https://mitobo.informatik.uni-halle.de/api.php?action=feedcontributions&user=Moeller&feedformat=atomMiToBo - User contributions [en]2024-03-29T10:37:59ZUser contributionsMediaWiki 1.38.2https://mitobo.informatik.uni-halle.de/index.php?title=Publications&diff=1035Publications2023-11-29T11:05:43Z<p>Moeller: </p>
<hr />
<div>MiToBo has been used in diverse research projects. Below you can find a selection of our publications about MiToBo itself and also several of our research papers in which MiToBo has successfully been applied to various tasks.<br/><br />
<br />
* S. Klemm, J. Buhl, B. Möller, and K. Bürstenbinder,<br>'''''Quantitative Analysis of Microtubule Organization in Leaf Epidermis Pavement Cells'''''.<br>In P. J. Hussey and P. Wang, editors, The Plant Cytoskeleton: Methods and Protocols, pages 43--61. Springer US, New York, NY, 2023.<br />
<br />
* Y. Poeschl, B. Möller, L. Müller, and K. Bürstenbinder,<br>'''''User-friendly assessment of pavement cell shape features with PaCeQuant: Novel functions and tools'''''.<br>In [https://doi.org/10.1016/bs.mcb.2020.04.010 Methods in Cell Biology], Academic Press, 2020.<br />
<br />
* B. Möller, L. Zergiebel, and K. Bürstenbinder,<br>'''''Quantitative and Comparative Analysis of Global Patterns of (Microtubule) Cytoskeleton Organization with CytoskeletonAnalyzer2D'''''.<br>In F. Cvrčková and V. Žárský, editors, [http://dx.doi.org/10.1007/978-1-4939-9469-4_10 Plant Cell Morphogenesis: Methods and Protocols, chapter 10, pp. 151-171], Springer New York, New York, NY, 2019.<br />
<br />
* B. Möller, Y. Poeschl, S. Klemm, and K. Bürstenbinder,<br>'''''Morphological Analysis of Leaf Epidermis Pavement Cells with PaCeQuant'''''.<br>In F. Cvrčková and V. Žárský, editors, [http://dx.doi.org/10.1007/978-1-4939-9469-4_22 Plant Cell Morphogenesis: Methods and Protocols, chapter 22, pages 329-349], Springer New York, New York, NY, 2019.<br />
<br />
* B. Möller and K. Bürstenbinder,<br>'''''Semi-automatic Cell Segmentation from Noisy Image Data for Quantification of Microtubule Organization on Single Cell Level'''''.<br>In Proc. of IEEE 16th International Symposium on Biomedical Imaging (ISBI '19), pp. 199-203, ISBN: 978-1-5386-3640-4, Venice, Italy, April 2019.<br />
<br />
* B. Möller and M. Schattat,<br>'''''Quantification of Stromule Frequencies in Microscope Images of Plastids combining Ridge Detection and Geometric Criteria'''''.<br>In Proc. of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 2: BIOIMAGING, pp. 38-48, ISBN: 978-989-758-353-7, INSTICC, SciTePress, Prague, Czech Republic, February 2019.<br />
<br />
* D. Mitra, S. Klemm, P. Kumari, J. Quegwer, B. Möller, Y. Poeschl, P. Pflug, G. Stamm, S. Abel, K. Bürstenbinder,<br>'''''Microtubule-associated protein IQ67 DOMAIN5 regulates morphogenesis of leaf pavement cells in Arabidopsis thaliana'''''.<br>In [https://academic.oup.com/jxb/article/70/2/529/5165408 Journal of Experimental Botany, 70(2):529-543, January 2019].<br />
<br />
* B. Möller, Y. Poeschl, R. Plötner, and K. Bürstenbinder,<br>'''''PaCeQuant: A Tool for High-Throughput Quantification of Pavement Cell Shape Characteristics'''''.<br>In [http://www.plantphysiol.org/content/early/2017/09/20/pp.17.00961 Plant Physiology, 175(1), September 2017].<br />
<br />
* K. Bürstenbinder, B. Möller, R. Plötner, G. Stamm, G. Hause, D. Mitra, and S. Abel,<br>'''''The IQD Family of Calmodulin-Binding Proteins Links Calcium Signaling to Microtubules, Membrane Subdomains, and the Nucleus'''''.<br>In [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5338658/# Plant Physiology, 173(3):1692-1708, March 2017].<br />
<br />
* B. Möller, M. Glaß, D. Misiak and S. Posch, '''''MiToBo – A Toolbox for Image Processing and Analysis''''',<br> In Journal of Open Research Software 4: e17, DOI: http://dx.doi.org/10.5334/jors.103, 2016.<br />
<br />
* L. Franke, B. Storbeck, J. L. Erickson, D. Rödel, D. Schröter, B. Möller, and M. H. Schattat, <br/> '''''The 'MTB Cell Counter' a versatile tool for the semi-automated quantification of sub-cellular phenotypes in fluorescence microscopy images. A case study on plastids, nuclei and peroxisomes''''', <br/>In [http://zs.thulb.uni-jena.de/receive/jportal_jparticle_00342296 Journal of Endocytobiosis and Cell Research, 26:31-42, 2015].<br />
<br />
* B. Möller, E. Piltz and N. Bley, '''''Quantification of Actin Structures using Unsupervised Pattern Analysis Techniques''''', <br/>In Proc. of Int. Conf. on Pattern Recognition (ICPR '14), IEEE, pp. 3251-3256, Stockholm, Sweden, August 2014. <br />
<br />
* D. Misiak, S. Posch, M. Lederer, C. Reinke, S. Hüttelmaier and B. Möller, '''''Extraction of Protein Profiles from Primary Neurons using Active Contour Models and Wavelets''''', <br/> In [http://www.sciencedirect.com/science/article/pii/S0165027013004330 Journal of Neuroscience Methods , vol. 225, pages 1-12, March 2014]. <br />
<br />
* M. Glaß, B. Möller and S. Posch, '''''Scratch Assay Analysis in ImageJ'''', <br/> In Proc. of ImageJ User & Developer Conference, pp. 211-214, ISBN 2-919941-18-6, Mondorf-les-Bains, Luxembourg, October 2012. <br />
<br />
* B. Möller and D. Misiak, '''''SnakeOptimizer - Object Segmentation with Parametric Active Contours in ImageJ''''', <br/> In Proc. of ImageJ User & Developer Conference, pp. 215-217/222, ISBN 2-919941-18-6, Mondorf-les-Bains, Luxembourg, October 2012.<br />
<br />
* M. Glaß, B. Möller, A. Zirkel, K. Wächter, S. Hüttelmaier and S. Posch, '''''Cell Migration Analysis: Segmenting Scratch Assay Images with Level Sets and Support Vector Machines''''',<br> In Pattern Recognition, vol. 45, no. 9, pp. 3154-3165, Elsevier, September 2012. <br />
<br />
* B. Möller and S. Posch, '''''Comparing Active Contours for the Segmentation of Biomedical Images''''',<br> In Proc. of IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI), pp. 736-739, IEEEXplore Digital Library, ISBN 978-1-4577-1856-4, Barcelona, Spain, May 2012.<br />
<br />
* B. Möller and S. Posch, '''''MiCA - Easy Cell Image Analysis with Normalized Snakes''''',<br> In Proc. of Workshop on Microscopic Image Analysis with Applications in Biology (MIAAB), Heidelberg, Germany, September 2011. <br />
<br />
* M. Glaß, B. Möller, A. Zirkel, K. Wächter, S. Hüttelmaier and S. Posch, '''''Scratch Assay Analysis with Topology-preserving Level Sets and Texture Measure''''',<br> In Proc. of 5th Iberian Conference on Pattern Recognition and Image Analysis (IbPRIA), Jordi Vitrià, João M. Sanches, and Mario Hernández, editors, Springer, LNCS 6669, pp. 100-108, Las Palmas de Gran Canaria, Spain, June 2011.</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Main_Page&diff=1034Main Page2023-11-29T11:04:15Z<p>Moeller: </p>
<hr />
<div>= MiToBo - A <span style="color:#CC0000">m</span>icroscope <span style="color:#CC0000">i</span>mage analysis <span style="color:#CC0000">to</span>ol<span style="color:#CC0000">bo</span>x =<br />
<br />
{|width="100%"<br />
|-<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''What is MiToBo?'''<br><br />
The Microscope Image Analysis Toolbox MiToBo is a toolbox with a large collection of basic and advanced functions and algorithms for processing and analyzing digital images. Many tools in MiToBo target at the analysis of various kinds of microscopy data, however, most of the functionality within MiToBo is generic (see [[Features|page of features]] for an overview). MiToBo is implemented as extension for the widely used image processing application [http://rsbweb.nih.gov/ij/ ImageJ]/[https://fiji.sc/ Fiji] and its new release [http://developer.imagej.net/ ImageJ 2.0]. All functions, operators and plugins of MiToBo are ready to be directly used as plugins in ImageJ and Fiji.<br /><br/><br />
<br />
'''Highlight operators and tools in MiToBo'''<br />
{|style="background-color:#f8f8ff"<br />
|style="text-align:left;width:10%|[[File:MiToBo_logo_CytoskeletonAnalyzer2D.png|border|72px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/CytoskeletonAnalyzer2D]]<br />
|style="text-align:left;width:80%|'''''[[Applications/CytoskeletonAnalyzer2D|CytoskeletonAnalyzer2D]]''''' for the quantification of cytoskeleton structural patterns in microscopy images with texture measures;<br><br />
to ease cell boundary extraction in data preparation we additionally provide the '''''[[Applications/CellBoundaryExtractor2D|CellBoundaryExtractor2D]]''''' and a handy '''''[[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]]'''''<br />
|-<br />
|style="text-align:left;width:10%|[[File:MiToBo_logo_PaCeQuant.png|border|72px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/PaCeQuantToolset]]<br />
|style="text-align:left;width:80%|'''''[[Applications/PaCeQuantToolset|PaCeQuant]]''''' and corresponding tools, i.e. the '''''[[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]]''''', the '''''[[Applications/FeatureColorMapper|FeatureColorMapper]]''''' and the R package '''''[[Applications/PaCeQuantAna|PaCeQuantAna]]''''', for quantification, visualization and statistical analysis of the morphology and shape characteristics of cells<br />
|-<br />
|style="text-align:left;width:10%|[[File:NeuronAnalyzer2D.png|border|72px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/NeuronAnalyzer2D]]<br />
|style="text-align:left;width:80%|'''''[[Applications/NeuronAnalyzer2D|Neuron Analyzer]]''''' for the segmentation of neurons in microscope images<br />
|-<br />
|style="text-align:left;width:10%|[[File:tracking_ES-2.gif|72px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/CellMigrationAnalyzer]]<br />
|style="text-align:left;width:80%|'''''[[Applications/CellMigrationAnalyzer|Cell Migration Analyzer]]''''' for analyzing single cell migration from time lapse image sequences<br />
|-<br />
|style="text-align:left;width:10%|[[File:GFP_U2OS_overlay.png|72px|left|border|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/ScratchAssayAnalyzer]]<br />
|style="text-align:left;width:80%|'''''[[Applications/ScratchAssayAnalyzer|Scratch Assay Analyzer]]''''' for analyzing microscope images from collective cell migration experiments<br />
|}<br />
For several other important operators and plugins documentation is available via the [[Operator_Documentation| Operator Documentation pages]] here in the Wiki.<br> <br />
The pages are structured according to the package structure of MiToBo which is also mirrored in the selection panel of MiToBo's operator runner.<br />
<br />
<br><br />
'''MiToBo for developers'''<br><br />
MiToBo aims not only to support users in analyzing their images, but also targets at developers by offering a programmer-friendly software framework and API for developing new algorithms.<br />
The MiToBo API completely separates the implementation of image processing algorithms from potential user interfaces based <br />
on [http://www.informatik.uni-halle.de/alida/ Alida] which is a library for easing the development of data analysis<br />
algorithms and tools. The main concept of Alida are <i>operators</i> as the core units for implementing data analysis algorithms. <br /><br />
Alida defines unified interfaces and execution procedures for operators which yield the fundament for its nice features like <br />
<ul><br />
<li> automatic documentation of complete analysis processes, e.g., leading from an input image to analysis results, in terms of processing graphs<br />
<li> automatic generation of commandline and graphical user interfaces<br />
<li> a graphical programming editor named '''''Grappa''''' automatically considering all implemented operators as potential processing nodes<br><br />
</ul><br />
<br />
<p><br />
MiToBo takes full advantage of Alida's features, hence, provides a framework for implementing image analysis algorithms allowing for automatic documentation and automatic user interface generation, and includes the graphical programming editor Grappa for user-friendly design of more complex processing pipelines.<br />
</p><br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Visit and follow MiToBo also at...'''<br><br />
{|<br />
|style="text-align:center;width:10%"|[[file:Imagej-128.png|90px|link=http://imagej.net/MiToBo]]<br />
|style="text-align:center;width:10%"|[[file:Git.png|90px|link=https://github.com/mitobo-hub]]<br />
|style="text-align:center;width:10%"|[[file:mtbtw.png|320px|link=https://twitter.com/MiToBo_Hal]]<br />
|style="text-align:center;width:10%"|[[file:logo.png|90px|link=http://imagejdocu.tudor.lu/doku.php?id=plugin:collections:mitobo_-_a_microscope_image_analysis_toolbox:start]]<br />
|style="text-align:center;width:10%"|[[file:logo-blue.png|90px|link=https://omictools.com/microscope-image-analysis-toolbox-tool]]<br />
|-<br />
|style="text-align:center;width:10%"|[http://imagej.net/MiToBo ImageJ.net]<br />
|style="text-align:center;width:10%"|[https://github.com/mitobo-hub GitHub]<br />
|style="text-align:center;width:10%"|[https://twitter.com/MiToBo_Hal Twitter]<br />
|style="text-align:center;width:10%"|[http://imagejdocu.tudor.lu/doku.php?id=plugin:collections:mitobo_-_a_microscope_image_analysis_toolbox:start ImageJ Docu Wiki]<br />
|style="text-align:center;width:10%"|[https://omictools.com/microscope-image-analysis-toolbox-tool OMIC Tools]<br />
|}<br />
</div><br />
</div><br />
|<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Latest News'''<br><br />
* 08/2023: MiToBo 2.3.1 has been released which fixes serious incompatibilities to Bioformats.<br />
* 07/2023: MiToBo 2.3 has been released.<br><br />
* 05/2021: MiToBo 2.2 has been released.<br><br />
* 12/2020: MiToBo 2.1 has been released.<br> <br />
* 05/2020: MiToBo 2.0 has been released.<br> From now on the online help system relies on operator class annotations, and the release includes a [https://mitobo.informatik.uni-halle.de/index.php/Applications/PaCeQuantToolset PaCeQuant] update with new shape features and improvements for supplemental tools like the [https://mitobo.informatik.uni-halle.de/index.php/Applications/FeatureColorMapper FeatureColorMapper] and the [https://mitobo.informatik.uni-halle.de/index.php/Operators/Tools/Interactive/LabelImageEditor LabelImageEditor].<br />
* 07/2019: MiToBo 1.8.15 has been released fixing several issues with handling images in MiToBo.<br />
* 02/2019: MiToBo 1.8.14 has been released.<br />
<br />
The news archive can be found [[News Archive | here]].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''How to get MiToBo?'''<br><br />
* ImageJ-Users:<br> download the [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/1.8.7.1/mitobo-plugins-1.8.7.1-bin.zip MiToBo-Plugins package] and follow the installation instructions to be found [[Installation | here]]. <br />
* Fiji-Users:<br> simply select MiToBo's update site [http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo] in FijiIs list of update sites in your installation<br />
* use in general:<br> you can download MiToBo and the MiToBo plugins package [[Downloads | here]]. <br/> <br />
<br />
You can find the API documentation for the current release [http://www.informatik.uni-halle.de/mitobo/api/index.html here].<br/> <br />
Furthermore MiToBo offers you a user and programmer guide which you can download [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual.pdf here].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Support, Bug reports & Feature requests'''<br />
{|style="background-color:#f8f8ff"<br />
|style="text-align:left;width:20%|[[File:forum-image-sc.png|border|64px|left|link=https://forum.image.sc/]]<br />
|style="text-align:left;width:60%|To get help on your questions about MiToBo tools, plugins and operators you can use the forum at [https://forum.image.sc/ image.sc] tagging your post with [https://forum.image.sc/tags/mitobo #mitobo].<br />
|-<br />
|style="text-align:left;width:20%|[[file:Git.png|64px|link=https://github.com/mitobo-hub]]<br />
|style="text-align:left;width:60%|Bug reports and feature requests can be submitted as issues on [https://github.com/mitobo-hub/mitobo/issues Github].<br />
|-<br />
|style="text-align:left;width:20%|[[file:Email.png|center|36px|link=]]<br />
|style="text-align:left;width:60%|Alternatively you can also write an email to [mailto:mitobo@informatik.uni-halle.de mitobo@informatik.uni-halle.de].<br />
|}<br />
Before reporting a new bug or requesting a new feature, please check if that bug has already been submitted in the forum or on Github.<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Licensing information'''<br><br />
MiToBo is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Gnu PGP Public Key'''<br><br />
Since version 1.8.7 MiToBo and MiToBo-Plugins releases are PGP signed. MiToBo's [https://pgp.mit.edu/pks/lookup?op=get&search=0x259F7DD171EFF7A9 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/.<br />
</div><br />
</div><br />
|}</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Downloads&diff=1033Downloads2023-11-29T11:02:16Z<p>Moeller: /* Quick Start */</p>
<hr />
<div>== Quick Start ==<br />
The easiest and fastest way to install and run MiToBo is to activate MiToBo's update site in Fiji:<br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br><br />
<br />
To enable this site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
<br />
<br><br />
For installing MiToBo this way you need to activate the following site:<br />
* MiToBo<br />
For some operators additional sites are required:<br />
* Biomedgroup (e.g., for PaCeQuant)<br />
<br />
<br><br />
More details how to install and run MiToBo can be found on our [[Installation]] page.<br />
<br><br />
<br />
== Downloads and Releases ==<br />
<br />
The current release of the MiToBo core distribution and also of the extended MiToBo-Plugins distribution is 2.3.1.<br />
<br />
Since release 1.3 we support Maven for managing MiToBo's resources.<br> You can download the MiToBo distributions as well as the Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/#browse/de.unihalle.informatik.MiToBo https://moon.informatik.uni-halle.de/#browse/de.unihalle.informatik.MiToBo]<br />
<br />
There are two MiToBo distributions available:<br />
* <b>MiToBo:</b><br> this package contains the core of MiToBo, i.e. all operators, the MiToBo runners for operator execution and also Grappa;<br> <b>not included</b> are the plugins to run MiToBo from within ImageJ 1.x, hence, this distribution is mainly for stand-alone usage of MiToBo and development purposes<br><br />
* <b>MiToBo-Plugins:</b><br> this package contains the complete MiToBo distribution, some special plugins like the [[Applications/MTBCellCounter | MTB Cell Counter]], and in addition some ImageJ plugins to run MiToBo operators from within ImageJ; you should download the MiToBo-Plugins distribution if you like to use MiToBo with ImageJ<br><br />
<br />
Since release 1.8 MiToBo's implementation requires at least Java 1.8.<br />
<br><br />
<br />
At the bottom of this page additional files are available for download:<br />
* Old distributions: complete distributions including all dependencies, scripts, documentation, etc.<br />
* Binaries only: only the jar archives, no dependencies neither documentation<br />
* APIs: Javadoc APIs<br />
<br><br />
<br />
== Maven Project Template ==<br />
Using MiToBo as a library for own developments can best be done by making use of Maven.<br><br />
Particularly, Maven automatically resolves all dependencies which otherwise would have to be installed manually.<br />
<br />
For getting started with MiToBo and Maven a project template is provided: <br />
<br />
[http://www.informatik.uni-halle.de/mitobo/downloads/maven/mitobo-demo-project-1.2-src.zip Maven project template [zip]]<br />
<br />
The project is readily configured and you can immediately start with own developments.<br><br />
It also contains a demo operator showing the basic usage of MiToBo data types and operators on the code level.<br />
<br />
Make sure that you have installed Maven and a Java Develpoment Kit (JDK) in version 1.8 or higher.<br><br />
You can check the Java version by running 'mvn --version' from command line.<br> <br />
If an older Java version is used, let the 'JAVA_HOME' environment variable point to a folder containing a more recent JDK.<br />
<br />
You can run Maven directly from within the extracted folder. Alternatively the Maven template project can easily be imported into an IDE like Eclipse.<br><br />
The zip file contains a README file containing more information about installing and configuring the project template.<br />
<br/><br />
<br />
<br />
== Manual ==<br />
<br />
Detailed information about MiToBo, its API and usage, can be found in MiToBo's User and Programmer Guide.<br />
<br />
* MiToBo-Guide, Version 1.0 [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual.pdf pdf]<br />
<br><br />
<br />
== Additional resources ==<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release:<br />
* Chipory binary [http://www.informatik.uni-halle.de/mitobo/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www.informatik.uni-halle.de/mitobo/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br><br />
<br />
<br />
== Logo ==<br />
<br />
* MiToBo logo as [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.pdf PDF] or [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.png PNG]<br />
<br />
<br />
== Earlier releases of MiToBo (< 1.5) ==<br />
<br />
Since release 1.3 MiToBo's resources are available from our Maven archive server: [https://moon.informatik.uni-halle.de/archiva/]<br>Binaries, sources and documentation for versions older than the current release, but at least of version 1.3 or newer can be found there.<br> All other releases can be accessed via the list below.<br><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 1.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3-javadoc.jar jar]<br />
| March 31st, 2015 (Support for callbacks)<br />
|-<br />
| 1.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 1.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 1.2<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-bin-v1.2.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-v1.2.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-v1.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
|-<br />
| 1.1<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-bin-v1.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-v1.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-v1.1.zip zip]<br />
| March 1st, 2013<br />
|-<br />
| 1.0.5<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.5.zip zip]<br />
| October 23rd, 2012<br />
|-<br />
| 1.0.1<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.1.zip zip]<br />
| July 6th, 2012<br />
|-<br />
| 1.0.0<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.0.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.0.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.0.zip zip]<br />
| April 26th, 2012<br />
|-<br />
| 0.96<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.6.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.6.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-0.9.6.zip zip]<br />
| September 01, 2011<br />
|-<br />
| 0.95<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-0.9.5.zip zip]<br />
| June 08, 2011 (updated June 22nd, 2011)<br />
|-<br />
| 0.9<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.tar.gz tar.gz]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.tar.gz tar.gz]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.tar.gz tar.gz]<br />
| October 26, 2010<br />
|}<br />
<br/><br />
<br />
=== Requirements (for MiToBo < 1.3) ===<br />
MiToBo requires Java 1.6 or later. <br />
<br />
'''Note''': Java 1.7 is currently not fully supported!<br />
<br />
The following external jars are needed to run MiToBo plugins and use the code.<br/><br />
<b>Note that the binary zip file already includes all jars required, there is no need for explicit download!</b><br />
<br />
MiToBo depends on the following external jars:<br />
<br />
* [http://rsbweb.nih.gov/ij/ ImageJ], >= Version 1.47d<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://www.csie.ntu.edu.tw/~cjlin/libsvm/ LIBSVM], Version 3.1<br />
* [http://www.loci.wisc.edu/software/bio-formats/ Loci Tools], Version 4.3.3<br />
* [http://math.nist.gov/javanumerics/jama/ Jama], Version 1.0.2 <br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
* [http://sezpoz.java.net/ SezPoz], Version 1.9<br />
* [http://www.jgraph.com/mxdownload.html JGraph], Version 1.7.1.8<br />
<br />
* [https://jai-imageio.dev.java.net/ JAI ImageIO], Version 1.1 (only required for MiToBo 0.9)<br />
<br />
=== Project internal libraries ===<br />
<br />
MiToBo also relies on some libraries provided by the MiToBo project itself.<br><br />
In particular XML schemes for representing the history graphs and MiToBo's online help are included in separate jar archives.<br />
<br />
'''[[Note]]:''' <br/><br />
''' You do not need to download these libraries explicitly. If you download the binary zip file all jars and libraries are already included.''' <br/><br />
<br />
The MiToBo internal archive files included in the zip file are the following ones:<br />
<br />
* ALDGraphml, Version 1.0.0 (Alida extensions for [http://graphml.graphdrawing.org/ graphML]):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/aldgraphml/aldgraphml.jar jar]<br />
* MTBXml, Version 1.0.0 (MiToBo XML I/O for several datatypes, based on XMLBeans):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbxml/mtbxml.jar jar] <br />
* MiToBo-Help, Version 1.0.0 (MiToBo JavaHelp pages):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mitoboHelp/MiToBo-Help.jar jar] <br />
<br />
The following library is only required for MiToBo-0.9: <br />
<br />
* MTBImageIO-Ext, Version 0.9 (improved image I/O based on ImageIO-Ext):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff-0.9.jar jar]<br />
** Source code [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff_src-0.9.zip zip]<br />
** Alternatively, the [https://imageio-ext.dev.java.net/ ImageIO-Ext] library can be used, which depends on the [https://jai-imageio.dev.java.net/ JAI ImageIO] library and the [https://jai.dev.java.net/ JAI] library.<br/>MTBImageIO-Ext is simply the TIFF part of ImageIO-Ext with slight adjustments to remove dependency on the JAI library.<br />
<br/></div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Downloads&diff=1032Downloads2023-11-29T11:01:48Z<p>Moeller: /* Releases and Downloads */</p>
<hr />
<div>== Quick Start ==<br />
The easiest and fastest way to install and run MiToBo is to activate MiToBo's update site in Fiji:<br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br><br />
<br />
To enable this site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
<br />
<br><br />
For installing MiToBo this way you need to activate the following site:<br />
* MiToBo<br />
For some operators additional sites are required:<br />
* Biomedgroup (e.g., PaCeQuant)<br />
<br />
<br><br />
More details how to install and run MiToBo can be found on our [[Installation]] page.<br />
<br><br />
<br />
== Downloads and Releases ==<br />
<br />
The current release of the MiToBo core distribution and also of the extended MiToBo-Plugins distribution is 2.3.1.<br />
<br />
Since release 1.3 we support Maven for managing MiToBo's resources.<br> You can download the MiToBo distributions as well as the Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/#browse/de.unihalle.informatik.MiToBo https://moon.informatik.uni-halle.de/#browse/de.unihalle.informatik.MiToBo]<br />
<br />
There are two MiToBo distributions available:<br />
* <b>MiToBo:</b><br> this package contains the core of MiToBo, i.e. all operators, the MiToBo runners for operator execution and also Grappa;<br> <b>not included</b> are the plugins to run MiToBo from within ImageJ 1.x, hence, this distribution is mainly for stand-alone usage of MiToBo and development purposes<br><br />
* <b>MiToBo-Plugins:</b><br> this package contains the complete MiToBo distribution, some special plugins like the [[Applications/MTBCellCounter | MTB Cell Counter]], and in addition some ImageJ plugins to run MiToBo operators from within ImageJ; you should download the MiToBo-Plugins distribution if you like to use MiToBo with ImageJ<br><br />
<br />
Since release 1.8 MiToBo's implementation requires at least Java 1.8.<br />
<br><br />
<br />
At the bottom of this page additional files are available for download:<br />
* Old distributions: complete distributions including all dependencies, scripts, documentation, etc.<br />
* Binaries only: only the jar archives, no dependencies neither documentation<br />
* APIs: Javadoc APIs<br />
<br><br />
<br />
== Maven Project Template ==<br />
Using MiToBo as a library for own developments can best be done by making use of Maven.<br><br />
Particularly, Maven automatically resolves all dependencies which otherwise would have to be installed manually.<br />
<br />
For getting started with MiToBo and Maven a project template is provided: <br />
<br />
[http://www.informatik.uni-halle.de/mitobo/downloads/maven/mitobo-demo-project-1.2-src.zip Maven project template [zip]]<br />
<br />
The project is readily configured and you can immediately start with own developments.<br><br />
It also contains a demo operator showing the basic usage of MiToBo data types and operators on the code level.<br />
<br />
Make sure that you have installed Maven and a Java Develpoment Kit (JDK) in version 1.8 or higher.<br><br />
You can check the Java version by running 'mvn --version' from command line.<br> <br />
If an older Java version is used, let the 'JAVA_HOME' environment variable point to a folder containing a more recent JDK.<br />
<br />
You can run Maven directly from within the extracted folder. Alternatively the Maven template project can easily be imported into an IDE like Eclipse.<br><br />
The zip file contains a README file containing more information about installing and configuring the project template.<br />
<br/><br />
<br />
<br />
== Manual ==<br />
<br />
Detailed information about MiToBo, its API and usage, can be found in MiToBo's User and Programmer Guide.<br />
<br />
* MiToBo-Guide, Version 1.0 [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual.pdf pdf]<br />
<br><br />
<br />
== Additional resources ==<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release:<br />
* Chipory binary [http://www.informatik.uni-halle.de/mitobo/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www.informatik.uni-halle.de/mitobo/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br><br />
<br />
<br />
== Logo ==<br />
<br />
* MiToBo logo as [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.pdf PDF] or [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.png PNG]<br />
<br />
<br />
== Earlier releases of MiToBo (< 1.5) ==<br />
<br />
Since release 1.3 MiToBo's resources are available from our Maven archive server: [https://moon.informatik.uni-halle.de/archiva/]<br>Binaries, sources and documentation for versions older than the current release, but at least of version 1.3 or newer can be found there.<br> All other releases can be accessed via the list below.<br><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 1.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3-javadoc.jar jar]<br />
| March 31st, 2015 (Support for callbacks)<br />
|-<br />
| 1.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 1.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 1.2<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-bin-v1.2.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-v1.2.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-v1.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
|-<br />
| 1.1<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-bin-v1.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-v1.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-v1.1.zip zip]<br />
| March 1st, 2013<br />
|-<br />
| 1.0.5<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.5.zip zip]<br />
| October 23rd, 2012<br />
|-<br />
| 1.0.1<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.1.zip zip]<br />
| July 6th, 2012<br />
|-<br />
| 1.0.0<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.0.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.0.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.0.zip zip]<br />
| April 26th, 2012<br />
|-<br />
| 0.96<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.6.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.6.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-0.9.6.zip zip]<br />
| September 01, 2011<br />
|-<br />
| 0.95<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-0.9.5.zip zip]<br />
| June 08, 2011 (updated June 22nd, 2011)<br />
|-<br />
| 0.9<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.tar.gz tar.gz]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.tar.gz tar.gz]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.tar.gz tar.gz]<br />
| October 26, 2010<br />
|}<br />
<br/><br />
<br />
=== Requirements (for MiToBo < 1.3) ===<br />
MiToBo requires Java 1.6 or later. <br />
<br />
'''Note''': Java 1.7 is currently not fully supported!<br />
<br />
The following external jars are needed to run MiToBo plugins and use the code.<br/><br />
<b>Note that the binary zip file already includes all jars required, there is no need for explicit download!</b><br />
<br />
MiToBo depends on the following external jars:<br />
<br />
* [http://rsbweb.nih.gov/ij/ ImageJ], >= Version 1.47d<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://www.csie.ntu.edu.tw/~cjlin/libsvm/ LIBSVM], Version 3.1<br />
* [http://www.loci.wisc.edu/software/bio-formats/ Loci Tools], Version 4.3.3<br />
* [http://math.nist.gov/javanumerics/jama/ Jama], Version 1.0.2 <br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
* [http://sezpoz.java.net/ SezPoz], Version 1.9<br />
* [http://www.jgraph.com/mxdownload.html JGraph], Version 1.7.1.8<br />
<br />
* [https://jai-imageio.dev.java.net/ JAI ImageIO], Version 1.1 (only required for MiToBo 0.9)<br />
<br />
=== Project internal libraries ===<br />
<br />
MiToBo also relies on some libraries provided by the MiToBo project itself.<br><br />
In particular XML schemes for representing the history graphs and MiToBo's online help are included in separate jar archives.<br />
<br />
'''[[Note]]:''' <br/><br />
''' You do not need to download these libraries explicitly. If you download the binary zip file all jars and libraries are already included.''' <br/><br />
<br />
The MiToBo internal archive files included in the zip file are the following ones:<br />
<br />
* ALDGraphml, Version 1.0.0 (Alida extensions for [http://graphml.graphdrawing.org/ graphML]):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/aldgraphml/aldgraphml.jar jar]<br />
* MTBXml, Version 1.0.0 (MiToBo XML I/O for several datatypes, based on XMLBeans):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbxml/mtbxml.jar jar] <br />
* MiToBo-Help, Version 1.0.0 (MiToBo JavaHelp pages):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mitoboHelp/MiToBo-Help.jar jar] <br />
<br />
The following library is only required for MiToBo-0.9: <br />
<br />
* MTBImageIO-Ext, Version 0.9 (improved image I/O based on ImageIO-Ext):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff-0.9.jar jar]<br />
** Source code [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff_src-0.9.zip zip]<br />
** Alternatively, the [https://imageio-ext.dev.java.net/ ImageIO-Ext] library can be used, which depends on the [https://jai-imageio.dev.java.net/ JAI ImageIO] library and the [https://jai.dev.java.net/ JAI] library.<br/>MTBImageIO-Ext is simply the TIFF part of ImageIO-Ext with slight adjustments to remove dependency on the JAI library.<br />
<br/></div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Downloads&diff=1031Downloads2023-11-29T11:01:02Z<p>Moeller: /* Quick Start */</p>
<hr />
<div>== Quick Start ==<br />
The easiest and fastest way to install and run MiToBo is to activate MiToBo's update site in Fiji:<br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br><br />
<br />
To enable this site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
<br />
<br><br />
For installing MiToBo this way you need to activate the following site:<br />
* MiToBo<br />
For some operators additional sites are required:<br />
* Biomedgroup (e.g., PaCeQuant)<br />
<br />
<br><br />
More details how to install and run MiToBo can be found on our [[Installation]] page.<br />
<br><br />
<br />
== Releases and Downloads ==<br />
<br />
The current release of the MiToBo core distribution and also of the extended MiToBo-Plugins distribution is 2.3.1.<br />
<br />
Since release 1.3 we support Maven for managing MiToBo's resources.<br> You can download the MiToBo distributions as well as the Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/#browse/de.unihalle.informatik.MiToBo https://moon.informatik.uni-halle.de/#browse/de.unihalle.informatik.MiToBo]<br />
<br />
There are two MiToBo distributions available:<br />
* <b>MiToBo:</b><br> this package contains the core of MiToBo, i.e. all operators, the MiToBo runners for operator execution and also Grappa;<br> <b>not included</b> are the plugins to run MiToBo from within ImageJ 1.x, hence, this distribution is mainly for stand-alone usage of MiToBo and development purposes<br><br />
* <b>MiToBo-Plugins:</b><br> this package contains the complete MiToBo distribution, some special plugins like the [[Applications/MTBCellCounter | MTB Cell Counter]], and in addition some ImageJ plugins to run MiToBo operators from within ImageJ; you should download the MiToBo-Plugins distribution if you like to use MiToBo with ImageJ<br><br />
<br />
Since release 1.8 MiToBo's implementation requires at least Java 1.8.<br />
<br><br />
<br />
At the bottom of this page additional files are available for download:<br />
* Old distributions: complete distributions including all dependencies, scripts, documentation, etc.<br />
* Binaries only: only the jar archives, no dependencies neither documentation<br />
* APIs: Javadoc APIs<br />
<br><br />
<br />
== Maven Project Template ==<br />
Using MiToBo as a library for own developments can best be done by making use of Maven.<br><br />
Particularly, Maven automatically resolves all dependencies which otherwise would have to be installed manually.<br />
<br />
For getting started with MiToBo and Maven a project template is provided: <br />
<br />
[http://www.informatik.uni-halle.de/mitobo/downloads/maven/mitobo-demo-project-1.2-src.zip Maven project template [zip]]<br />
<br />
The project is readily configured and you can immediately start with own developments.<br><br />
It also contains a demo operator showing the basic usage of MiToBo data types and operators on the code level.<br />
<br />
Make sure that you have installed Maven and a Java Develpoment Kit (JDK) in version 1.8 or higher.<br><br />
You can check the Java version by running 'mvn --version' from command line.<br> <br />
If an older Java version is used, let the 'JAVA_HOME' environment variable point to a folder containing a more recent JDK.<br />
<br />
You can run Maven directly from within the extracted folder. Alternatively the Maven template project can easily be imported into an IDE like Eclipse.<br><br />
The zip file contains a README file containing more information about installing and configuring the project template.<br />
<br/><br />
<br />
<br />
== Manual ==<br />
<br />
Detailed information about MiToBo, its API and usage, can be found in MiToBo's User and Programmer Guide.<br />
<br />
* MiToBo-Guide, Version 1.0 [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual.pdf pdf]<br />
<br><br />
<br />
== Additional resources ==<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release:<br />
* Chipory binary [http://www.informatik.uni-halle.de/mitobo/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www.informatik.uni-halle.de/mitobo/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br><br />
<br />
<br />
== Logo ==<br />
<br />
* MiToBo logo as [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.pdf PDF] or [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.png PNG]<br />
<br />
<br />
== Earlier releases of MiToBo (< 1.5) ==<br />
<br />
Since release 1.3 MiToBo's resources are available from our Maven archive server: [https://moon.informatik.uni-halle.de/archiva/]<br>Binaries, sources and documentation for versions older than the current release, but at least of version 1.3 or newer can be found there.<br> All other releases can be accessed via the list below.<br><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 1.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3-javadoc.jar jar]<br />
| March 31st, 2015 (Support for callbacks)<br />
|-<br />
| 1.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 1.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 1.2<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-bin-v1.2.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-v1.2.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-v1.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
|-<br />
| 1.1<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-bin-v1.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-v1.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-v1.1.zip zip]<br />
| March 1st, 2013<br />
|-<br />
| 1.0.5<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.5.zip zip]<br />
| October 23rd, 2012<br />
|-<br />
| 1.0.1<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.1.zip zip]<br />
| July 6th, 2012<br />
|-<br />
| 1.0.0<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.0.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.0.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.0.zip zip]<br />
| April 26th, 2012<br />
|-<br />
| 0.96<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.6.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.6.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-0.9.6.zip zip]<br />
| September 01, 2011<br />
|-<br />
| 0.95<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-0.9.5.zip zip]<br />
| June 08, 2011 (updated June 22nd, 2011)<br />
|-<br />
| 0.9<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.tar.gz tar.gz]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.tar.gz tar.gz]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.tar.gz tar.gz]<br />
| October 26, 2010<br />
|}<br />
<br/><br />
<br />
=== Requirements (for MiToBo < 1.3) ===<br />
MiToBo requires Java 1.6 or later. <br />
<br />
'''Note''': Java 1.7 is currently not fully supported!<br />
<br />
The following external jars are needed to run MiToBo plugins and use the code.<br/><br />
<b>Note that the binary zip file already includes all jars required, there is no need for explicit download!</b><br />
<br />
MiToBo depends on the following external jars:<br />
<br />
* [http://rsbweb.nih.gov/ij/ ImageJ], >= Version 1.47d<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://www.csie.ntu.edu.tw/~cjlin/libsvm/ LIBSVM], Version 3.1<br />
* [http://www.loci.wisc.edu/software/bio-formats/ Loci Tools], Version 4.3.3<br />
* [http://math.nist.gov/javanumerics/jama/ Jama], Version 1.0.2 <br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
* [http://sezpoz.java.net/ SezPoz], Version 1.9<br />
* [http://www.jgraph.com/mxdownload.html JGraph], Version 1.7.1.8<br />
<br />
* [https://jai-imageio.dev.java.net/ JAI ImageIO], Version 1.1 (only required for MiToBo 0.9)<br />
<br />
=== Project internal libraries ===<br />
<br />
MiToBo also relies on some libraries provided by the MiToBo project itself.<br><br />
In particular XML schemes for representing the history graphs and MiToBo's online help are included in separate jar archives.<br />
<br />
'''[[Note]]:''' <br/><br />
''' You do not need to download these libraries explicitly. If you download the binary zip file all jars and libraries are already included.''' <br/><br />
<br />
The MiToBo internal archive files included in the zip file are the following ones:<br />
<br />
* ALDGraphml, Version 1.0.0 (Alida extensions for [http://graphml.graphdrawing.org/ graphML]):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/aldgraphml/aldgraphml.jar jar]<br />
* MTBXml, Version 1.0.0 (MiToBo XML I/O for several datatypes, based on XMLBeans):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbxml/mtbxml.jar jar] <br />
* MiToBo-Help, Version 1.0.0 (MiToBo JavaHelp pages):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mitoboHelp/MiToBo-Help.jar jar] <br />
<br />
The following library is only required for MiToBo-0.9: <br />
<br />
* MTBImageIO-Ext, Version 0.9 (improved image I/O based on ImageIO-Ext):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff-0.9.jar jar]<br />
** Source code [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff_src-0.9.zip zip]<br />
** Alternatively, the [https://imageio-ext.dev.java.net/ ImageIO-Ext] library can be used, which depends on the [https://jai-imageio.dev.java.net/ JAI ImageIO] library and the [https://jai.dev.java.net/ JAI] library.<br/>MTBImageIO-Ext is simply the TIFF part of ImageIO-Ext with slight adjustments to remove dependency on the JAI library.<br />
<br/></div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Installation&diff=1030Installation2023-11-29T10:59:17Z<p>Moeller: /* Using MiToBo with ImageJ */</p>
<hr />
<div>== General remarks ==<br />
<br />
There are two common ways to work with MiToBo:<br />
<ul><br />
<li> just using the operators included in MiToBo for improving your work and easing image processing tasks, e.g., via ImageJ or Fiji<br />
<li> using the MiToBo API to write operators, plugins and other image analysis applications on your own<br />
</ul><br />
The functionality of MiToBo is best used from within ImageJ or Fiji. In case that you aim to use MiToBo for your own development, you need to download the binaries explicitly. The actual installation instructions differ in some parts depending on which way of using MiToBo you have in mind.<br> Below we will first outline more details about the installation steps required for simply using MiToBo's operators in ImageJ and Fiji, and then provide some notes regarding the binary zip file. Finally we will present some details for using MiToBo's API with your own code.<br />
<br />
<blockquote style="background-color: lightgrey; border: solid thin grey;"><br />
'''[[The recommended way to install and run MiToBo and its operators/plugins is via Fiji!]]'''<br><br />
MiToBo has its own Fiji update site named "MiToBo".<br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br><br />
<br />
To enable this site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
<br />
Note that for some plugins (e.g., PaCeQuant) also the "Biomedgroup" update site needs to be activated.<br />
</blockquote><br />
<br />
== Using MiToBo with Fiji ==<br />
Since release 1.5 MiToBo features a Fiji update site and the easiest way to use MiToBo's operators and plugins is to enable the update site in your Fiji installation. <br> The MiToBo update site is<br><br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br />
<br />
To enable the site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
<br />
'''Important notices:'''<br> <br />
<ul><br />
<li> Occasionally MiToBo '''operators crash when run from within Fiji'''. The reason for this behaviour are most of the time '''conflicting jar archives''' delivered with the Fiji distribution.<br> We figured out that particularly the jar file<br />
<br />
* jars/bio-formats/formats-common-5.1.x.jar<br />
<br />
often causes such trouble. Thus, if you encounter problems running MiToBo operators, please try to locally delete or uninstall the abovementioned jar archive from your local Fiji installation and then re-run the MiToBo operator.<br />
<li> For some of our operators special issues exist and require special treatment:<br />
<ul><br />
<li> [[Applications/CellBoundaryExtractor2D| CellBoundaryExtractor2D]]: there are version conflicts with regard to the '''JGraphT library''' used by this operator and also by default included in every Fiji distribution; please refer to installation instructions on the [[Applications/CellBoundaryExtractor2D|webpage of the operator]] for a workaround<br />
</ul><br />
</ul><br />
<br />
<br><br />
<br />
== Using MiToBo with ImageJ ==<br />
<br />
'''Important Note 1:''' Before you consider installing MiToBo manually within ImageJ, check if it could not be an option to use Fiji and activate MiToBo's update site - in most cases this will be significantly less painful...<br />
<br />
'''Important Note 2:''' These instructions refer to ImageJ 1.<br />
<br />
<br><br />
General remarks:<br><br />
For using MiToBo with ImageJ it is the easiest to download the latest distribution zipfile (*-bin.zip) from<br><br />
<br />
[https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/ https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/]<br><br />
<br />
which already includes '''''all''''' dependencies and ships with some scripts to run MiToBo's operators and plugins out of the box.<br />
<br />
=== Linux ===<br />
<br />
Using MiToBo with a [[Installation/Linux|Linux operating system]].<br />
<br />
<br><br />
<br />
=== Windows ===<br />
<br />
Using MiToBo with a [[Installation/Windows|Windows operating system]].</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Installation&diff=1029Installation2023-11-29T10:56:44Z<p>Moeller: </p>
<hr />
<div>== General remarks ==<br />
<br />
There are two common ways to work with MiToBo:<br />
<ul><br />
<li> just using the operators included in MiToBo for improving your work and easing image processing tasks, e.g., via ImageJ or Fiji<br />
<li> using the MiToBo API to write operators, plugins and other image analysis applications on your own<br />
</ul><br />
The functionality of MiToBo is best used from within ImageJ or Fiji. In case that you aim to use MiToBo for your own development, you need to download the binaries explicitly. The actual installation instructions differ in some parts depending on which way of using MiToBo you have in mind.<br> Below we will first outline more details about the installation steps required for simply using MiToBo's operators in ImageJ and Fiji, and then provide some notes regarding the binary zip file. Finally we will present some details for using MiToBo's API with your own code.<br />
<br />
<blockquote style="background-color: lightgrey; border: solid thin grey;"><br />
'''[[The recommended way to install and run MiToBo and its operators/plugins is via Fiji!]]'''<br><br />
MiToBo has its own Fiji update site named "MiToBo".<br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br><br />
<br />
To enable this site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
<br />
Note that for some plugins (e.g., PaCeQuant) also the "Biomedgroup" update site needs to be activated.<br />
</blockquote><br />
<br />
== Using MiToBo with Fiji ==<br />
Since release 1.5 MiToBo features a Fiji update site and the easiest way to use MiToBo's operators and plugins is to enable the update site in your Fiji installation. <br> The MiToBo update site is<br><br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br />
<br />
To enable the site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
<br />
'''Important notices:'''<br> <br />
<ul><br />
<li> Occasionally MiToBo '''operators crash when run from within Fiji'''. The reason for this behaviour are most of the time '''conflicting jar archives''' delivered with the Fiji distribution.<br> We figured out that particularly the jar file<br />
<br />
* jars/bio-formats/formats-common-5.1.x.jar<br />
<br />
often causes such trouble. Thus, if you encounter problems running MiToBo operators, please try to locally delete or uninstall the abovementioned jar archive from your local Fiji installation and then re-run the MiToBo operator.<br />
<li> For some of our operators special issues exist and require special treatment:<br />
<ul><br />
<li> [[Applications/CellBoundaryExtractor2D| CellBoundaryExtractor2D]]: there are version conflicts with regard to the '''JGraphT library''' used by this operator and also by default included in every Fiji distribution; please refer to installation instructions on the [[Applications/CellBoundaryExtractor2D|webpage of the operator]] for a workaround<br />
</ul><br />
</ul><br />
<br />
<br><br />
<br />
== Using MiToBo with ImageJ ==<br />
<br />
'''Important Note:''' These instructions refer to ImageJ 1.<br />
<br />
<br><br />
General remarks:<br><br />
For using MiToBo with ImageJ it is the easiest to download the latest distribution zipfile (*-bin.zip) from<br><br />
<br />
[https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/ https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/]<br><br />
<br />
which already includes '''''all''''' dependencies and ships with some scripts to run MiToBo's operators and plugins out of the box.<br />
<br />
=== Linux ===<br />
<br />
Using MiToBo with a [[Installation/Linux|Linux operating system]].<br />
<br />
<br><br />
<br />
=== Windows ===<br />
<br />
Using MiToBo with a [[Installation/Windows|Windows operating system]].</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Installation&diff=1028Installation2023-11-29T10:56:20Z<p>Moeller: /* The MiToBo Binary Zip File */</p>
<hr />
<div>== General remarks ==<br />
<br />
There are two common ways to work with MiToBo:<br />
<ul><br />
<li> just using the operators included in MiToBo for improving your work and easing image processing tasks, e.g., via ImageJ or Fiji<br />
<li> using the MiToBo API to write operators, plugins and other image analysis applications on your own<br />
</ul><br />
The functionality of MiToBo is best used from within ImageJ or Fiji. In case that you aim to use MiToBo for your own development, you need to download the binaries explicitly. The actual installation instructions differ in some parts depending on which way of using MiToBo you have in mind.<br> Below we will first outline more details about the installation steps required for simply using MiToBo's operators in ImageJ and Fiji, and then provide some notes regarding the binary zip file. Finally we will present some details for using MiToBo's API with your own code.<br />
<br />
<blockquote style="background-color: lightgrey; border: solid thin grey;"><br />
'''[[The recommended way to install and run MiToBo and its operators/plugins is via Fiji!]]'''<br><br />
MiToBo has its own Fiji update site named "MiToBo".<br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br><br />
<br />
To enable this site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
<br />
Note that for some plugins (e.g., PaCeQuant) also the "Biomedgroup" update site needs to be activated.<br />
</blockquote><br />
<br />
== Using MiToBo with Fiji ==<br />
Since release 1.5 MiToBo features a Fiji update site and the easiest way to use MiToBo's operators and plugins is to enable the update site in your Fiji installation. <br> The MiToBo update site is<br><br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br />
<br />
To enable the site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
<br />
'''Important notices:'''<br> <br />
<ul><br />
<li> Occasionally MiToBo '''operators crash when run from within Fiji'''. The reason for this behaviour are most of the time '''conflicting jar archives''' delivered with the Fiji distribution.<br> We figured out that particularly the jar file<br />
<br />
* jars/bio-formats/formats-common-5.1.x.jar<br />
<br />
often causes such trouble. Thus, if you encounter problems running MiToBo operators, please try to locally delete or uninstall the abovementioned jar archive from your local Fiji installation and then re-run the MiToBo operator.<br />
<li> For some of our operators special issues exist and require special treatment:<br />
<ul><br />
<li> [[Applications/CellBoundaryExtractor2D| CellBoundaryExtractor2D]]: there are version conflicts with regard to the '''JGraphT library''' used by this operator and also by default included in every Fiji distribution; please refer to installation instructions on the [[Applications/CellBoundaryExtractor2D|webpage of the operator]] for a workaround<br />
</ul><br />
</ul><br />
<br />
<br><br />
<br />
== Using MiToBo with ImageJ ==<br />
<br />
'''Important Note:''' These instructions refer to ImageJ 1.<br />
<br />
<br><br />
General remarks:<br><br />
For using MiToBo with ImageJ it is the easiest to download the latest distribution zipfile (*-bin.zip) from<br><br />
<br />
[https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/ https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/]<br><br />
<br />
which already includes '''''all''''' dependencies and ships with some scripts to run MiToBo's operators and plugins out of the box.<br />
<br />
=== Linux ===<br />
<br />
Using MiToBo with a [[Installation/Linux|Linux operating system]].<br />
<br />
<br><br />
<br />
=== Windows ===<br />
<br />
Using MiToBo with a [[Installation/Windows|Windows operating system]].<br />
<br />
<br><br />
<br />
== The MiToBo Binary Zip File ==<br />
<br />
To get the current release of MiToBo (e.g. for using it as a library for your own developments) either download and extract the MiToBo Binary zip file from [https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo/ https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo/] or clone our Github repository [https://github.com/mitobo-hub/mitobo https://github.com/mitobo-hub/mitobo].<br> You will find the following structure of directories and files:<br />
* lib - includes nesessary libaries for Linux and Windows<br />
* licences - includes MiToBo license and licences for other software used by MiToBo<br />
* macros - includes the MiToBo macro toolset<br />
* plugins - includes MiToBo jar and other jars used by MiToBo<br />
* testimages - some sample images<br />
* ''MiToBo-Guide-1.0.pdf'' - the user and programmer guide for MiToBo<br />
* ''oprunner.sh'' - shell script to run MiToBo operators from commandline (Linux only)<br />
* ''run.sh'' - shell script to run ImageJ with MiToBo (Linux only)<br />
* ''README'' - with basic information<br />
<br />
== Using MiToBo's APIs ==<br />
To use the API of MiToBo and benefit from MiToBo's functionality in your own code you just need to make the jar archive to be found in the zip file available on your classpath. In addition, make sure that all jar archives MiToBo depends on and which are listed on the [[downloads|Download page]] are also in your classpath.<br> Note that the jars are also included in the MiToBo's binary zip file, thus, you don't need to download them manually.</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Installation&diff=1027Installation2023-11-29T10:54:25Z<p>Moeller: </p>
<hr />
<div>== General remarks ==<br />
<br />
There are two common ways to work with MiToBo:<br />
<ul><br />
<li> just using the operators included in MiToBo for improving your work and easing image processing tasks, e.g., via ImageJ or Fiji<br />
<li> using the MiToBo API to write operators, plugins and other image analysis applications on your own<br />
</ul><br />
The functionality of MiToBo is best used from within ImageJ or Fiji. In case that you aim to use MiToBo for your own development, you need to download the binaries explicitly. The actual installation instructions differ in some parts depending on which way of using MiToBo you have in mind.<br> Below we will first outline more details about the installation steps required for simply using MiToBo's operators in ImageJ and Fiji, and then provide some notes regarding the binary zip file. Finally we will present some details for using MiToBo's API with your own code.<br />
<br />
<blockquote style="background-color: lightgrey; border: solid thin grey;"><br />
'''[[The recommended way to install and run MiToBo and its operators/plugins is via Fiji!]]'''<br><br />
MiToBo has its own Fiji update site named "MiToBo".<br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br><br />
<br />
To enable this site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
<br />
Note that for some plugins (e.g., PaCeQuant) also the "Biomedgroup" update site needs to be activated.<br />
</blockquote><br />
<br />
== Using MiToBo with Fiji ==<br />
Since release 1.5 MiToBo features a Fiji update site and the easiest way to use MiToBo's operators and plugins is to enable the update site in your Fiji installation. <br> The MiToBo update site is<br><br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br />
<br />
To enable the site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
<br />
'''Important notices:'''<br> <br />
<ul><br />
<li> Occasionally MiToBo '''operators crash when run from within Fiji'''. The reason for this behaviour are most of the time '''conflicting jar archives''' delivered with the Fiji distribution.<br> We figured out that particularly the jar file<br />
<br />
* jars/bio-formats/formats-common-5.1.x.jar<br />
<br />
often causes such trouble. Thus, if you encounter problems running MiToBo operators, please try to locally delete or uninstall the abovementioned jar archive from your local Fiji installation and then re-run the MiToBo operator.<br />
<li> For some of our operators special issues exist and require special treatment:<br />
<ul><br />
<li> [[Applications/CellBoundaryExtractor2D| CellBoundaryExtractor2D]]: there are version conflicts with regard to the '''JGraphT library''' used by this operator and also by default included in every Fiji distribution; please refer to installation instructions on the [[Applications/CellBoundaryExtractor2D|webpage of the operator]] for a workaround<br />
</ul><br />
</ul><br />
<br />
<br><br />
<br />
== Using MiToBo with ImageJ ==<br />
<br />
'''Important Note:''' These instructions refer to ImageJ 1.<br />
<br />
<br><br />
General remarks:<br><br />
For using MiToBo with ImageJ it is the easiest to download the latest distribution zipfile (*-bin.zip) from<br><br />
<br />
[https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/ https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/]<br><br />
<br />
which already includes '''''all''''' dependencies and ships with some scripts to run MiToBo's operators and plugins out of the box.<br />
<br />
=== Linux ===<br />
<br />
Using MiToBo with a [[Installation/Linux|Linux operating system]].<br />
<br />
<br><br />
<br />
=== Windows ===<br />
<br />
Using MiToBo with a [[Installation/Windows|Windows operating system]].<br />
<br />
<br><br />
<br />
== The MiToBo Binary Zip File ==<br />
<br />
To get the current release of MiToBo download and extract the MiToBo Binary zip file from [https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo/ https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo/].<br> You will find the following structure of directories and files:<br />
* lib - includes nesessary libaries for Linux and Windows<br />
* licences - includes MiToBo license and licences for other software used by MiToBo<br />
* macros - includes the MiToBo macro toolset<br />
* plugins - includes MiToBo jar and other jars used by MiToBo<br />
* testimages - some sample images<br />
* ''MiToBo-Guide-1.0.pdf'' - the user and programmer guide for MiToBo<br />
* ''oprunner.sh'' - shell script to run MiToBo operators from commandline (Linux only)<br />
* ''run.sh'' - shell script to run ImageJ with MiToBo (Linux only)<br />
* ''README'' - with basic information<br />
<br />
== Using MiToBo's APIs ==<br />
To use the API of MiToBo and benefit from MiToBo's functionality in your own code you just need to make the jar archive to be found in the zip file available on your classpath. In addition, make sure that all jar archives MiToBo depends on and which are listed on the [[downloads|Download page]] are also in your classpath.<br> Note that the jars are also included in the MiToBo's binary zip file, thus, you don't need to download them manually.</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Installation&diff=1026Installation2023-11-29T10:53:20Z<p>Moeller: /* The MiToBo Binary Zip File */</p>
<hr />
<div>== General remarks ==<br />
<br />
There are two common ways to work with MiToBo:<br />
<ul><br />
<li> just using the operators included in MiToBo for improving your work and easing image processing tasks, e.g., via ImageJ or Fiji<br />
<li> using the MiToBo API to write operators, plugins and other image analysis applications on your own<br />
</ul><br />
The functionality of MiToBo is best used from within ImageJ or Fiji. In case that you aim to use MiToBo for your own development, you need to download the binaries explicitly. The actual installation instructions differ in some parts depending on which way of using MiToBo you have in mind.<br> Below we will first outline more details about the installation steps required for simply using MiToBo's operators in ImageJ and Fiji, and then provide some notes regarding the binary zip file. Finally we will present some details for using MiToBo's API with your own code.<br />
<br />
<blockquote style="background-color: lightgrey; border: solid thin grey;"><br />
'''[[The recommended way to install and run MiToBo and its operators/plugins is via Fiji!]]'''<br><br />
MiToBo has its own Fiji update site named "MiToBo".<br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br><br />
<br />
To enable this site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
<br />
Note that for some plugins (e.g., PaCeQuant) also the "Biomedgroup" update site needs to be activated.<br />
</blockquote><br />
<br />
== Using MiToBo with Fiji ==<br />
Since release 1.5 MiToBo features a Fiji update site and the easiest way to use MiToBo's operators and plugins is to enable the update site in your Fiji installation. <br> The MiToBo update site is<br><br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br />
<br />
To enable the site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
<br />
'''Important notices:'''<br> <br />
<ul><br />
<li> Occasionally MiToBo '''operators crash when run from within Fiji'''. The reason for this behaviour are most of the time '''conflicting jar archives''' delivered with the Fiji distribution.<br> We figured out that particularly the jar file<br />
<br />
* jars/bio-formats/formats-common-5.1.x.jar<br />
<br />
often causes such trouble. Thus, if you encounter problems running MiToBo operators, please try to locally delete or uninstall the abovementioned jar archive from your local Fiji installation and then re-run the MiToBo operator.<br />
<li> For some of our operators special issues exist and require special treatment:<br />
<ul><br />
<li> [[Applications/CellBoundaryExtractor2D| CellBoundaryExtractor2D]]: there are version conflicts with regard to the '''JGraphT library''' used by this operator and also by default included in every Fiji distribution; please refer to installation instructions on the [[Applications/CellBoundaryExtractor2D|webpage of the operator]] for a workaround<br />
</ul><br />
</ul><br />
<br />
<br><br />
<br />
== Using MiToBo with ImageJ ==<br />
<br />
'''Important Note:''' These instructions refer to ImageJ 1.<br />
<br />
<br><br />
General remarks:<br><br />
For using MiToBo with ImageJ it is the easiest to download the latest distribution zipfile (*-bin.zip) from<br><br />
<br />
[https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/ https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/]<br><br />
<br />
which already includes '''''all''''' dependencies and ships with some scripts to run MiToBo's operators and plugins out of the box.<br />
<br />
=== Linux ===<br />
<br />
Using MiToBo with a [[Installation/Linux|Linux operating system]].<br />
<br />
<br><br />
<br />
=== Windows ===<br />
<br />
Using MiToBo with a [[Installation/Windows|Windows operating system]].<br />
<br />
<br><br />
<br />
== The MiToBo Binary Zip File ==<br />
<br />
To get the current release of MiToBo download and extract the MiToBo Binary zip file from .<br> You will find the following structure of directories and files:<br />
* lib - includes nesessary libaries for Linux and Windows<br />
* licences - includes MiToBo license and licences for other software used by MiToBo<br />
* macros - includes the MiToBo macro toolset<br />
* plugins - includes MiToBo jar and other jars used by MiToBo<br />
* testimages - some sample images<br />
* ''MiToBo-Guide-1.0.pdf'' - the user and programmer guide for MiToBo<br />
* ''oprunner.sh'' - shell script to run MiToBo operators from commandline (Linux only)<br />
* ''run.sh'' - shell script to run ImageJ with MiToBo (Linux only)<br />
* ''README'' - with basic information<br />
<br />
== Using MiToBo's APIs ==<br />
To use the API of MiToBo and benefit from MiToBo's functionality in your own code you just need to make the jar archive to be found in the zip file available on your classpath. In addition, make sure that all jar archives MiToBo depends on and which are listed on the [[downloads|Download page]] are also in your classpath.<br> Note that the jars are also included in the MiToBo's binary zip file, thus, you don't need to download them manually.</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Installation&diff=1025Installation2023-11-29T10:51:55Z<p>Moeller: /* Using MiToBo with ImageJ */</p>
<hr />
<div>== General remarks ==<br />
<br />
There are two common ways to work with MiToBo:<br />
<ul><br />
<li> just using the operators included in MiToBo for improving your work and easing image processing tasks, e.g., via ImageJ or Fiji<br />
<li> using the MiToBo API to write operators, plugins and other image analysis applications on your own<br />
</ul><br />
The functionality of MiToBo is best used from within ImageJ or Fiji. In case that you aim to use MiToBo for your own development, you need to download the binaries explicitly. The actual installation instructions differ in some parts depending on which way of using MiToBo you have in mind.<br> Below we will first outline more details about the installation steps required for simply using MiToBo's operators in ImageJ and Fiji, and then provide some notes regarding the binary zip file. Finally we will present some details for using MiToBo's API with your own code.<br />
<br />
<blockquote style="background-color: lightgrey; border: solid thin grey;"><br />
'''[[The recommended way to install and run MiToBo and its operators/plugins is via Fiji!]]'''<br><br />
MiToBo has its own Fiji update site named "MiToBo".<br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br><br />
<br />
To enable this site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
<br />
Note that for some plugins (e.g., PaCeQuant) also the "Biomedgroup" update site needs to be activated.<br />
</blockquote><br />
<br />
== Using MiToBo with Fiji ==<br />
Since release 1.5 MiToBo features a Fiji update site and the easiest way to use MiToBo's operators and plugins is to enable the update site in your Fiji installation. <br> The MiToBo update site is<br><br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br />
<br />
To enable the site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
<br />
'''Important notices:'''<br> <br />
<ul><br />
<li> Occasionally MiToBo '''operators crash when run from within Fiji'''. The reason for this behaviour are most of the time '''conflicting jar archives''' delivered with the Fiji distribution.<br> We figured out that particularly the jar file<br />
<br />
* jars/bio-formats/formats-common-5.1.x.jar<br />
<br />
often causes such trouble. Thus, if you encounter problems running MiToBo operators, please try to locally delete or uninstall the abovementioned jar archive from your local Fiji installation and then re-run the MiToBo operator.<br />
<li> For some of our operators special issues exist and require special treatment:<br />
<ul><br />
<li> [[Applications/CellBoundaryExtractor2D| CellBoundaryExtractor2D]]: there are version conflicts with regard to the '''JGraphT library''' used by this operator and also by default included in every Fiji distribution; please refer to installation instructions on the [[Applications/CellBoundaryExtractor2D|webpage of the operator]] for a workaround<br />
</ul><br />
</ul><br />
<br />
<br><br />
<br />
== Using MiToBo with ImageJ ==<br />
<br />
'''Important Note:''' These instructions refer to ImageJ 1.<br />
<br />
<br><br />
General remarks:<br><br />
For using MiToBo with ImageJ it is the easiest to download the latest distribution zipfile (*-bin.zip) from<br><br />
<br />
[https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/ https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/]<br><br />
<br />
which already includes '''''all''''' dependencies and ships with some scripts to run MiToBo's operators and plugins out of the box.<br />
<br />
=== Linux ===<br />
<br />
Using MiToBo with a [[Installation/Linux|Linux operating system]].<br />
<br />
<br><br />
<br />
=== Windows ===<br />
<br />
Using MiToBo with a [[Installation/Windows|Windows operating system]].<br />
<br />
<br><br />
<br />
== The [[downloads|MiToBo Binary]] Zip File ==<br />
<br />
To get the current release of MiToBo download and extract the [[downloads|MiToBo Binary zip file]].<br> You will find the following structure of directories and files:<br />
* lib - includes nesessary libaries for Linux and Windows<br />
* licences - includes MiToBo license and licences for other software used by MiToBo<br />
* macros - includes the MiToBo macro toolset<br />
* plugins - includes MiToBo jar and other jars used by MiToBo<br />
* testimages - some sample images<br />
* ''MiToBo-Guide-1.0.pdf'' - the user and programmer guide for MiToBo<br />
* ''oprunner.sh'' - shell script to run MiToBo operators from commandline (Linux only)<br />
* ''run.sh'' - shell script to run ImageJ with MiToBo (Linux only)<br />
* ''README'' - with basic information<br />
<br />
== Using MiToBo's APIs ==<br />
To use the API of MiToBo and benefit from MiToBo's functionality in your own code you just need to make the jar archive to be found in the zip file available on your classpath. In addition, make sure that all jar archives MiToBo depends on and which are listed on the [[downloads|Download page]] are also in your classpath.<br> Note that the jars are also included in the MiToBo's binary zip file, thus, you don't need to download them manually.</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Installation&diff=1024Installation2023-11-29T10:48:24Z<p>Moeller: /* General remarks */</p>
<hr />
<div>== General remarks ==<br />
<br />
There are two common ways to work with MiToBo:<br />
<ul><br />
<li> just using the operators included in MiToBo for improving your work and easing image processing tasks, e.g., via ImageJ or Fiji<br />
<li> using the MiToBo API to write operators, plugins and other image analysis applications on your own<br />
</ul><br />
The functionality of MiToBo is best used from within ImageJ or Fiji. In case that you aim to use MiToBo for your own development, you need to download the binaries explicitly. The actual installation instructions differ in some parts depending on which way of using MiToBo you have in mind.<br> Below we will first outline more details about the installation steps required for simply using MiToBo's operators in ImageJ and Fiji, and then provide some notes regarding the binary zip file. Finally we will present some details for using MiToBo's API with your own code.<br />
<br />
<blockquote style="background-color: lightgrey; border: solid thin grey;"><br />
'''[[The recommended way to install and run MiToBo and its operators/plugins is via Fiji!]]'''<br><br />
MiToBo has its own Fiji update site named "MiToBo".<br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br><br />
<br />
To enable this site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
<br />
Note that for some plugins (e.g., PaCeQuant) also the "Biomedgroup" update site needs to be activated.<br />
</blockquote><br />
<br />
== Using MiToBo with Fiji ==<br />
Since release 1.5 MiToBo features a Fiji update site and the easiest way to use MiToBo's operators and plugins is to enable the update site in your Fiji installation. <br> The MiToBo update site is<br><br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br />
<br />
To enable the site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
<br />
'''Important notices:'''<br> <br />
<ul><br />
<li> Occasionally MiToBo '''operators crash when run from within Fiji'''. The reason for this behaviour are most of the time '''conflicting jar archives''' delivered with the Fiji distribution.<br> We figured out that particularly the jar file<br />
<br />
* jars/bio-formats/formats-common-5.1.x.jar<br />
<br />
often causes such trouble. Thus, if you encounter problems running MiToBo operators, please try to locally delete or uninstall the abovementioned jar archive from your local Fiji installation and then re-run the MiToBo operator.<br />
<li> For some of our operators special issues exist and require special treatment:<br />
<ul><br />
<li> [[Applications/CellBoundaryExtractor2D| CellBoundaryExtractor2D]]: there are version conflicts with regard to the '''JGraphT library''' used by this operator and also by default included in every Fiji distribution; please refer to installation instructions on the [[Applications/CellBoundaryExtractor2D|webpage of the operator]] for a workaround<br />
</ul><br />
</ul><br />
<br />
<br><br />
<br />
== Using MiToBo with ImageJ ==<br />
<br />
'''Important Note:''' These instructions refer to ImageJ 1 only, instructions for ImageJ 2.0 will follow soon.<br />
<br />
<br><br />
<br />
=== Linux ===<br />
<br />
Using MiToBo with a [[Installation/Linux|Linux operating system]].<br />
<br />
<br><br />
<br />
=== Windows ===<br />
<br />
Using MiToBo with a [[Installation/Windows|Windows operating system]].<br />
<br />
<br><br />
<br />
== The [[downloads|MiToBo Binary]] Zip File ==<br />
<br />
To get the current release of MiToBo download and extract the [[downloads|MiToBo Binary zip file]].<br> You will find the following structure of directories and files:<br />
* lib - includes nesessary libaries for Linux and Windows<br />
* licences - includes MiToBo license and licences for other software used by MiToBo<br />
* macros - includes the MiToBo macro toolset<br />
* plugins - includes MiToBo jar and other jars used by MiToBo<br />
* testimages - some sample images<br />
* ''MiToBo-Guide-1.0.pdf'' - the user and programmer guide for MiToBo<br />
* ''oprunner.sh'' - shell script to run MiToBo operators from commandline (Linux only)<br />
* ''run.sh'' - shell script to run ImageJ with MiToBo (Linux only)<br />
* ''README'' - with basic information<br />
<br />
== Using MiToBo's APIs ==<br />
To use the API of MiToBo and benefit from MiToBo's functionality in your own code you just need to make the jar archive to be found in the zip file available on your classpath. In addition, make sure that all jar archives MiToBo depends on and which are listed on the [[downloads|Download page]] are also in your classpath.<br> Note that the jars are also included in the MiToBo's binary zip file, thus, you don't need to download them manually.</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Installation&diff=1023Installation2023-11-29T10:44:18Z<p>Moeller: /* General remarks */</p>
<hr />
<div>== General remarks ==<br />
<br />
There are two common ways to work with MiToBo:<br />
<ul><br />
<li> just using the operators included in MiToBo for improving your work and easing image processing tasks, e.g., via ImageJ or Fiji<br />
<li> using the MiToBo API to write operators, plugins and other image analysis applications on your own<br />
</ul><br />
The functionality of MiToBo is best used from within ImageJ or Fiji. In case that you aim to use MiToBo for your own development, you need to download the binaries explicitly. The actual installation instructions differ in some parts depending on which way of using MiToBo you have in mind.<br> Below we will first outline more details about the installation steps required for simply using MiToBo's operators in ImageJ and Fiji, and then provide some notes regarding the binary zip file. Finally we will present some details for using MiToBo's API with your own code.<br />
<br />
<br><br />
<br />
== Using MiToBo with Fiji ==<br />
Since release 1.5 MiToBo features a Fiji update site and the easiest way to use MiToBo's operators and plugins is to enable the update site in your Fiji installation. <br> The MiToBo update site is<br><br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br />
<br />
To enable the site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
<br />
'''Important notices:'''<br> <br />
<ul><br />
<li> Occasionally MiToBo '''operators crash when run from within Fiji'''. The reason for this behaviour are most of the time '''conflicting jar archives''' delivered with the Fiji distribution.<br> We figured out that particularly the jar file<br />
<br />
* jars/bio-formats/formats-common-5.1.x.jar<br />
<br />
often causes such trouble. Thus, if you encounter problems running MiToBo operators, please try to locally delete or uninstall the abovementioned jar archive from your local Fiji installation and then re-run the MiToBo operator.<br />
<li> For some of our operators special issues exist and require special treatment:<br />
<ul><br />
<li> [[Applications/CellBoundaryExtractor2D| CellBoundaryExtractor2D]]: there are version conflicts with regard to the '''JGraphT library''' used by this operator and also by default included in every Fiji distribution; please refer to installation instructions on the [[Applications/CellBoundaryExtractor2D|webpage of the operator]] for a workaround<br />
</ul><br />
</ul><br />
<br />
<br><br />
<br />
== Using MiToBo with ImageJ ==<br />
<br />
'''Important Note:''' These instructions refer to ImageJ 1 only, instructions for ImageJ 2.0 will follow soon.<br />
<br />
<br><br />
<br />
=== Linux ===<br />
<br />
Using MiToBo with a [[Installation/Linux|Linux operating system]].<br />
<br />
<br><br />
<br />
=== Windows ===<br />
<br />
Using MiToBo with a [[Installation/Windows|Windows operating system]].<br />
<br />
<br><br />
<br />
== The [[downloads|MiToBo Binary]] Zip File ==<br />
<br />
To get the current release of MiToBo download and extract the [[downloads|MiToBo Binary zip file]].<br> You will find the following structure of directories and files:<br />
* lib - includes nesessary libaries for Linux and Windows<br />
* licences - includes MiToBo license and licences for other software used by MiToBo<br />
* macros - includes the MiToBo macro toolset<br />
* plugins - includes MiToBo jar and other jars used by MiToBo<br />
* testimages - some sample images<br />
* ''MiToBo-Guide-1.0.pdf'' - the user and programmer guide for MiToBo<br />
* ''oprunner.sh'' - shell script to run MiToBo operators from commandline (Linux only)<br />
* ''run.sh'' - shell script to run ImageJ with MiToBo (Linux only)<br />
* ''README'' - with basic information<br />
<br />
== Using MiToBo's APIs ==<br />
To use the API of MiToBo and benefit from MiToBo's functionality in your own code you just need to make the jar archive to be found in the zip file available on your classpath. In addition, make sure that all jar archives MiToBo depends on and which are listed on the [[downloads|Download page]] are also in your classpath.<br> Note that the jars are also included in the MiToBo's binary zip file, thus, you don't need to download them manually.</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Downloads&diff=1022Downloads2023-11-29T10:43:18Z<p>Moeller: /* Quick Start */</p>
<hr />
<div>== Quick Start ==<br />
The easiest and fastest way to install and run MiToBo is to activate MiToBo's update site in Fiji:<br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br><br />
<br />
To enable this site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
<br />
More details how to install and run MiToBo can be found on our [[Installation]] page.<br />
<br><br />
<br />
== Releases and Downloads ==<br />
<br />
The current release of the MiToBo core distribution and also of the extended MiToBo-Plugins distribution is 2.3.1.<br />
<br />
Since release 1.3 we support Maven for managing MiToBo's resources.<br> You can download the MiToBo distributions as well as the Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/#browse/de.unihalle.informatik.MiToBo https://moon.informatik.uni-halle.de/#browse/de.unihalle.informatik.MiToBo]<br />
<br />
There are two MiToBo distributions available:<br />
* <b>MiToBo:</b><br> this package contains the core of MiToBo, i.e. all operators, the MiToBo runners for operator execution and also Grappa;<br> <b>not included</b> are the plugins to run MiToBo from within ImageJ 1.x, hence, this distribution is mainly for stand-alone usage of MiToBo and development purposes<br><br />
* <b>MiToBo-Plugins:</b><br> this package contains the complete MiToBo distribution, some special plugins like the [[Applications/MTBCellCounter | MTB Cell Counter]], and in addition some ImageJ plugins to run MiToBo operators from within ImageJ; you should download the MiToBo-Plugins distribution if you like to use MiToBo with ImageJ<br><br />
<br />
Since release 1.8 MiToBo's implementation requires at least Java 1.8.<br />
<br><br />
<br />
At the bottom of this page additional files are available for download:<br />
* Old distributions: complete distributions including all dependencies, scripts, documentation, etc.<br />
* Binaries only: only the jar archives, no dependencies neither documentation<br />
* APIs: Javadoc APIs<br />
<br><br />
<br />
== Maven Project Template ==<br />
Using MiToBo as a library for own developments can best be done by making use of Maven.<br><br />
Particularly, Maven automatically resolves all dependencies which otherwise would have to be installed manually.<br />
<br />
For getting started with MiToBo and Maven a project template is provided: <br />
<br />
[http://www.informatik.uni-halle.de/mitobo/downloads/maven/mitobo-demo-project-1.2-src.zip Maven project template [zip]]<br />
<br />
The project is readily configured and you can immediately start with own developments.<br><br />
It also contains a demo operator showing the basic usage of MiToBo data types and operators on the code level.<br />
<br />
Make sure that you have installed Maven and a Java Develpoment Kit (JDK) in version 1.8 or higher.<br><br />
You can check the Java version by running 'mvn --version' from command line.<br> <br />
If an older Java version is used, let the 'JAVA_HOME' environment variable point to a folder containing a more recent JDK.<br />
<br />
You can run Maven directly from within the extracted folder. Alternatively the Maven template project can easily be imported into an IDE like Eclipse.<br><br />
The zip file contains a README file containing more information about installing and configuring the project template.<br />
<br/><br />
<br />
<br />
== Manual ==<br />
<br />
Detailed information about MiToBo, its API and usage, can be found in MiToBo's User and Programmer Guide.<br />
<br />
* MiToBo-Guide, Version 1.0 [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual.pdf pdf]<br />
<br><br />
<br />
== Additional resources ==<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release:<br />
* Chipory binary [http://www.informatik.uni-halle.de/mitobo/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www.informatik.uni-halle.de/mitobo/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br><br />
<br />
<br />
== Logo ==<br />
<br />
* MiToBo logo as [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.pdf PDF] or [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.png PNG]<br />
<br />
<br />
== Earlier releases of MiToBo (< 1.5) ==<br />
<br />
Since release 1.3 MiToBo's resources are available from our Maven archive server: [https://moon.informatik.uni-halle.de/archiva/]<br>Binaries, sources and documentation for versions older than the current release, but at least of version 1.3 or newer can be found there.<br> All other releases can be accessed via the list below.<br><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 1.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3-javadoc.jar jar]<br />
| March 31st, 2015 (Support for callbacks)<br />
|-<br />
| 1.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 1.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 1.2<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-bin-v1.2.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-v1.2.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-v1.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
|-<br />
| 1.1<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-bin-v1.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-v1.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-v1.1.zip zip]<br />
| March 1st, 2013<br />
|-<br />
| 1.0.5<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.5.zip zip]<br />
| October 23rd, 2012<br />
|-<br />
| 1.0.1<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.1.zip zip]<br />
| July 6th, 2012<br />
|-<br />
| 1.0.0<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.0.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.0.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.0.zip zip]<br />
| April 26th, 2012<br />
|-<br />
| 0.96<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.6.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.6.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-0.9.6.zip zip]<br />
| September 01, 2011<br />
|-<br />
| 0.95<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-0.9.5.zip zip]<br />
| June 08, 2011 (updated June 22nd, 2011)<br />
|-<br />
| 0.9<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.tar.gz tar.gz]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.tar.gz tar.gz]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.tar.gz tar.gz]<br />
| October 26, 2010<br />
|}<br />
<br/><br />
<br />
=== Requirements (for MiToBo < 1.3) ===<br />
MiToBo requires Java 1.6 or later. <br />
<br />
'''Note''': Java 1.7 is currently not fully supported!<br />
<br />
The following external jars are needed to run MiToBo plugins and use the code.<br/><br />
<b>Note that the binary zip file already includes all jars required, there is no need for explicit download!</b><br />
<br />
MiToBo depends on the following external jars:<br />
<br />
* [http://rsbweb.nih.gov/ij/ ImageJ], >= Version 1.47d<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://www.csie.ntu.edu.tw/~cjlin/libsvm/ LIBSVM], Version 3.1<br />
* [http://www.loci.wisc.edu/software/bio-formats/ Loci Tools], Version 4.3.3<br />
* [http://math.nist.gov/javanumerics/jama/ Jama], Version 1.0.2 <br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
* [http://sezpoz.java.net/ SezPoz], Version 1.9<br />
* [http://www.jgraph.com/mxdownload.html JGraph], Version 1.7.1.8<br />
<br />
* [https://jai-imageio.dev.java.net/ JAI ImageIO], Version 1.1 (only required for MiToBo 0.9)<br />
<br />
=== Project internal libraries ===<br />
<br />
MiToBo also relies on some libraries provided by the MiToBo project itself.<br><br />
In particular XML schemes for representing the history graphs and MiToBo's online help are included in separate jar archives.<br />
<br />
'''[[Note]]:''' <br/><br />
''' You do not need to download these libraries explicitly. If you download the binary zip file all jars and libraries are already included.''' <br/><br />
<br />
The MiToBo internal archive files included in the zip file are the following ones:<br />
<br />
* ALDGraphml, Version 1.0.0 (Alida extensions for [http://graphml.graphdrawing.org/ graphML]):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/aldgraphml/aldgraphml.jar jar]<br />
* MTBXml, Version 1.0.0 (MiToBo XML I/O for several datatypes, based on XMLBeans):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbxml/mtbxml.jar jar] <br />
* MiToBo-Help, Version 1.0.0 (MiToBo JavaHelp pages):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mitoboHelp/MiToBo-Help.jar jar] <br />
<br />
The following library is only required for MiToBo-0.9: <br />
<br />
* MTBImageIO-Ext, Version 0.9 (improved image I/O based on ImageIO-Ext):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff-0.9.jar jar]<br />
** Source code [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff_src-0.9.zip zip]<br />
** Alternatively, the [https://imageio-ext.dev.java.net/ ImageIO-Ext] library can be used, which depends on the [https://jai-imageio.dev.java.net/ JAI ImageIO] library and the [https://jai.dev.java.net/ JAI] library.<br/>MTBImageIO-Ext is simply the TIFF part of ImageIO-Ext with slight adjustments to remove dependency on the JAI library.<br />
<br/></div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Downloads&diff=1021Downloads2023-11-29T10:41:23Z<p>Moeller: </p>
<hr />
<div>== Quick Start ==<br />
The easiest and fastest way to run MiToBo is to activate MiToBo's update site in Fiji:<br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br><br />
<br />
To enable this site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
<br />
More details how to install and run MiToBo can be found on our [[Installation]] page.<br />
<br><br />
<br />
<br />
== Releases and Downloads ==<br />
<br />
The current release of the MiToBo core distribution and also of the extended MiToBo-Plugins distribution is 2.3.1.<br />
<br />
Since release 1.3 we support Maven for managing MiToBo's resources.<br> You can download the MiToBo distributions as well as the Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/#browse/de.unihalle.informatik.MiToBo https://moon.informatik.uni-halle.de/#browse/de.unihalle.informatik.MiToBo]<br />
<br />
There are two MiToBo distributions available:<br />
* <b>MiToBo:</b><br> this package contains the core of MiToBo, i.e. all operators, the MiToBo runners for operator execution and also Grappa;<br> <b>not included</b> are the plugins to run MiToBo from within ImageJ 1.x, hence, this distribution is mainly for stand-alone usage of MiToBo and development purposes<br><br />
* <b>MiToBo-Plugins:</b><br> this package contains the complete MiToBo distribution, some special plugins like the [[Applications/MTBCellCounter | MTB Cell Counter]], and in addition some ImageJ plugins to run MiToBo operators from within ImageJ; you should download the MiToBo-Plugins distribution if you like to use MiToBo with ImageJ<br><br />
<br />
Since release 1.8 MiToBo's implementation requires at least Java 1.8.<br />
<br><br />
<br />
At the bottom of this page additional files are available for download:<br />
* Old distributions: complete distributions including all dependencies, scripts, documentation, etc.<br />
* Binaries only: only the jar archives, no dependencies neither documentation<br />
* APIs: Javadoc APIs<br />
<br><br />
<br />
== Maven Project Template ==<br />
Using MiToBo as a library for own developments can best be done by making use of Maven.<br><br />
Particularly, Maven automatically resolves all dependencies which otherwise would have to be installed manually.<br />
<br />
For getting started with MiToBo and Maven a project template is provided: <br />
<br />
[http://www.informatik.uni-halle.de/mitobo/downloads/maven/mitobo-demo-project-1.2-src.zip Maven project template [zip]]<br />
<br />
The project is readily configured and you can immediately start with own developments.<br><br />
It also contains a demo operator showing the basic usage of MiToBo data types and operators on the code level.<br />
<br />
Make sure that you have installed Maven and a Java Develpoment Kit (JDK) in version 1.8 or higher.<br><br />
You can check the Java version by running 'mvn --version' from command line.<br> <br />
If an older Java version is used, let the 'JAVA_HOME' environment variable point to a folder containing a more recent JDK.<br />
<br />
You can run Maven directly from within the extracted folder. Alternatively the Maven template project can easily be imported into an IDE like Eclipse.<br><br />
The zip file contains a README file containing more information about installing and configuring the project template.<br />
<br/><br />
<br />
<br />
== Manual ==<br />
<br />
Detailed information about MiToBo, its API and usage, can be found in MiToBo's User and Programmer Guide.<br />
<br />
* MiToBo-Guide, Version 1.0 [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual.pdf pdf]<br />
<br><br />
<br />
== Additional resources ==<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release:<br />
* Chipory binary [http://www.informatik.uni-halle.de/mitobo/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www.informatik.uni-halle.de/mitobo/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br><br />
<br />
<br />
== Logo ==<br />
<br />
* MiToBo logo as [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.pdf PDF] or [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.png PNG]<br />
<br />
<br />
== Earlier releases of MiToBo (< 1.5) ==<br />
<br />
Since release 1.3 MiToBo's resources are available from our Maven archive server: [https://moon.informatik.uni-halle.de/archiva/]<br>Binaries, sources and documentation for versions older than the current release, but at least of version 1.3 or newer can be found there.<br> All other releases can be accessed via the list below.<br><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 1.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3-javadoc.jar jar]<br />
| March 31st, 2015 (Support for callbacks)<br />
|-<br />
| 1.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 1.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 1.2<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-bin-v1.2.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-v1.2.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-v1.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
|-<br />
| 1.1<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-bin-v1.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-v1.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-v1.1.zip zip]<br />
| March 1st, 2013<br />
|-<br />
| 1.0.5<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.5.zip zip]<br />
| October 23rd, 2012<br />
|-<br />
| 1.0.1<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.1.zip zip]<br />
| July 6th, 2012<br />
|-<br />
| 1.0.0<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.0.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.0.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.0.zip zip]<br />
| April 26th, 2012<br />
|-<br />
| 0.96<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.6.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.6.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-0.9.6.zip zip]<br />
| September 01, 2011<br />
|-<br />
| 0.95<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-0.9.5.zip zip]<br />
| June 08, 2011 (updated June 22nd, 2011)<br />
|-<br />
| 0.9<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.tar.gz tar.gz]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.tar.gz tar.gz]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.tar.gz tar.gz]<br />
| October 26, 2010<br />
|}<br />
<br/><br />
<br />
=== Requirements (for MiToBo < 1.3) ===<br />
MiToBo requires Java 1.6 or later. <br />
<br />
'''Note''': Java 1.7 is currently not fully supported!<br />
<br />
The following external jars are needed to run MiToBo plugins and use the code.<br/><br />
<b>Note that the binary zip file already includes all jars required, there is no need for explicit download!</b><br />
<br />
MiToBo depends on the following external jars:<br />
<br />
* [http://rsbweb.nih.gov/ij/ ImageJ], >= Version 1.47d<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://www.csie.ntu.edu.tw/~cjlin/libsvm/ LIBSVM], Version 3.1<br />
* [http://www.loci.wisc.edu/software/bio-formats/ Loci Tools], Version 4.3.3<br />
* [http://math.nist.gov/javanumerics/jama/ Jama], Version 1.0.2 <br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
* [http://sezpoz.java.net/ SezPoz], Version 1.9<br />
* [http://www.jgraph.com/mxdownload.html JGraph], Version 1.7.1.8<br />
<br />
* [https://jai-imageio.dev.java.net/ JAI ImageIO], Version 1.1 (only required for MiToBo 0.9)<br />
<br />
=== Project internal libraries ===<br />
<br />
MiToBo also relies on some libraries provided by the MiToBo project itself.<br><br />
In particular XML schemes for representing the history graphs and MiToBo's online help are included in separate jar archives.<br />
<br />
'''[[Note]]:''' <br/><br />
''' You do not need to download these libraries explicitly. If you download the binary zip file all jars and libraries are already included.''' <br/><br />
<br />
The MiToBo internal archive files included in the zip file are the following ones:<br />
<br />
* ALDGraphml, Version 1.0.0 (Alida extensions for [http://graphml.graphdrawing.org/ graphML]):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/aldgraphml/aldgraphml.jar jar]<br />
* MTBXml, Version 1.0.0 (MiToBo XML I/O for several datatypes, based on XMLBeans):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbxml/mtbxml.jar jar] <br />
* MiToBo-Help, Version 1.0.0 (MiToBo JavaHelp pages):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mitoboHelp/MiToBo-Help.jar jar] <br />
<br />
The following library is only required for MiToBo-0.9: <br />
<br />
* MTBImageIO-Ext, Version 0.9 (improved image I/O based on ImageIO-Ext):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff-0.9.jar jar]<br />
** Source code [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff_src-0.9.zip zip]<br />
** Alternatively, the [https://imageio-ext.dev.java.net/ ImageIO-Ext] library can be used, which depends on the [https://jai-imageio.dev.java.net/ JAI ImageIO] library and the [https://jai.dev.java.net/ JAI] library.<br/>MTBImageIO-Ext is simply the TIFF part of ImageIO-Ext with slight adjustments to remove dependency on the JAI library.<br />
<br/></div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Downloads&diff=1020Downloads2023-11-29T10:38:27Z<p>Moeller: </p>
<hr />
<div>== Quick Start ==<br />
The easiest and fastest way to run MiToBo is to activate MiToBo's update site in Fiji:<br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br><br />
<br />
To enable this site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
<br />
More details how to install and run MiToBo can be found on our [[Installation]] page.<br />
<br />
== Releases and Downloads ==<br />
<br />
The current release of the MiToBo core distribution and also of the extended MiToBo-Plugins distribution is 2.3.1.<br />
<br />
Since release 1.3 we support Maven for managing MiToBo's resources.<br> You can download the MiToBo distributions as well as the Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/#browse/de.unihalle.informatik.MiToBo https://moon.informatik.uni-halle.de/#browse/de.unihalle.informatik.MiToBo]<br />
<br />
There are two MiToBo distributions available:<br />
* <b>MiToBo:</b><br> this package contains the core of MiToBo, i.e. all operators, the MiToBo runners for operator execution and also Grappa;<br> <b>not included</b> are the plugins to run MiToBo from within ImageJ 1.x, hence, this distribution is mainly for stand-alone usage of MiToBo and development purposes<br><br />
* <b>MiToBo-Plugins:</b><br> this package contains the complete MiToBo distribution, some special plugins like the [[Applications/MTBCellCounter | MTB Cell Counter]], and in addition some ImageJ plugins to run MiToBo operators from within ImageJ; you should download the MiToBo-Plugins distribution if you like to use MiToBo with ImageJ<br><br />
<br />
Since release 1.8 MiToBo's implementation requires at least Java 1.8.<br />
<br><br />
<br />
At the bottom of this page additional files are available for download:<br />
* Old distributions: complete distributions including all dependencies, scripts, documentation, etc.<br />
* Binaries only: only the jar archives, no dependencies neither documentation<br />
* APIs: Javadoc APIs<br />
<br><br />
<br />
== Maven Project Template ==<br />
Using MiToBo as a library for own developments can best be done by making use of Maven.<br><br />
Particularly, Maven automatically resolves all dependencies which otherwise would have to be installed manually.<br />
<br />
For getting started with MiToBo and Maven a project template is provided: <br />
<br />
[http://www.informatik.uni-halle.de/mitobo/downloads/maven/mitobo-demo-project-1.2-src.zip Maven project template [zip]]<br />
<br />
The project is readily configured and you can immediately start with own developments.<br><br />
It also contains a demo operator showing the basic usage of MiToBo data types and operators on the code level.<br />
<br />
Make sure that you have installed Maven and a Java Develpoment Kit (JDK) in version 1.8 or higher.<br><br />
You can check the Java version by running 'mvn --version' from command line.<br> <br />
If an older Java version is used, let the 'JAVA_HOME' environment variable point to a folder containing a more recent JDK.<br />
<br />
You can run Maven directly from within the extracted folder. Alternatively the Maven template project can easily be imported into an IDE like Eclipse.<br><br />
The zip file contains a README file containing more information about installing and configuring the project template.<br />
<br/><br />
<br />
== Manual ==<br />
<br />
Detailed information about MiToBo, its API and usage, can be found in MiToBo's User and Programmer Guide.<br />
<br />
* MiToBo-Guide, Version 1.0 [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual.pdf pdf]<br />
<br/><br />
<br />
<br />
== Additional resources ==<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release:<br />
* Chipory binary [http://www.informatik.uni-halle.de/mitobo/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www.informatik.uni-halle.de/mitobo/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br/><br />
<br />
<br />
== Logo ==<br />
<br />
* MiToBo logo as [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.pdf PDF] or [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.png PNG]<br />
<br />
<br />
== Earlier releases of MiToBo (< 1.5) ==<br />
<br />
Since release 1.3 MiToBo's resources are available from our Maven archive server: [https://moon.informatik.uni-halle.de/archiva/]<br>Binaries, sources and documentation for versions older than the current release, but at least of version 1.3 or newer can be found there.<br> All other releases can be accessed via the list below.<br><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 1.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3-javadoc.jar jar]<br />
| March 31st, 2015 (Support for callbacks)<br />
|-<br />
| 1.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 1.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 1.2<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-bin-v1.2.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-v1.2.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-v1.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
|-<br />
| 1.1<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-bin-v1.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-v1.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-v1.1.zip zip]<br />
| March 1st, 2013<br />
|-<br />
| 1.0.5<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.5.zip zip]<br />
| October 23rd, 2012<br />
|-<br />
| 1.0.1<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.1.zip zip]<br />
| July 6th, 2012<br />
|-<br />
| 1.0.0<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.0.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.0.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.0.zip zip]<br />
| April 26th, 2012<br />
|-<br />
| 0.96<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.6.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.6.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-0.9.6.zip zip]<br />
| September 01, 2011<br />
|-<br />
| 0.95<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-0.9.5.zip zip]<br />
| June 08, 2011 (updated June 22nd, 2011)<br />
|-<br />
| 0.9<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.tar.gz tar.gz]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.tar.gz tar.gz]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.tar.gz tar.gz]<br />
| October 26, 2010<br />
|}<br />
<br/><br />
<br />
=== Requirements (for MiToBo < 1.3) ===<br />
MiToBo requires Java 1.6 or later. <br />
<br />
'''Note''': Java 1.7 is currently not fully supported!<br />
<br />
The following external jars are needed to run MiToBo plugins and use the code.<br/><br />
<b>Note that the binary zip file already includes all jars required, there is no need for explicit download!</b><br />
<br />
MiToBo depends on the following external jars:<br />
<br />
* [http://rsbweb.nih.gov/ij/ ImageJ], >= Version 1.47d<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://www.csie.ntu.edu.tw/~cjlin/libsvm/ LIBSVM], Version 3.1<br />
* [http://www.loci.wisc.edu/software/bio-formats/ Loci Tools], Version 4.3.3<br />
* [http://math.nist.gov/javanumerics/jama/ Jama], Version 1.0.2 <br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
* [http://sezpoz.java.net/ SezPoz], Version 1.9<br />
* [http://www.jgraph.com/mxdownload.html JGraph], Version 1.7.1.8<br />
<br />
* [https://jai-imageio.dev.java.net/ JAI ImageIO], Version 1.1 (only required for MiToBo 0.9)<br />
<br />
=== Project internal libraries ===<br />
<br />
MiToBo also relies on some libraries provided by the MiToBo project itself.<br><br />
In particular XML schemes for representing the history graphs and MiToBo's online help are included in separate jar archives.<br />
<br />
'''[[Note]]:''' <br/><br />
''' You do not need to download these libraries explicitly. If you download the binary zip file all jars and libraries are already included.''' <br/><br />
<br />
The MiToBo internal archive files included in the zip file are the following ones:<br />
<br />
* ALDGraphml, Version 1.0.0 (Alida extensions for [http://graphml.graphdrawing.org/ graphML]):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/aldgraphml/aldgraphml.jar jar]<br />
* MTBXml, Version 1.0.0 (MiToBo XML I/O for several datatypes, based on XMLBeans):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbxml/mtbxml.jar jar] <br />
* MiToBo-Help, Version 1.0.0 (MiToBo JavaHelp pages):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mitoboHelp/MiToBo-Help.jar jar] <br />
<br />
The following library is only required for MiToBo-0.9: <br />
<br />
* MTBImageIO-Ext, Version 0.9 (improved image I/O based on ImageIO-Ext):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff-0.9.jar jar]<br />
** Source code [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff_src-0.9.zip zip]<br />
** Alternatively, the [https://imageio-ext.dev.java.net/ ImageIO-Ext] library can be used, which depends on the [https://jai-imageio.dev.java.net/ JAI ImageIO] library and the [https://jai.dev.java.net/ JAI] library.<br/>MTBImageIO-Ext is simply the TIFF part of ImageIO-Ext with slight adjustments to remove dependency on the JAI library.<br />
<br/></div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Main_Page&diff=1019Main Page2023-11-29T10:27:17Z<p>Moeller: </p>
<hr />
<div>= MiToBo - A <span style="color:#CC0000">m</span>icroscope <span style="color:#CC0000">i</span>mage analysis <span style="color:#CC0000">to</span>ol<span style="color:#CC0000">bo</span>x =<br />
<br />
{|width="100%"<br />
|-<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''What is MiToBo?'''<br><br />
The Microscope Image Analysis Toolbox MiToBo is a toolbox with a large collection of basic and advanced functions and algorithms for processing and analyzing digital images. Many tools in MiToBo target at the analysis of various kinds of microscopy data, however, most of the functionality within MiToBo is generic (see [[Features|page of features]] for an overview). MiToBo is implemented as extension for the widely used image processing application [http://rsbweb.nih.gov/ij/ ImageJ]/[https://fiji.sc/ Fiji] and its new release [http://developer.imagej.net/ ImageJ 2.0]. All functions, operators and plugins of MiToBo are ready to be directly used as plugins in ImageJ and Fiji.<br /><br/><br />
<br />
'''Highlight operators and tools in MiToBo'''<br />
{|style="background-color:#f8f8ff"<br />
|style="text-align:left;width:10%|[[File:MiToBo_logo_CytoskeletonAnalyzer2D.png|border|72px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/CytoskeletonAnalyzer2D]]<br />
|style="text-align:left;width:80%|'''''[[Applications/CytoskeletonAnalyzer2D|CytoskeletonAnalyzer2D]]''''' for the quantification of cytoskeleton structural patterns in microscopy images with texture measures;<br><br />
to ease cell boundary extraction in data preparation we additionally provide the '''''[[Applications/CellBoundaryExtractor2D|CellBoundaryExtractor2D]]''''' and a handy '''''[[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]]'''''<br />
|-<br />
|style="text-align:left;width:10%|[[File:MiToBo_logo_PaCeQuant.png|border|72px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/PaCeQuantToolset]]<br />
|style="text-align:left;width:80%|'''''[[Applications/PaCeQuantToolset|PaCeQuant]]''''' and corresponding tools, i.e. the '''''[[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]]''''', the '''''[[Applications/FeatureColorMapper|FeatureColorMapper]]''''' and the R package '''''[[Applications/PaCeQuantAna|PaCeQuantAna]]''''', for quantification, visualization and statistical analysis of the morphology and shape characteristics of cells<br />
|-<br />
|style="text-align:left;width:10%|[[File:NeuronAnalyzer2D.png|border|72px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/NeuronAnalyzer2D]]<br />
|style="text-align:left;width:80%|'''''[[Applications/NeuronAnalyzer2D|Neuron Analyzer]]''''' for the segmentation of neurons in microscope images<br />
|-<br />
|style="text-align:left;width:10%|[[File:tracking_ES-2.gif|72px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/CellMigrationAnalyzer]]<br />
|style="text-align:left;width:80%|'''''[[Applications/CellMigrationAnalyzer|Cell Migration Analyzer]]''''' for analyzing single cell migration from time lapse image sequences<br />
|-<br />
|style="text-align:left;width:10%|[[File:GFP_U2OS_overlay.png|72px|left|border|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/ScratchAssayAnalyzer]]<br />
|style="text-align:left;width:80%|'''''[[Applications/ScratchAssayAnalyzer|Scratch Assay Analyzer]]''''' for analyzing microscope images from collective cell migration experiments<br />
|}<br />
For several other important operators and plugins documentation is available via the [[Operator_Documentation| Operator Documentation pages]] here in the Wiki.<br> <br />
The pages are structured according to the package structure of MiToBo which is also mirrored in the selection panel of MiToBo's operator runner.<br />
<br />
<br><br />
'''MiToBo for developers'''<br><br />
MiToBo aims not only to support users in analyzing their images, but also targets at developers by offering a programmer-friendly software framework and API for developing new algorithms.<br />
The MiToBo API completely separates the implementation of image processing algorithms from potential user interfaces based <br />
on [http://www.informatik.uni-halle.de/alida/ Alida] which is a library for easing the development of data analysis<br />
algorithms and tools. The main concept of Alida are <i>operators</i> as the core units for implementing data analysis algorithms. <br /><br />
Alida defines unified interfaces and execution procedures for operators which yield the fundament for its nice features like <br />
<ul><br />
<li> automatic documentation of complete analysis processes, e.g., leading from an input image to analysis results, in terms of processing graphs<br />
<li> automatic generation of commandline and graphical user interfaces<br />
<li> a graphical programming editor named '''''Grappa''''' automatically considering all implemented operators as potential processing nodes<br><br />
</ul><br />
<br />
<p><br />
MiToBo takes full advantage of Alida's features, hence, provides a framework for implementing image analysis algorithms allowing for automatic documentation and automatic user interface generation, and includes the graphical programming editor Grappa for user-friendly design of more complex processing pipelines.<br />
</p><br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Visit and follow MiToBo also at...'''<br><br />
{|<br />
|style="text-align:center;width:10%"|[[file:Imagej-128.png|90px|link=http://imagej.net/MiToBo]]<br />
|style="text-align:center;width:10%"|[[file:Git.png|90px|link=https://github.com/mitobo-hub]]<br />
|style="text-align:center;width:10%"|[[file:mtbtw.png|320px|link=https://twitter.com/MiToBo_Hal]]<br />
|style="text-align:center;width:10%"|[[file:logo.png|90px|link=http://imagejdocu.tudor.lu/doku.php?id=plugin:collections:mitobo_-_a_microscope_image_analysis_toolbox:start]]<br />
|style="text-align:center;width:10%"|[[file:logo-blue.png|90px|link=https://omictools.com/microscope-image-analysis-toolbox-tool]]<br />
|-<br />
|style="text-align:center;width:10%"|[http://imagej.net/MiToBo ImageJ.net]<br />
|style="text-align:center;width:10%"|[https://github.com/mitobo-hub GitHub]<br />
|style="text-align:center;width:10%"|[https://twitter.com/MiToBo_Hal Twitter]<br />
|style="text-align:center;width:10%"|[http://imagejdocu.tudor.lu/doku.php?id=plugin:collections:mitobo_-_a_microscope_image_analysis_toolbox:start ImageJ Docu Wiki]<br />
|style="text-align:center;width:10%"|[https://omictools.com/microscope-image-analysis-toolbox-tool OMIC Tools]<br />
|}<br />
</div><br />
</div><br />
|<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Latest News'''<br><br />
* 08/2023: MiToBo 2.3.1 has been released which fixes serious incompatibilities to Bioformats.<br />
* 07/2023: MiToBo 2.3 has been releases.<br><br />
* 05/2021: MiToBo 2.2 has been released.<br><br />
* 12/2020: MiToBo 2.1 has been released.<br> <br />
* 05/2020: MiToBo 2.0 has been released.<br> From now on the online help system relies on operator class annotations, and the release includes a [https://mitobo.informatik.uni-halle.de/index.php/Applications/PaCeQuantToolset PaCeQuant] update with new shape features and improvements for supplemental tools like the [https://mitobo.informatik.uni-halle.de/index.php/Applications/FeatureColorMapper FeatureColorMapper] and the [https://mitobo.informatik.uni-halle.de/index.php/Operators/Tools/Interactive/LabelImageEditor LabelImageEditor].<br />
* 07/2019: MiToBo 1.8.15 has been released fixing several issues with handling images in MiToBo.<br />
* 02/2019: MiToBo 1.8.14 has been released.<br />
<br />
The news archive can be found [[News Archive | here]].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''How to get MiToBo?'''<br><br />
* ImageJ-Users:<br> download the [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/1.8.7.1/mitobo-plugins-1.8.7.1-bin.zip MiToBo-Plugins package] and follow the installation instructions to be found [[Installation | here]]. <br />
* Fiji-Users:<br> simply select MiToBo's update site [http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo] in FijiIs list of update sites in your installation<br />
* use in general:<br> you can download MiToBo and the MiToBo plugins package [[Downloads | here]]. <br/> <br />
<br />
You can find the API documentation for the current release [http://www.informatik.uni-halle.de/mitobo/api/index.html here].<br/> <br />
Furthermore MiToBo offers you a user and programmer guide which you can download [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual.pdf here].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Support, Bug reports & Feature requests'''<br />
{|style="background-color:#f8f8ff"<br />
|style="text-align:left;width:20%|[[File:forum-image-sc.png|border|64px|left|link=https://forum.image.sc/]]<br />
|style="text-align:left;width:60%|To get help on your questions about MiToBo tools, plugins and operators you can use the forum at [https://forum.image.sc/ image.sc] tagging your post with [https://forum.image.sc/tags/mitobo #mitobo].<br />
|-<br />
|style="text-align:left;width:20%|[[file:Git.png|64px|link=https://github.com/mitobo-hub]]<br />
|style="text-align:left;width:60%|Bug reports and feature requests can be submitted as issues on [https://github.com/mitobo-hub/mitobo/issues Github].<br />
|-<br />
|style="text-align:left;width:20%|[[file:Email.png|center|36px|link=]]<br />
|style="text-align:left;width:60%|Alternatively you can also write an email to [mailto:mitobo@informatik.uni-halle.de mitobo@informatik.uni-halle.de].<br />
|}<br />
Before reporting a new bug or requesting a new feature, please check if that bug has already been submitted in the forum or on Github.<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Licensing information'''<br><br />
MiToBo is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Gnu PGP Public Key'''<br><br />
Since version 1.8.7 MiToBo and MiToBo-Plugins releases are PGP signed. MiToBo's [https://pgp.mit.edu/pks/lookup?op=get&search=0x259F7DD171EFF7A9 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/.<br />
</div><br />
</div><br />
|}</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Acknowledgements&diff=1018Acknowledgements2023-06-05T06:49:29Z<p>Moeller: </p>
<hr />
<div>__NOTOC__<br />
<br />
* The development of [http://mitobo.informatik.uni-halle.de/index.php/Applications/PaCeQuant PaCeQuant], the [http://mitobo.informatik.uni-halle.de/index.php/Applications/CytoskeletonAnalyzer2D CytoskeletonAnalyzer2D] and several other tools and operators have greatly profited from the image acquisition and user feedback as well as the overall intense scientific support of the group of [https://www.ipb-halle.de/en/employee/katharina-buerstenbinder/ Dr. Katharina Bürstenbinder], [https://www.ipb-halle.de/en/research/molecular-signal-processing/ Department of Molecular Signal Processing], [https://www.ipb-halle.de/en/ Leibniz Institute of Plant Biochemistry], Halle (Saale), Germany.<br/><br/><br />
<br />
* We thank [https://www.landw.uni-halle.de/prof/biom_ai/ Dr. Yvonne Pöschl-Grau], formerly member of the [https://www.idiv.de/en/groups_and_people/central_management/bioinformatics_unit_biu.html Bioinformatics Unit (BIU)] of the [https://www.idiv.de/en.html German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig] and now member of the [https://www.landw.uni-halle.de/prof/biom_ai/ Working Group for Biometry and Agricultural Informatics] of the Martin Luther University Halle-Wittenberg, for close collaboration in developing [http://mitobo.informatik.uni-halle.de/index.php/Applications/PaCeQuant PaCeQuant].<br/><br/><br />
<br />
* We greatfully acknowledge [https://www.biologie.uni-halle.de/institutsbereich_pflanzenphys/ag_schattat/2678173_2678352/#anchor2691932 Dr. Martin Schattat], Plant Organelle Shape and Dynamics Lab, [https://www.biologie.uni-halle.de/institutsbereich_pflanzenphys/ Institute of Plant Physiology], Martin Luther University Halle-Wittenberg, for the close collaboration, scientific support, image acquisition and comprehensive user feedback during the development of the MTBCellCounter and various other plant cell related operators.<br/><br/><br />
<br />
* Many thanks to the workgroup of Prof. Dr. Stefan Hüttelmaier ([http://www.medizin.uni-halle.de/index.php?id=326&L=1 Division for Molecular Cell Biology]) of the Martin Luther University Halle-Wittenberg) for their scientific support and image acquisition.<br/><br/><br />
<br />
* MiToBo builds on top of [https://imagej.net/Welcome ImageJ] and [https://fiji.sc/ Fiji] and takes great benefit from the infrastructure and very active community of theses tools. Hence, a big thanks goes to the ImageJ/Fiji development team around Wayne Rasband, Curtis Rueden and all the others for their never ending efforts to steadily push forward the tools.<br/><br/><br />
<br />
* We thank the [http://www.eclipse.org Eclipse Foundation] for developing the Eclipse IDE, which greatly accelerates the development of MiToBo.<br/><br/><br />
<br />
== Active MiToBo maintainers and core developers ==<br />
* Stefan Posch<br />
* Birgit Möller<br />
<br><br />
<br />
== Former members of the development team ==<br />
* Markus Glaß<br />
* Oliver Greß<br />
* Danny Misiak</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Applications/PaCeQuantAna&diff=1017Applications/PaCeQuantAna2023-06-05T06:41:30Z<p>Moeller: /* Email */</p>
<hr />
<div>== PaCeQuantAna: R package for Visualization and Statistical Analysis of Cell Shape Featues ==<br />
We provide an R package for visualizing and analyzing features extracted by PaCeQuant.<br><br />
<br />
<br />
The new version compatible with PaCeQuant as released in MiToBo 2.0 in May 2020 is out now! It can be downloaded here:<br />
<br />
* [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/paceQuant/paceQuantAna/PaCeQuantAna_1.0.3.tar.gz R package v1.0.3]<br />
<br />
<br />
=== Installation ===<br />
For installation in RStudio download the package and follow the instructions below:<br />
<br />
<ol><br />
<li> Install the following packages:<br />
<ul><br />
<li> '''caroline'''<br />
<li> '''gplots'''<br />
<li> '''dunn.test'''<br />
<li> '''sm'''<br />
<li> '''RColorBrewer'''<br />
</ul><br />
To this end start RStudio, select<br />
<blockquote>“Tools” → “Install Packages…” </blockquote><br />
from the menu bar.<br> Choose <blockquote>“Install from: Repository (CRAN)”</blockquote> and enter the names of the packages.<br> Activate <blockquote>“Install dependencies”.</blockquote><br />
<li> The multtest package can be installed via the following Bioconductor installation script:<br><br />
<ul> '''R versions < 3.5.0''':<br />
<blockquote>source ("<nowiki>http://bioconductor.org/biocLite.R</nowiki>")</blockquote><br />
<blockquote>biocLite("multtest")</blockquote><br />
</ul><br />
<ul> '''R versions >= 3.5.0''':<br />
<ul>If you do not have used Bioconductor before and have not installed any [http://bioconductor.org/install/ Bioconductor] packages yet, then:<br />
<blockquote>Install BiocManager and core packages from Bioconductor:<br />
<blockquote>if (!requireNamespace("BiocManager", quietly = TRUE))</blockquote><br />
<blockquote>install.packages("BiocManager")</blockquote><br />
<blockquote>BiocManager::install()</blockquote><br />
</ul><br />
<ul>Install specific packages e.g. "multtest"<br />
<blockquote>BiocManager::install("multtest")</blockquote><br />
</ul><br />
</ul><br />
<li> Install the PaCeQuantAna package selecting <br />
<blockquote>“Tools” → “Install Packages…”</blockquote> <br />
from the menu bar.<br> <br />
Choose <blockquote>“Install from: Package Archive File (.tgz; .tar.gz)"</blockquote> <br />
and select the tar.gz file of PaCeQuantAna via <blockquote>"Browse...".</blockquote><br />
</ol><br />
<br><br />
We use Arial or Helvetica fonts when creating the plots, which is often recommended for publication. Therefore you will need to prepare your working environment by once running <br><br />
<blockquote>library(extrafont)</blockquote><br />
<blockquote>font_import()</blockquote><br />
<blockquote>loadfonts()</blockquote><br />
This will initialize the creation of a font database.<br><br />
You can check which fonts where found and load by <br><br />
<blockquote>fonts()</blockquote><br />
<br />
=== Documentation ===<br />
<br />
Find more details of how to use the package and details about the general workflow in the vignette of the package by either navigating to the vignette in the Rstudio package manager tab or by typing <br />
<blockquote>vignette("PaCeQuantAna")</blockquote><br />
in the console.<br />
<br />
'''Please note:'''<br><br />
'''The vignette is currently under construction. An updated version will be released soon.'''<br><br />
<br />
The vignette contains comprehensive documentation of the various functions and options of the package.<br><br />
In addition, a sample workflow R script is provided which shows all commands to load your data, configure the output and do the analysis.<br><br />
You can directly copy the script into a file and load this file into the Rstudio editor to run it completely or line-wise.<br />
<br />
You can test the new version of the package with sample data and small workflows (R scripts) for analyses of developmental stages and mutant screening. Therefore we provide two archives:<br />
<br />
* [http://informatik.uni-halle.de/~poeschl/PaCeQuantAna/BookChapter2020/developmentalStages.zip Sample data and R scripts for analyses of developmental stages]<br />
<br />
* [http://informatik.uni-halle.de/~poeschl/PaCeQuantAna/BookChapter2020/mutantScreening.zip Sample data and R scripts for mutant screening]<br />
<br />
Both archives contain the specific <br><br />
<ul><br />
<li> sample data<br />
<li> workflows and <br />
<li> data description files<br />
</ul><br />
. <br />
The sample data sets are reduced to 2 microscopy images per group (time point or species). The workflows contain the function calls depicted in Fig. 5 in Poeschl et al 2020. The data description files are customized to fit e.g. the species and time points included in our analyses, color used or font face used.<br><br />
<br />
Both archives include ready to use workflows for provided sample data sets. Only the path to the folder of the extracted archive needs to be set as working directory in the corresponding R-scripts. <br> <br />
In detail '''developmentalStages.zip''' contains<br />
<ul><br />
<li> sample data: Time-series_2-3-5-7, a folder containing the data organised into folders<br />
<li> 3 workflows: 1 general workflow for analyses of developmental stages and 2 specific workflows for<br />
<ul><br />
<li> Col-0: including prepared outputFolder containing the customised data description file<br />
<li> Col-0_iqd5-1_iqd5-2: including prepared outputFolder containing the customised data description file<br />
</ul><br />
</ul><br />
<br><br />
In detail '''mutantScreening.zip''' contains<br />
<ul><br />
<li> sample data: Mutants, a folder containing the data organised into folders<br />
<li> 2 workflows: 1 general workflow for screening mutants and 1 specific workflow for<br />
<ul><br />
<li> mutant_screening: including prepared outputFolder containing the customised data description file<br />
</ul><br />
</ul><br />
<br />
=== Important notes ===<br />
<ul><br />
<li> By default the working directory (set with ''setwd(...)'') where the output folder will be created, and the data directory (set with ''dataDir'') must not be identical!<br> <br />
If you require these folders to be identical for whatever reason you need to manually edit the file ''data_description.csv'' in the output folder and delete the row referring to the output folder.<br />
<li> On Windows operating systems you may encounter problems with missing fonts, i.e., error messages like the following one:<br />
<blockquote>...</blockquote><br />
<blockquote>Error in pdf(file = paste0(outdir, fsep, base_file_name,</blockquote><br />
<blockquote>"_dunn_test_heatmap_adjusted_pvalues.pdf"),&nbsp; :</blockquote><br />
<blockquote>&nbsp; unknown family 'Arial'</blockquote> <br />
<blockquote>...</blockquote><br />
Initialize each of your workflows using PaCeQuantAna with<br />
<blockquote>library(extrafont)</blockquote><br />
This will initialize the Windows font database and should solve the problems.<br />
</ul><br />
<br />
<br />
<br><br />
===== Email =====<br />
[[file:Email.png|left|36px|link=]]<br />
Don't hesitate to send an email when you encounter a problem or when you have questions: [mailto:yvonne.poeschl-grau@landw.uni-halle.de yvonne.poeschl-grau@landw.uni-halle.de]<br><br />
<br />
<br><br />
<br />
=== Old versions ===<br />
The old version of PaCeQuantAna compatible with PaCeQuant results generated with MiToBo 1.8.x can be downloaded here:<br />
<br />
* [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/paceQuantEval/PaCeQuantAna_1.0.0.tar.gz R package v1.0.0]<br />
<br />
You can test the package on these sample data: [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/time_series.zip sample data for PaCeQuantAna]<br><br />
<br />
<br />
<!--<br />
== R script for Visualization and Statistical Analysis of Results ==<br />
We provide an R script for visualizing and analyzing results generated by PaCeQuant:<br />
<br />
* [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/paceQuantEval/PaCeQuantEval_version0.1.zip R script v0.1]<br />
* [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/paceQuantEval/README.PaCeQuantEval README]<br />
<br />
Before running the script you need to set some path variables in the header of the script file which, e.g., specify where to find the PaCeQuant result data and where to save the final plots. <br />
<br />
The script will include result data from the current directory and from all direct sub-directories of the current folder into its analysis.<br> Each folder is treated as one group of cells, and the analysis is designed to compare different groups of cells against each other.<br />
<br />
You can test the script on the sample data provided on this page.<br />
--></div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Applications/PaCeQuantAna&diff=1016Applications/PaCeQuantAna2023-03-23T16:13:37Z<p>Moeller: /* PaCeQuantAna: R package for Visualization and Statistical Analysis of Cell Shape Featues */</p>
<hr />
<div>== PaCeQuantAna: R package for Visualization and Statistical Analysis of Cell Shape Featues ==<br />
We provide an R package for visualizing and analyzing features extracted by PaCeQuant.<br><br />
<br />
<br />
The new version compatible with PaCeQuant as released in MiToBo 2.0 in May 2020 is out now! It can be downloaded here:<br />
<br />
* [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/paceQuant/paceQuantAna/PaCeQuantAna_1.0.3.tar.gz R package v1.0.3]<br />
<br />
<br />
=== Installation ===<br />
For installation in RStudio download the package and follow the instructions below:<br />
<br />
<ol><br />
<li> Install the following packages:<br />
<ul><br />
<li> '''caroline'''<br />
<li> '''gplots'''<br />
<li> '''dunn.test'''<br />
<li> '''sm'''<br />
<li> '''RColorBrewer'''<br />
</ul><br />
To this end start RStudio, select<br />
<blockquote>“Tools” → “Install Packages…” </blockquote><br />
from the menu bar.<br> Choose <blockquote>“Install from: Repository (CRAN)”</blockquote> and enter the names of the packages.<br> Activate <blockquote>“Install dependencies”.</blockquote><br />
<li> The multtest package can be installed via the following Bioconductor installation script:<br><br />
<ul> '''R versions < 3.5.0''':<br />
<blockquote>source ("<nowiki>http://bioconductor.org/biocLite.R</nowiki>")</blockquote><br />
<blockquote>biocLite("multtest")</blockquote><br />
</ul><br />
<ul> '''R versions >= 3.5.0''':<br />
<ul>If you do not have used Bioconductor before and have not installed any [http://bioconductor.org/install/ Bioconductor] packages yet, then:<br />
<blockquote>Install BiocManager and core packages from Bioconductor:<br />
<blockquote>if (!requireNamespace("BiocManager", quietly = TRUE))</blockquote><br />
<blockquote>install.packages("BiocManager")</blockquote><br />
<blockquote>BiocManager::install()</blockquote><br />
</ul><br />
<ul>Install specific packages e.g. "multtest"<br />
<blockquote>BiocManager::install("multtest")</blockquote><br />
</ul><br />
</ul><br />
<li> Install the PaCeQuantAna package selecting <br />
<blockquote>“Tools” → “Install Packages…”</blockquote> <br />
from the menu bar.<br> <br />
Choose <blockquote>“Install from: Package Archive File (.tgz; .tar.gz)"</blockquote> <br />
and select the tar.gz file of PaCeQuantAna via <blockquote>"Browse...".</blockquote><br />
</ol><br />
<br><br />
We use Arial or Helvetica fonts when creating the plots, which is often recommended for publication. Therefore you will need to prepare your working environment by once running <br><br />
<blockquote>library(extrafont)</blockquote><br />
<blockquote>font_import()</blockquote><br />
<blockquote>loadfonts()</blockquote><br />
This will initialize the creation of a font database.<br><br />
You can check which fonts where found and load by <br><br />
<blockquote>fonts()</blockquote><br />
<br />
=== Documentation ===<br />
<br />
Find more details of how to use the package and details about the general workflow in the vignette of the package by either navigating to the vignette in the Rstudio package manager tab or by typing <br />
<blockquote>vignette("PaCeQuantAna")</blockquote><br />
in the console.<br />
<br />
'''Please note:'''<br><br />
'''The vignette is currently under construction. An updated version will be released soon.'''<br><br />
<br />
The vignette contains comprehensive documentation of the various functions and options of the package.<br><br />
In addition, a sample workflow R script is provided which shows all commands to load your data, configure the output and do the analysis.<br><br />
You can directly copy the script into a file and load this file into the Rstudio editor to run it completely or line-wise.<br />
<br />
You can test the new version of the package with sample data and small workflows (R scripts) for analyses of developmental stages and mutant screening. Therefore we provide two archives:<br />
<br />
* [http://informatik.uni-halle.de/~poeschl/PaCeQuantAna/BookChapter2020/developmentalStages.zip Sample data and R scripts for analyses of developmental stages]<br />
<br />
* [http://informatik.uni-halle.de/~poeschl/PaCeQuantAna/BookChapter2020/mutantScreening.zip Sample data and R scripts for mutant screening]<br />
<br />
Both archives contain the specific <br><br />
<ul><br />
<li> sample data<br />
<li> workflows and <br />
<li> data description files<br />
</ul><br />
. <br />
The sample data sets are reduced to 2 microscopy images per group (time point or species). The workflows contain the function calls depicted in Fig. 5 in Poeschl et al 2020. The data description files are customized to fit e.g. the species and time points included in our analyses, color used or font face used.<br><br />
<br />
Both archives include ready to use workflows for provided sample data sets. Only the path to the folder of the extracted archive needs to be set as working directory in the corresponding R-scripts. <br> <br />
In detail '''developmentalStages.zip''' contains<br />
<ul><br />
<li> sample data: Time-series_2-3-5-7, a folder containing the data organised into folders<br />
<li> 3 workflows: 1 general workflow for analyses of developmental stages and 2 specific workflows for<br />
<ul><br />
<li> Col-0: including prepared outputFolder containing the customised data description file<br />
<li> Col-0_iqd5-1_iqd5-2: including prepared outputFolder containing the customised data description file<br />
</ul><br />
</ul><br />
<br><br />
In detail '''mutantScreening.zip''' contains<br />
<ul><br />
<li> sample data: Mutants, a folder containing the data organised into folders<br />
<li> 2 workflows: 1 general workflow for screening mutants and 1 specific workflow for<br />
<ul><br />
<li> mutant_screening: including prepared outputFolder containing the customised data description file<br />
</ul><br />
</ul><br />
<br />
=== Important notes ===<br />
<ul><br />
<li> By default the working directory (set with ''setwd(...)'') where the output folder will be created, and the data directory (set with ''dataDir'') must not be identical!<br> <br />
If you require these folders to be identical for whatever reason you need to manually edit the file ''data_description.csv'' in the output folder and delete the row referring to the output folder.<br />
<li> On Windows operating systems you may encounter problems with missing fonts, i.e., error messages like the following one:<br />
<blockquote>...</blockquote><br />
<blockquote>Error in pdf(file = paste0(outdir, fsep, base_file_name,</blockquote><br />
<blockquote>"_dunn_test_heatmap_adjusted_pvalues.pdf"),&nbsp; :</blockquote><br />
<blockquote>&nbsp; unknown family 'Arial'</blockquote> <br />
<blockquote>...</blockquote><br />
Initialize each of your workflows using PaCeQuantAna with<br />
<blockquote>library(extrafont)</blockquote><br />
This will initialize the Windows font database and should solve the problems.<br />
</ul><br />
<br />
<br />
<br><br />
===== Email =====<br />
[[file:Email.png|left|36px|link=]]<br />
Don't hesitate to send an email when you encounter a problem or when you have questions: [mailto:poeschl@informatik.uni-halle.de poeschl@informatik.uni-halle.de]<br><br />
<br />
<br><br />
<br />
=== Old versions ===<br />
The old version of PaCeQuantAna compatible with PaCeQuant results generated with MiToBo 1.8.x can be downloaded here:<br />
<br />
* [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/paceQuantEval/PaCeQuantAna_1.0.0.tar.gz R package v1.0.0]<br />
<br />
You can test the package on these sample data: [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/time_series.zip sample data for PaCeQuantAna]<br><br />
<br />
<br />
<!--<br />
== R script for Visualization and Statistical Analysis of Results ==<br />
We provide an R script for visualizing and analyzing results generated by PaCeQuant:<br />
<br />
* [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/paceQuantEval/PaCeQuantEval_version0.1.zip R script v0.1]<br />
* [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/paceQuantEval/README.PaCeQuantEval README]<br />
<br />
Before running the script you need to set some path variables in the header of the script file which, e.g., specify where to find the PaCeQuant result data and where to save the final plots. <br />
<br />
The script will include result data from the current directory and from all direct sub-directories of the current folder into its analysis.<br> Each folder is treated as one group of cells, and the analysis is designed to compare different groups of cells against each other.<br />
<br />
You can test the script on the sample data provided on this page.<br />
--></div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Operators/Tools/Interactive/LabelImageEditor&diff=1015Operators/Tools/Interactive/LabelImageEditor2021-04-09T14:26:48Z<p>Moeller: /* Label Image Editor */</p>
<hr />
<div><br/><br />
<br/><br />
<br />
== Label Image Editor ==<br />
[[File:LabelImageEditor-MTBOperatorControlFrame.png|400px|right|link=]]<br />
<br />
The ''Label Image Editor'' is available since release version 1.8.8 of MiToBo.<br/><br />
In MiToBo/MiToBo plugins releases 1.8.13.1 and 2.1.2 it got rich feature updates.<br />
<br />
===== Latest News =====<br />
The editor got latest updates in MiToBo/MiToBo plugins 2.1.2 (April 2021).<br />
<br />
===== Name of Plugin/Operator =====<br />
<code><br />
de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor<br />
</code><br />
<br><br />
(available since MiToBo version 1.8.8)<br />
<br><br />
<br />
===== Main features ===== <br />
* images provided in an input folder are subsequently displayed to the user<br />
* regions, i.e. connected components, can be removed and joined by simple mouse-clicks<br />
* additional boundaries can be added by drawing free-hand lines with configurable line width<br />
* region labels can be adjusted to enhance visibility <br />
* region re-labeling is supported to guarantee unique labels<br />
* holes within regions can be filled <br />
* missing regions in terms of small holes can automatically filled in <br />
* support for up to 65535 labels<br />
<br />
===== Usage =====<br />
The editor is dedicated to the analysis of label images. In a label image each region or connected component, respectively, is assumed to be marked with a unique intensity or color value, i.e. all of its pixels should share this value.<br />
The editor provides various editing functions to remove or join regions within such images.<br><br><br />
Note that the editor can also handle label images with one-pixel wide black boundaries between regions.<br><br><br />
The editor takes as input a directory from where the images are loaded one after the other.<br><br />
Once an image is displayed to the user edit operations can be performed. Afterwards the changes are saved to a new image file and the next label image is read from the given input directory. <br />
<br />
<br><br />
To run the LabelImageEditor perform the following steps:<br />
* install MiToBo by following the instructions on the [[Installation]] page<br />
* run MiToBo and start the operator runner by selecting the menu item '''''MiToBo Runner''''' from '''''Plugins -> MiToBo''''' <br />
* in the selection menu navigate to '''de.unihalle.informatik.MiToBo.tool.interactive''' and select the operator '''''LabelImageEditor'''''<br />
This will bring up the operator window of the LabelImageEditor (see figure on the right, top) where the basic configuration parameters can be added. Clicking the "Run" button will open the editor window with the first image loaded (figure on the right, bottom).<br />
<br />
<br><br />
* Input data:<br>The operator reads the contents of a given input image directory and displays all images one after the other to the user. <br>The user can edit the images, i.e. remove labeled regions, by clicking with the left mouse button somewhere into the region to remove.<br> Clicking the "Next" button at the top of the editor window will save the current image to disk and proceed with the next image in the folder. <br><br><br />
* Output data:<br>For each input image the operator will save a corresponding output image, either in the same folder or a specific output folder if provided.<br> Output images will share the name of the corresponding input image extended with substring "-edited".<br> Note, all images are relabeled automatically before saving to ensure consecutive labels in the resulting edited images. <br> Consecutive labels are a pre-requisite for some other MiToBo tools which can be used in further processing steps, like the [[Applications/FeatureColorMapper|FeatureColorMapper]].<br />
<br />
<br><br />
* Parameters:<br />
{|class="wikitable"<br />
|Name<br />
|Description<br />
|-<br />
|''Input Directory''<br />
|directory from where the images to process will be loaded<br />
|-<br />
|''File Filter''<br />
|Optional string to filter image files to be processed. If the string is empty all files are processed. <br>If a non-empty string is provided, files with names not containing the pattern will be skipped.<br> For example, if the string ".tif" is provided, only images ending with ".tif", i.e. in TIFF format, will be considered.<br> The string "cell" would select only images containing the word "cell" somewhere in their names.<br> Note that as string any valid Java regular expression is admissible. See for example [http://www.vogella.com/tutorials/JavaRegularExpressions/article.html this website] for more details on regular expressions.<br />
|-<br />
|''Output directory''<br />
|optional; edited result label images will be saved to this directory; if not provided the result images will be stored in the input folder<br />
|}<br />
<br />
[[File:LabelImageEditor-EditorWindow.png|500px|right|link=]]<br />
<br />
<br><br />
The following table lists all available operations available in the editor window:<br />
{|class="wikitable" <br />
|style="width: 15%;"|Operation <br />
|How to do it<br />
|-<br />
|''remove a region''<br />
|click with left mouse button somewhere into the region to be removed;<br>the region will then be removed by setting all its pixels to a value of zero<br />
|-<br />
|''join two regions''<br />
|press 'Shift' and left-click into the first region to remember its label, then release 'Shift' and left-click into the second region;<br>the label of the first region will be transferred to the second region; black pixels between both parts can be removed afterwards using the "Fix borders" button<br />
|-<br />
|''draw a new boundary''<br />
| keep left mouse button pressed and drag the mouse, this will add a one-pixel wide free-hand line to the label image; note that you can configure the line width via the 'Options' button<br />
|-<br />
|''fill-in a missing region<br> (new in version 2.1.2)''<br />
|press 'Ctrl' and 'Shift' and left-click into the missing region area; be sure that the area is fully enclosed by other regions, open background sections cannot be filled properly<br />
|}<br />
<br />
<br><br />
The buttons in the editor window have the following functions:<br />
{|class="wikitable"<br />
|Button<br />
|Function<br />
|Keyboard Shortcut<br />
|-<br />
|''Next''<br />
|save current changes and jump to next image<br />
|''Alt + n''<br />
|-<br />
|''Skip''<br />
|cancel current image, don't save anything and jump to next image<br />
|''Alt + s''<br />
|-<br />
|''Contrast''<br />
|adjust labels to optimize visibility, i.e., shift labels into upper third of gray-scale range with maximal distances between them<br />
|''Alt + c''<br />
|-<br />
|''Relabel''<br />
|relabel the image, i.e., make sure that every region gets a unique label<br />
|''Alt + r''<br />
|-<br />
|''Fix Borders''<br />
|remove all background pixels with more than one foreground label in their neighborhood; the size of the neighborhood to be considered can be configured via the 'Options' button, and sometimes it is necessary to re-run the command several times to remove all non-border pixels between two region parts<br />
|''Alt + b''<br />
|-<br />
|''Fill Holes''<br />
|fill background regions enclosed by a single region with the region label<br />
|''Alt + h''<br />
|-<br />
|''Undo''<br />
|undo the last action; IMPORTANT: only the most recent action can be undone!<br />
|''Alt + u''<br />
|-<br />
|''Options''<br />
|opens a window with configuration options, e.g., for setting the line width in drawing or the maximum boundary width<br />
|''Alt + o''<br />
|-<br />
|''Quit''<br />
|save current changes and quit the editor window<br />
|''Alt + q''<br />
|}<br />
<br />
<br><br><br />
'''Hint:''' The ''Undo'' function has currently only a history of length one. If you accidentally deleted too many regions or want to undo more than one action, either run the editor once again on the complete directory or copy the corresponding image to a separate folder and run the editor on that folder. Results of a former run will be overwritten without further inquiry.<br />
<br />
=== Updates ===<br />
----<br><br />
<br />
'''April 2021'''<br />
* The editor got some updates in MiToBo 2.1.2 and MiToBo-plugins 2.1.2, respectively. Background regions can now be filled-in, more labels are supported and some parameters be configured by the user.<br />
<br />
'''January 2019'''<br />
* The editor got a comprehensive update in MiToBo 1.8.13.1 and MiToBo-plugins 1.8.13.1, respectively. There is now much more editing functionality available, e.g., filling holes or drawing of free-hand lines.<br />
<br />
'''March 2018'''<br />
* The LabelImageEditor has been released in MiToBo 1.8.8 and MiToBo-plugins 1.8.8, respectively.<br><br><br />
<p><br />
<br />
=== Technical Details ===<br />
----<br><br />
The label editor relies on analyzing and manipulating the grayscale values of segmented regions in a given image.<br> In detail, the most important functions are implemented as follows:<br />
* deleting regions:<br> the grayscale value at the mouse-click position is determined and all pixels in the image sharing this value are set to black<br />
* joining regions:<br> upon clicking into the first region its grayscale value is internally stored;<br> when the user clicks into the second region which is to be merged with the first one<br> the grayscale value at the click position is extracted and all pixels with this value are relabeled with the formerly stored grayscale value of the first region;<br> important: after doing the join both joined regions share the same grayscale value, however, are not connected to each other; hence, to get a valid label image again you should run the "Fix Borders" function<br />
* relabel image:<br> the image is thresholded with a threshold of zero to get a binary image of background and labeled regions;<br> then a sequential component labeling is run on the image which assigns consecutive grayscale labels to all connected components in the foreground of the image<br />
* adjust contrast:<br> the image is relabeled, however, the target labels are equidistantly spread over just the upper two third of the available grayscale range;<br> the underlying motivation for this is given by the observation that low grayscale values are hard to distinguish from the background, thus, brighter labels improve visibility<br />
* fix borders:<br> this functions seeks to eliminate borders between regions with identical labels which may for example occur after joining two regions;<br> for removing borders for each background pixel in the image the grayscale values in a 7x7 neighborhood of the pixel are analyzed,<br> and if there is only a single grayscale value found and more than half of the analyzed neighborhood pixels share this value, the corresponding background pixel gets the value as well;<br> the neighborhood is currently fixed to 7x7, thus, borders which are wider cannot be closed, and it has to be noted that sometimes the function has to be run several times to remove all pixels belonging to a single border</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Applications/PaCeQuant&diff=1014Applications/PaCeQuant2021-03-05T08:40:27Z<p>Moeller: /* Sample data */</p>
<hr />
<div><br/><br />
<br/><br />
<br />
== PaCeQuant Plugin ==<br />
[[File:MiToBo_logo_PaCeQuant.png|border|150px|left|link=]]<br />
<br />
PaCeQuant is available since release version 1.8.6 of MiToBo.<br />
<br/><br />
<br />
In MiToBo version 2.0 released in May 2020 it got an update which added the largest empty circle as shape criterion to PaCeQuant's feature set.<br />
<br><br />
<br />
The PaCeQuant plugin as part of MiToBo as well as the R script for the visualization of result data are published under the terms of [https://www.gnu.org/licenses/gpl-3.0.en.html GNU General Public License v3.0].<br />
<br />
[[File:sampleImage-inverse.png|300px|right|link=]]<br />
[[File:sampleImage-colorResult-inverse.png|300px|right|link=]]<br />
[[File:sampleImage-features-white.png|300px|right|link=]]<br />
<br />
==== Name of Plugin/Operator ====<br />
<code><br />
de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant<br />
</code><br />
<br><br />
(available since MiToBo version 1.8.6)<br />
<br><br><br />
<br />
==== Related Publications ====<br />
<br />
When using PaCeQuant, please cite us:<br />
* Y. Poeschl, B. Möller, L. Müller, and K. Bürstenbinder,<br>'''''User-friendly assessment of pavement cell shape features with PaCeQuant: Novel functions and tools'''''.<br>In [https://www.sciencedirect.com/science/article/pii/S0091679X20300741?via%3Dihub Methods in Cell Biology], Academic Press, 2020.<br />
* B. Möller, Y. Poeschl, S. Klemm, and K. Bürstenbinder,<br>'''''Morphological Analysis of Leaf Epidermis Pavement Cells with PaCeQuant'''''.<br>In F. Cvrčková and V. Žárský, editors, [https://link.springer.com/protocol/10.1007%2F978-1-4939-9469-4_22 Plant Cell Morphogenesis: Methods and Protocols, chapter 22, pages 329-349], Springer New York, New York, NY, 2019.<br />
* B. Möller, Y. Poeschl, R. Plötner, and K. Bürstenbinder,<br> '''''PaCeQuant: A Tool for High-Throughput Quantification of Pavement Cell Shape Characteristics'''''.<br> [http://www.plantphysiol.org/content/early/2017/09/20/pp.17.00961 Plant Physiology, 175(1), September 2017].<br />
<br><br />
<br />
<br />
==== Main Features ==== <br />
* extraction of 28 characteristic shape features to quantify pavement cell shape<br />
* fully automatic segmentation of cell regions from input images<br />
* optional import of external/manual cell segmentation data<br />
* classification of lobes into type I (2-cell contact) and type II (3-cell contact)<br />
* additional R scripts for feature visualization<br />
<br />
<br />
==== Supplemental Tools ====<br />
The core PaCeQuant plugin has been supplemented by additional tools to ease feature visualization and analysis:<br />
* the [[Applications/FeatureColorMapper|FeatureColorMapper]] plugin for creating heatmap visualizations of cell features<br />
<p><p><br />
* the [[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]] for handy manual post-processing of segmentation results<br />
<p><p><br />
* the R package [[Applications/PaCeQuantAna|PaCeQuantAna]] for statistical analysis of feature data and creation of publication-ready plots of feature distributions and statistical analysis results<br><br><br />
<br />
<br />
==== Usage - Parameters ====<br />
To run PaCeQuant perform the following steps:<br />
* install MiToBo by following the instructions on the [[Installation]] page<br />
* run MiToBo and start the operator runner by selecting the menu item '''''PaCeQuant''''' from '''''Plugins -> MiToBo''''' <br />
This will bring up the operator window of PaCeQuant.<br />
<br />
===== Phases and Operation modes ===== <br />
PaCeQuant supports three different options for running listed below:<br />
* ''SEGMENTATION_AND_FEATURES:''<br> expects images as input, segments the images and extracts features<br />
* ''SEGMENTATION_ONLY:''<br> expects images as input, just segments the cell regions, no feature extraction<br />
* ''FEATURES_ONLY:''<br> works on binary or label images or ImageJ regions, extracts features for the given regions<br />
<br />
In addition PaCeQuant can be run in either of two modes:<br />
* ''INTERACTIVE:''<br> PaCeQuant processes the data provided directly within the graphical environment of ImageJ, i.e. reads regions from the ROI manager, and directly shows results<br />
* ''BATCH:''<br> PaCeQuant processes all files (images or ROI files) in a given folder and writes results to disk<br />
For batch mode the user can specify an input directory, in interactive mode PaCeQuant expects an input image or regions to be available in ImageJ.<br />
<br />
Depending on the chosen phase and operation mode the graphical user interface is dynamically re-configured to show only the options relevant for the selected options.<br />
<br />
===== Input Image/Directory =====<br />
Depending on the chosen phases and operation modes here you need to specify either input data already loaded in ImageJ/Fiji or a directory where PaCeQuant can find the data to process. In detail, you have to provide the following information for the various configurations:<br />
{|class="wikitable"<br />
|style="width:20%;"|Operation Mode <br />
| Phase(s) to Run <br />
| Input Data <br />
|-<br />
|''INTERACTIVE'' <br />
|''SEGMENTATION_ONLY'' <br />
|Gray-scale input image already opened in ImageJ/Fiji.<br />
|-<br />
| <br />
|''SEGMENTATION_AND_FEATURES'' <br />
|Gray-scale input image already opened in ImageJ/Fiji.<br />
|-<br />
| <br />
|''FEATURES_ONLY'' <br />
|Binary or label image already opened in ImageJ/Fiji, or ImageJ ROI set from ROI manager.<br />
|-<br />
|''BATCH'' <br />
|''SEGMENTATION_ONLY'' <br />
|Directory containing gray-scale input images.<br> First-level sub-folders are also processed.<br />
|-<br />
| <br />
|''SEGMENTATION_AND_FEATURES'' <br />
|Directory containing gray-scale input images.<br> First-level sub-folders are also processed.<br />
|-<br />
| <br />
|''FEATURES_ONLY'' <br />
|Directory containing either binary or label images to process, a collection of ImageJ ROI files (with ending '.roi'), or an archive of multiple ImageJ ROIs (with ending '.zip').<br />
|}<br />
<span style="color:#ff0000">'''Important notice''':</span><br> In ''BATCH'' mode PaCeQuant tries to analyze ''all'' image files present in the given folder or any of its direct sub-folders. In particular, PaCeQuant will also analyze data from a potential result folder of a previous run, if it is present in the given folder. To avoid problems resulting from analyzing wrong data you should ensure that the provided directory only contains native input images or segmentation data and no other image data not suitable for processing with PaCeQuant.<br />
<br />
===== Calibration =====<br />
As PaCeQuant measures lengths and areas from the given data it is important that the tool is properly calibrated, i.e. the physical size of a pixel is known. PaCeQuant supports two calibration modes:<br />
* AUTO:<br> here PaCeQuant seeks to extract calibration information from the given input data<br />
* MANUAL:<br> the user can enter calibration data, i.e. the physical size of a pixel and the units to use<br />
<span style="color:#ff0000">'''Important notice''':</span><br> Please note that in ImageJ ROI files no calibration data is stored. Thus, when using PaCeQuant to extract features from external segmentation data provided as ImageJ ROIs, you always need to manually provide calibration data. And this also holds when manually post-processing segmentation data extracted with PaCeQuant as all calibration data of the original images will get lost.<br />
<br />
===== Configuration of Segmentation Phase =====<br />
For detailed configuration of the algorithms applied during the segmentation phase the following parameters are available:<br />
{|class="wikitable"<br />
|style="width:20%;"|Name<br />
|Description<br />
|-<br />
|''Border Contrast''<br />
|Allows to select whether the boundaries of the cells are darker or brighter than the background.<br />
|-<br />
|''Heuristic for Gap Closing''<br />
|During segmentation sometimes small gaps in the boundaries remain which can be closed by PaCeQuant applying one of the following heuristics:<br />
* WATERSHED (recommended): calculates a distance image from the binary boundary image extracted so far and then applies a watershed transformation to find additional boundaries<br />
* NAIVE_HEURISTIC: just calculates the distance between two end-points and links them if the distance is below a threshold<br />
|-<br />
|''Unit for Size Thresholds''<br />
|Unit in which the size thresholds for filtering valid regions (see next two parameters) are specified, i.e. either PIXELS or MICRONS.<br />
|-<br />
|''Minimal Size of Cells''<br />
|Segmented cells being too small can automatically be excluded by specifying a minimal size for valid cells.<br />
|-<br />
|''Maximal Size of Cells''<br />
|Segmented cells being too large can also automatically be excluded by specifying a maximal size for valid cells.<br />
|}<br />
<br />
===== Configuration of Feature Extraction Phase =====<br />
{|class="wikitable"<br />
|style="width:20%;"|Name<br />
|Description<br />
|-<br />
|''Feature Extraction''<br />
|For changing various parameters used in feature extraction the [[Operators/Features/MorphologyAnalyzer2D | MorphologyAnalyzer2D]] operator of MiToBo is used and can be configured here. Note that changing parameters might hamper comparison of PaCeQuant results among different work groups or laboratories.<br />
|-<br />
|''Analyze lobe types?''<br />
|Activates the optional classification of individual lobes into type I (2-cell contact) or type II (3-cell contact) lobes.<br />
|}<br />
<br />
===== Additional Configuration Parameters =====<br />
{|class="wikitable"<br />
|style="width:20%;"|Name<br />
|Description<br />
|-<br />
|''Niblack threshold''<br />
|Allows to configure the binarization step in the segmentation phase, i.e., to increase or decrease the sensitivity of PaCeQuant for cell boundaries. The lower the threshold the more potential boundary candidate pixels will be extracted which might add to an improved segmentation in case of low contrast.<br />
|-<br />
|''Draw region IDs to output image?''<br />
|If the segmentation phase is run PaCeQuant outputs a label image showing segmented cell regions. If this option is activated region IDs are drawn to that image for easier interpretation. But note that this renders the image unsuitable for any further automatic analysis.<br />
|-<br />
|''Verbose''<br />
|If enabled additional log messages will be printed to console.<br />
|-<br />
|''Show/save additional results?''<br />
|If enabled an additional image stack with a collection of intermediate images will be generated. The images in this stack might help to get a deeper insight into PaCeQuant and might help to identify problems in case that the segmentation of input images fails.<br />
|-<br />
|''Show/save feature stack?''<br />
|If enabled a stack of images is generated where each image visualizes the values of a specific feature. For most images in this stack the feature values of individual cells are mapped to the intensity value of the corresponding cell (e.g., for features like area, solidity, width, length, branch count, etc.). <br />
|}<br />
<br />
==== Usage - Output data ====<br />
If PaCeQuant is run in ''INTERACTIVE'' mode all results are directly shown in ImageJ/Fiji, while in ''BATCH'' mode all result data is saved to a folder named ''results'' in the input folder. Which kinds of output data are resulting from running PaCeQuant depends on the selected phases:<br />
<br />
* list of result files from '''''SEGMENTATION''''' phase:<br />
** *-allRois.zip: ImageJ ROI archive containing all ROIs extracted from a single image<br />
** *_<number>.roi: ROI file containing only ROI with ID ''number''extracted from single image<br />
** *-grayscale-result.tif: gray-scale label image of extracted cell regions <br />
** *-color-result.tif: overlay of extracted cell regions (in pseudo-color) over input image<br />
** *-intermediate-result-stack.tif: (optional) stack of intermediate result images<br />
* list of result files from '''''FEATURES''''' phase:<br />
** *-allRois-table.txt: extracted feature values for all cells in a given image<br />
** *-allRois-grayscale-result.tif: gray-scale label image showing analyzed regions<br />
** *-intermediate-result-stack.tif: (optional) stack of intermediate result images<br />
** *-feature-stack.tif: (optional) stack of images visualizing feature values for cells<br />
** *-allRois-lobe-types.tif: (if lobe type classification is enabled) image visualizing the type of each lobe of all cells analyzed<br />
** *-allRois-cell-<number>-lobe-table.txt: (if lobe type classification is enabled) file containing features for lobes of cell with ID ''number'' <br />
<br />
Note that the asterisk in the above file names represents a single image, i.e. the set of files exists for each image present in the given folder.<br> All files with ending ''*.ald'' are internal MiToBo log files in XML format where, e.g., parameter settings are stored and which usually can be ignored or just preserved for later reference.<br />
<br />
==== Sample data ====<br />
Here we provide some sample data with which you can test your local PaCeQuant installation:<br />
<br />
* [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/sampleData/sampleData.zip sample data]<br />
<br />
To apply PaCeQuant to the test data simply unpack the data archive to a folder of your choice and set the input directory parameter of PaCeQuant to the sample data folder.<br><br />
<br />
The following archives contain result data extracted from the sample data with PaCeQuant and default settings for validating if your local PaCeQuant installation yields correct results.<br><br />
Depending on the PaCeQuant version the result data slightly differs:<br />
<br />
* Result data PaCeQuant v2.0 (May 2020): [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/sampleData/sampleDataResults-v2.0.zip sampleDataResults-v2.0.zip] (Java version: 1.8) <br> Starting with version 2.0 PaCeQuant provides the Largest Empty Circle feature, and in this version also an issue with measurement units in lobe measurings has been fixed.<br />
<br />
* Result data PaCeQuant v1.0 (Sep 2017): [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/sampleData/sampleDataResults-v1.0.zip sampleDataResults-v1.0.zip]<br />
<br />
Please note that we occasionally encountered marginal deviations in numerical feature measurements in the last decimals between different versions of Java.<br> In particular with regard to curvature based measures which rely on trigonometric functions small changes in the values below the sixth decimal were sometimes observed.<br />
<p><br />
<br />
== Complementary Tools: FeatureColorMapper, LabelImageEditor and PaCeQuantAna ==<br />
Over the time several complementary tools for PaCeQuant have been developed which ease manual correction of segmentation results and simplify analysis and exploration of extracted shape features:<br />
<br><br />
* the [[Applications/FeatureColorMapper|FeatureColorMapper]] plugin for creating heatmap visualizations of cell features<br />
<p><p><br />
* the [[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]] for handy manual post-processing of segmentation results<br />
<p><p><br />
* the R package [[Applications/PaCeQuantAna|PaCeQuantAna]] for statistical analysis of feature data and creation of publication-ready plots of feature distributions and statistical analysis results<br><br><br />
<br />
<br />
<p><br />
== Notes on manual or semi-automatic segmentation of cells ==<br />
PaCeQuant supports extracting features from externally provided segmentation data.<br> This can be helpful in cases where the original input images are not suitable for automatic segmentation by PaCeQuant,<br> e.g., due to a general low image quality or image acquisition techniques for which PaCeQuant is not optimized.<br />
<br />
The segmentation data can be provided in different formats:<br />
* an 8-bit binary image where all cell regions are labeled white (intensity = 255)<br />
* an 8-bit gray-scale image where each cell region is marked with an individual label (intensity larger than zero) and the background in black (intensity = 0)<br />
* ImageJ ROI files<br />
Note that when providing binary images neighboring regions must not touch each other. Optimally the margins between neighboring cell regions will have a width of at least 3 pixels.<br />
<br />
=== ImageJ ROI files ===<br />
For providing segmentation data in terms of ImageJ ROI files the easiest way to do this is to segment regions directly in ImageJ/Fiji.<br />
<br />
Use the [https://imagej.nih.gov/ij/docs/guide/146-19.html#sub:Polygon-Selection-Tool Polygon Section Tool] for segmenting individual cells, add each of the polygons to the <br />
[https://imagej.nih.gov/ij/docs/guide/146-30.html#sub:ROI-Manager... ROI manager], and finally save all ROIs to a file.<br />
<br />
In case that you aim to improve an initial segmentation result of PaCeQuant, open the ROI files generated by PaCeQuant during the segmentation phase with ImageJ's ROI manager and edit the ROIs. <br />
<br />
For editing polygon selections ImageJ offers a large variety of possibilities, e.g.:<br />
* single points can be removed (Ctrl + click)<br />
* new points can be added by splitting segments (Shift + click)<br />
* the complete region can be moved<br />
* the polygon can be interpolated, i.e. sub-sampled<br />
More information on the various options can be found in the ImageJ documentation:<br />
* [https://imagej.nih.gov/ij/docs/guide/146-19.html#sub:Polygon-Selection-Tool Polygon Section Tool]<br />
* [https://imagej.nih.gov/ij/docs/guide/146-30.html#sub:ROI-Manager... ROI manager]<br />
Probably of interest might also be the macro [http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Modify_Polygon_Selection 'Modifying Polygon Selections'].</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Downloads&diff=1013Downloads2020-12-01T14:55:37Z<p>Moeller: </p>
<hr />
<div>Here you can find the current release of MiToBo for download. Likewise older versions and additional libraries required to run MiToBo can be found here.<br />
<br />
For detailed information on the installation process take a look at the [[Installation]] page.<br />
<br />
== Current release ==<br />
<br />
The current release of the MiToBo core distribution is 2.1 and of the extended MiToBo-Plugins distribution 2.1.<br />
<br />
Since release 1.3 we support Maven for managing MiToBo's resources.<br> You can download the MiToBo distributions as well as the Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/archiva/#browse/de.unihalle.informatik.MiToBo https://moon.informatik.uni-halle.de/archiva/#browse/de.unihalle.informatik.MiToBo]<br />
<br />
<blockquote style="background-color: lightgrey; border: solid thin grey;"><br />
'''[[Using MiToBo with ImageJ 1.x:]]'''<br><br />
For using MiToBo with ImageJ it is the easiest to download the distribution zipfile,<br><br />
<br />
[https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/1.8.15/mitobo-plugins-1.8.15-bin.zip https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/1.8.15/mitobo-plugins-1.8.15-bin.zip]<br><br />
<br />
which already includes '''''all''''' dependencies and ships with some scripts to run MiToBo's operators and plugins out of the box.<br> See the [http://www2.informatik.uni-halle.de/agprbio/mitobo/index.php/Installation installation instructions] for further information.<br />
</blockquote><br />
<br />
<blockquote style="background-color: lightgrey; border: solid thin grey;"><br />
'''[[Using MiToBo with Fiji:]]'''<br><br />
Since release 1.5 MiToBo is available via a Fiji update site:<br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br><br />
<br />
To enable this site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
</blockquote><br />
<br />
There are two MiToBo distributions available:<br />
* <b>MiToBo:</b><br> this package contains the core of MiToBo, i.e. all operators, the MiToBo runners for operator execution and also Grappa;<br> <b>not included</b> are the plugins to run MiToBo from within ImageJ 1.x, hence, this distribution is mainly for stand-alone usage of MiToBo and development purposes<br><br />
* <b>MiToBo-Plugins:</b><br> this package contains the complete MiToBo distribution, some special plugins like the [[Applications/MTBCellCounter | MTB Cell Counter]], and in addition some ImageJ plugins to run MiToBo operators from within ImageJ; you should download the MiToBo-Plugins distribution if you like to use MiToBo with ImageJ<br />
<br />
<br><br />
<br />
Since release 1.8 MiToBo's implementation requires at least Java 1.8.<br />
<br><br />
<br />
Below the following kinds of files are available for download:<br />
* Distribution: complete distributions including all dependencies, scripts, documentation, etc.<br />
* Binaries only: only the jar archives, no dependencies nor documentation<br />
* API: Javadoc API<br />
<br><br />
<br />
== Maven Project Template ==<br />
Using MiToBo as a library for own developments can best be done by making use of Maven.<br><br />
Particularly, Maven automatically resolves all dependencies which otherwise would have to be installed manually.<br />
<br />
For getting started with MiToBo and Maven a project template is provided: <br />
<br />
[http://www.informatik.uni-halle.de/mitobo/downloads/maven/mitobo-demo-project-1.2-src.zip Maven project template [zip]]<br />
<br />
The project is readily configured and you can immediately start with own developments.<br><br />
It also contains a demo operator showing the basic usage of MiToBo data types and operators on the code level.<br />
<br />
Make sure that you have installed Maven and a Java Develpoment Kit (JDK) in version 1.8 or higher.<br><br />
You can check the Java version by running 'mvn --version' from command line.<br> <br />
If an older Java version is used, let the 'JAVA_HOME' environment variable point to a folder containing a more recent JDK.<br />
<br />
You can run Maven directly from within the extracted folder. Alternatively the Maven template project can easily be imported into an IDE like Eclipse.<br><br />
The zip file contains a README file containing more information about installing and configuring the project template.<br />
<br/><br />
<br />
== Manual ==<br />
<br />
Detailed information about MiToBo, its API and usage, can be found in MiToBo's User and Programmer Guide.<br />
<br />
* MiToBo-Guide, Version 1.0 [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual.pdf pdf]<br />
<br/><br />
<br />
<br />
== Additional resources ==<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release:<br />
* Chipory binary [http://www.informatik.uni-halle.de/mitobo/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www.informatik.uni-halle.de/mitobo/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br/><br />
<br />
<br />
== Logo ==<br />
<br />
* MiToBo logo as [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.pdf PDF] or [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.png PNG]<br />
<br />
<br />
== Earlier releases of MiToBo (< 1.5) ==<br />
<br />
Since release 1.3 MiToBo's resources are available from our Maven archive server: [https://moon.informatik.uni-halle.de/archiva/]<br>Binaries, sources and documentation for versions older than the current release, but at least of version 1.3 or newer can be found there.<br> All other releases can be accessed via the list below.<br><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 1.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3-javadoc.jar jar]<br />
| March 31st, 2015 (Support for callbacks)<br />
|-<br />
| 1.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 1.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 1.2<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-bin-v1.2.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-v1.2.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-v1.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
|-<br />
| 1.1<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-bin-v1.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-v1.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-v1.1.zip zip]<br />
| March 1st, 2013<br />
|-<br />
| 1.0.5<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.5.zip zip]<br />
| October 23rd, 2012<br />
|-<br />
| 1.0.1<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.1.zip zip]<br />
| July 6th, 2012<br />
|-<br />
| 1.0.0<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.0.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.0.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.0.zip zip]<br />
| April 26th, 2012<br />
|-<br />
| 0.96<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.6.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.6.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-0.9.6.zip zip]<br />
| September 01, 2011<br />
|-<br />
| 0.95<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-0.9.5.zip zip]<br />
| June 08, 2011 (updated June 22nd, 2011)<br />
|-<br />
| 0.9<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.tar.gz tar.gz]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.tar.gz tar.gz]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.tar.gz tar.gz]<br />
| October 26, 2010<br />
|}<br />
<br/><br />
<br />
=== Requirements (for MiToBo < 1.3) ===<br />
MiToBo requires Java 1.6 or later. <br />
<br />
'''Note''': Java 1.7 is currently not fully supported!<br />
<br />
The following external jars are needed to run MiToBo plugins and use the code.<br/><br />
<b>Note that the binary zip file already includes all jars required, there is no need for explicit download!</b><br />
<br />
MiToBo depends on the following external jars:<br />
<br />
* [http://rsbweb.nih.gov/ij/ ImageJ], >= Version 1.47d<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://www.csie.ntu.edu.tw/~cjlin/libsvm/ LIBSVM], Version 3.1<br />
* [http://www.loci.wisc.edu/software/bio-formats/ Loci Tools], Version 4.3.3<br />
* [http://math.nist.gov/javanumerics/jama/ Jama], Version 1.0.2 <br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
* [http://sezpoz.java.net/ SezPoz], Version 1.9<br />
* [http://www.jgraph.com/mxdownload.html JGraph], Version 1.7.1.8<br />
<br />
* [https://jai-imageio.dev.java.net/ JAI ImageIO], Version 1.1 (only required for MiToBo 0.9)<br />
<br />
=== Project internal libraries ===<br />
<br />
MiToBo also relies on some libraries provided by the MiToBo project itself.<br><br />
In particular XML schemes for representing the history graphs and MiToBo's online help are included in separate jar archives.<br />
<br />
'''[[Note]]:''' <br/><br />
''' You do not need to download these libraries explicitly. If you download the binary zip file all jars and libraries are already included.''' <br/><br />
<br />
The MiToBo internal archive files included in the zip file are the following ones:<br />
<br />
* ALDGraphml, Version 1.0.0 (Alida extensions for [http://graphml.graphdrawing.org/ graphML]):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/aldgraphml/aldgraphml.jar jar]<br />
* MTBXml, Version 1.0.0 (MiToBo XML I/O for several datatypes, based on XMLBeans):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbxml/mtbxml.jar jar] <br />
* MiToBo-Help, Version 1.0.0 (MiToBo JavaHelp pages):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mitoboHelp/MiToBo-Help.jar jar] <br />
<br />
The following library is only required for MiToBo-0.9: <br />
<br />
* MTBImageIO-Ext, Version 0.9 (improved image I/O based on ImageIO-Ext):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff-0.9.jar jar]<br />
** Source code [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff_src-0.9.zip zip]<br />
** Alternatively, the [https://imageio-ext.dev.java.net/ ImageIO-Ext] library can be used, which depends on the [https://jai-imageio.dev.java.net/ JAI ImageIO] library and the [https://jai.dev.java.net/ JAI] library.<br/>MTBImageIO-Ext is simply the TIFF part of ImageIO-Ext with slight adjustments to remove dependency on the JAI library.<br />
<br/></div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Main_Page&diff=1012Main Page2020-12-01T14:55:17Z<p>Moeller: /* MiToBo - A microscope image analysis toolbox */</p>
<hr />
<div>= MiToBo - A <span style="color:#CC0000">m</span>icroscope <span style="color:#CC0000">i</span>mage analysis <span style="color:#CC0000">to</span>ol<span style="color:#CC0000">bo</span>x =<br />
<br />
{|width="100%"<br />
|-<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''What is MiToBo?'''<br><br />
The Microscope Image Analysis Toolbox MiToBo is a toolbox with a large collection of basic and advanced functions and algorithms for processing and analyzing digital images. Many tools in MiToBo target at the analysis of various kinds of microscopy data, however, most of the functionality within MiToBo is generic (see [[Features|page of features]] for an overview). MiToBo is implemented as extension for the widely used image processing application [http://rsbweb.nih.gov/ij/ ImageJ]/[https://fiji.sc/ Fiji] and its new release [http://developer.imagej.net/ ImageJ 2.0]. All functions, operators and plugins of MiToBo are ready to be directly used as plugins in ImageJ and Fiji.<br /><br/><br />
<br />
'''Highlight operators and tools in MiToBo'''<br />
{|style="background-color:#f8f8ff"<br />
|style="text-align:left;width:10%|[[File:MiToBo_logo_CytoskeletonAnalyzer2D.png|border|72px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/CytoskeletonAnalyzer2D]]<br />
|style="text-align:left;width:80%|'''''[[Applications/CytoskeletonAnalyzer2D|CytoskeletonAnalyzer2D]]''''' for the quantification of cytoskeleton structural patterns in microscopy images with texture measures;<br><br />
to ease cell boundary extraction in data preparation we additionally provide the '''''[[Applications/CellBoundaryExtractor2D|CellBoundaryExtractor2D]]''''' and a handy '''''[[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]]'''''<br />
|-<br />
|style="text-align:left;width:10%|[[File:MiToBo_logo_PaCeQuant.png|border|72px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/PaCeQuantToolset]]<br />
|style="text-align:left;width:80%|'''''[[Applications/PaCeQuantToolset|PaCeQuant]]''''' and corresponding tools, i.e. the '''''[[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]]''''', the '''''[[Applications/FeatureColorMapper|FeatureColorMapper]]''''' and the R package '''''[[Applications/PaCeQuantAna|PaCeQuantAna]]''''', for quantification, visualization and statistical analysis of the morphology and shape characteristics of cells<br />
|-<br />
|style="text-align:left;width:10%|[[File:NeuronAnalyzer2D.png|border|72px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/NeuronAnalyzer2D]]<br />
|style="text-align:left;width:80%|'''''[[Applications/NeuronAnalyzer2D|Neuron Analyzer]]''''' for the segmentation of neurons in microscope images<br />
|-<br />
|style="text-align:left;width:10%|[[File:tracking_ES-2.gif|72px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/CellMigrationAnalyzer]]<br />
|style="text-align:left;width:80%|'''''[[Applications/CellMigrationAnalyzer|Cell Migration Analyzer]]''''' for analyzing single cell migration from time lapse image sequences<br />
|-<br />
|style="text-align:left;width:10%|[[File:GFP_U2OS_overlay.png|72px|left|border|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/ScratchAssayAnalyzer]]<br />
|style="text-align:left;width:80%|'''''[[Applications/ScratchAssayAnalyzer|Scratch Assay Analyzer]]''''' for analyzing microscope images from collective cell migration experiments<br />
|}<br />
For several other important operators and plugins documentation is available via the [[Operator_Documentation| Operator Documentation pages]] here in the Wiki.<br> <br />
The pages are structured according to the package structure of MiToBo which is also mirrored in the selection panel of MiToBo's operator runner.<br />
<br />
<br><br />
'''MiToBo for developers'''<br><br />
MiToBo aims not only to support users in analyzing their images, but also targets at developers by offering a programmer-friendly software framework and API for developing new algorithms.<br />
The MiToBo API completely separates the implementation of image processing algorithms from potential user interfaces based <br />
on [http://www.informatik.uni-halle.de/alida/ Alida] which is a library for easing the development of data analysis<br />
algorithms and tools. The main concept of Alida are <i>operators</i> as the core units for implementing data analysis algorithms. <br /><br />
Alida defines unified interfaces and execution procedures for operators which yield the fundament for its nice features like <br />
<ul><br />
<li> automatic documentation of complete analysis processes, e.g., leading from an input image to analysis results, in terms of processing graphs<br />
<li> automatic generation of commandline and graphical user interfaces<br />
<li> a graphical programming editor named '''''Grappa''''' automatically considering all implemented operators as potential processing nodes<br><br />
</ul><br />
<br />
<p><br />
MiToBo takes full advantage of Alida's features, hence, provides a framework for implementing image analysis algorithms allowing for automatic documentation and automatic user interface generation, and includes the graphical programming editor Grappa for user-friendly design of more complex processing pipelines.<br />
</p><br />
</div><br />
</div><br />
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'''Visit and follow MiToBo also at...'''<br><br />
{|<br />
|style="text-align:center;width:10%"|[[file:Imagej-128.png|90px|link=http://imagej.net/MiToBo]]<br />
|style="text-align:center;width:10%"|[[file:Git.png|90px|link=https://github.com/mitobo-hub]]<br />
|style="text-align:center;width:10%"|[[file:mtbtw.png|320px|link=https://twitter.com/MiToBo_Hal]]<br />
|style="text-align:center;width:10%"|[[file:logo.png|90px|link=http://imagejdocu.tudor.lu/doku.php?id=plugin:collections:mitobo_-_a_microscope_image_analysis_toolbox:start]]<br />
|style="text-align:center;width:10%"|[[file:logo-blue.png|90px|link=https://omictools.com/microscope-image-analysis-toolbox-tool]]<br />
|-<br />
|style="text-align:center;width:10%"|[http://imagej.net/MiToBo ImageJ.net]<br />
|style="text-align:center;width:10%"|[https://github.com/mitobo-hub GitHub]<br />
|style="text-align:center;width:10%"|[https://twitter.com/MiToBo_Hal Twitter]<br />
|style="text-align:center;width:10%"|[http://imagejdocu.tudor.lu/doku.php?id=plugin:collections:mitobo_-_a_microscope_image_analysis_toolbox:start ImageJ Docu Wiki]<br />
|style="text-align:center;width:10%"|[https://omictools.com/microscope-image-analysis-toolbox-tool OMIC Tools]<br />
|}<br />
</div><br />
</div><br />
|<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Latest News'''<br><br />
* 12/2020: MiToBo 2.1 has been released.<br> <br />
* 05/2020: MiToBo 2.0 has been released.<br> From now on the online help system relies on operator class annotations, and the release includes a [https://mitobo.informatik.uni-halle.de/index.php/Applications/PaCeQuantToolset PaCeQuant] update with new shape features and improvements for supplemental tools like the [https://mitobo.informatik.uni-halle.de/index.php/Applications/FeatureColorMapper FeatureColorMapper] and the [https://mitobo.informatik.uni-halle.de/index.php/Operators/Tools/Interactive/LabelImageEditor LabelImageEditor].<br />
* 07/2019: MiToBo 1.8.15 has been released fixing several issues with handling images in MiToBo.<br />
* 02/2019: MiToBo 1.8.14 has been released.<br />
<br />
The news archive can be found [[News Archive | here]].<br />
</div><br />
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<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
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'''How to get MiToBo?'''<br><br />
* ImageJ-Users:<br> download the [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/1.8.7.1/mitobo-plugins-1.8.7.1-bin.zip MiToBo-Plugins package] and follow the installation instructions to be found [[Installation | here]]. <br />
* Fiji-Users:<br> simply select MiToBo's update site [http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo] in FijiIs list of update sites in your installation<br />
* use in general:<br> you can download MiToBo and the MiToBo plugins package [[Downloads | here]]. <br/> <br />
<br />
You can find the API documentation for the current release [http://www.informatik.uni-halle.de/mitobo/api/index.html here].<br/> <br />
Furthermore MiToBo offers you a user and programmer guide which you can download [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual.pdf here].<br />
</div><br />
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'''Support, Bug reports & Feature requests'''<br />
{|style="background-color:#f8f8ff"<br />
|style="text-align:left;width:20%|[[File:forum-image-sc.png|border|64px|left|link=https://forum.image.sc/]]<br />
|style="text-align:left;width:60%|To get help on your questions about MiToBo tools, plugins and operators you can use the forum at [https://forum.image.sc/ image.sc] tagging your post with [https://forum.image.sc/tags/mitobo #mitobo].<br />
|-<br />
|style="text-align:left;width:20%|[[file:Git.png|64px|link=https://github.com/mitobo-hub]]<br />
|style="text-align:left;width:60%|Bug reports and feature requests can be submitted as issues on [https://github.com/mitobo-hub/mitobo/issues Github].<br />
|-<br />
|style="text-align:left;width:20%|[[file:Email.png|center|36px|link=]]<br />
|style="text-align:left;width:60%|Alternatively you can also write an email to [mailto:mitobo@informatik.uni-halle.de mitobo@informatik.uni-halle.de].<br />
|}<br />
Before reporting a new bug or requesting a new feature, please check if that bug has already been submitted in the forum or on Github.<br />
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'''Licensing information'''<br><br />
MiToBo is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].<br />
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<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Gnu PGP Public Key'''<br><br />
Since version 1.8.7 MiToBo and MiToBo-Plugins releases are PGP signed. MiToBo's [https://pgp.mit.edu/pks/lookup?op=get&search=0x259F7DD171EFF7A9 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/.<br />
</div><br />
</div><br />
|}</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Applications/CytoskeletonAnalyzer2D&diff=1011Applications/CytoskeletonAnalyzer2D2020-12-01T14:53:53Z<p>Moeller: /* Cytoskeleton Analyzer 2D */</p>
<hr />
<div><br/><br />
<br/><br />
<br />
== Cytoskeleton Analyzer 2D ==<br />
[[File:MiToBo_logo_CytoskeletonAnalyzer2D.png|border|150px|left|link=]]<br />
<br />
[[File:ActinExample.png|150px|right|link=]]<br />
[[File:HT144-shC-Series010-clusters.png|150px|right|link=]]<br />
[[File:ActinDistro.png|150px|right|link=]]<br />
<br />
The ''Cytoskeleton Analyzer 2D'' is available since release version 1.8.13 of MiToBo.<br/><br/><br />
This operator is an extended version of the [[Applications/ActinAnalyzer2D | Actin Analyzer 2D]] operator which was released in MiToBo version 1.4. The new version provides local binary patterns as new texture features and has received improvements with regard to user-friendliness. In addition, to ease the annotation of cell areas which is an essential prerequisite for applying the Cytoskeleton Analyzer, a supplemental plugin for cell contour segmentation and a handy [[Operators/Tools/Interactive/LabelImageEditor | interactive editor]] for label images have been released.<br />
<br />
===== Latest News =====<br />
The Cytoskeleton Analyzer Plugin has been released in MiToBo and MiToBo-Plugins 1.8.13.<br />
<br />
===== Related Publications=====<br />
* ''K. Bürstenbinder, B. Möller, R. Plötner, G. Stamm, G. Hause, D. Mitra, and S. Abel,<br/> '''"The IQD Family of Calmodulin-Binding Proteins Links Calcium Signaling to Microtubules, Membrane Subdomains, and the Nucleus"'''.<br/>In Plant Physiology, 173(3):1692-1708, March 2017.''<br />
<br />
===== Name of Plugin/Operator =====<br />
<code><br />
de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D<br />
</code><br />
<br><br />
(available since MiToBo version 1.8.13)<br />
<br><br />
<br />
===== Main features ===== <br />
* automatic extraction of different structural patterns by unsupervised texture analysis and clustering<br />
* co-occurence matrices and Haralick features as well as local binary patterns are available for texture characterization<br />
* structure quantification performed based on cell-wise cluster distributions<br />
<br />
===== Usage =====<br />
To run the CytoskeletonAnalyzer2D perform the following steps:<br />
* install MiToBo by following the instructions on the [[Installation]] page<br />
* run MiToBo and start the operator runner by selecting the menu item '''''MiToBo Runner''''' from '''''Plugins -> MiToBo''''' <br />
* in the selection menu navigate to 'de.unihalle.informatik.MiToBo.apps.cytoskeleton' and select the operator '''''CytoskeletonAnalyzer2D'''''<br />
This will bring up the operator window of the CytoskeletonAnalyzer2D.<br><br><br />
<br />
* '''<u>Input data:</u>'''<br>The operator expects a special organization of the input image data which is shown in the figure below. All the data should be contained in a common top-level folder, here named ''"experiment"''.<br> The images for each treatment/genotype/protein have to be put into separate sub-folders of this top-level folder, here named ''"group-1"'', ''"group-2"'' and so on. Besides the set of corresponding images,<br> each sub-folder is required to contain an additional sub-folder named ''"results_segmentation"'' where the annotation files with the cell areas or boundaries, respectively, are stored.<br><br> <br />
[[File:FolderStructure.png|1200px|center|link=]]<br />
:For each image named ''"<imagename>.tif"'' a corresponding mask file is expected to be found in that folder. The mask file should have the same basename like the corresponding image file,<br> but either end on "-mask.tif" (e.g., ''"<imagename>-mask.tif"'') in case of using label images as masks, or on ''"-mask.zip"'' or ''"-mask.roi"'' (e.g., ''"<imagename>-mask.zip"''), respectively, in case of using region sets as mask data.<br> Note that the operator currently only accepts '''ImageJ 1.x ROI sets''' as input. If label images are used as segmentation masks, the labels of individual cells in the label images are used as unique identifiers for the cells, i.e.,<br> are used as labels in the various plots. If the segmentation data is given in terms of ROIs a unique identifier is derived from the order of the cell boundaries in the ROI set.<br> Note that in the latter case a mask image is written to the output directory as additional output where the cells are marked by their identifiers to allow for easier assessment of the results.<br><br> Each of the sub-folders in the top-level folder is treated as a separate group of cells or experimental condition, thus, the cells of all images within one sub-folder are collected in a single set.<br> The names of the folders are used to label the different groups in the various output data files.<br> If the input images contain more than one channel you can select the channel on which the Cytoskeleton Analyzer should work. By default the first channel is used. <br><br><br />
<br />
* '''<u>Output data:</u>'''<br>The operator generates image- or group-specific output data files as listed in the table below. All data files specific to a single input image are stored in a new sub-folder named ''"results_features"'' in the sub-folder of each group. All global output data files are stored directly in the top-level folder. The string ''imageID'' below represents the name of a single input image, the string ''groupID'' refers to a specific group. In addition to saving the output data to file bar charts and box-whisker plots are directly shown in the graphical user interface of ImageJ/Fiji upon termination of the analysis process. <br> <br><br />
<br />
{|class="wikitable" style="margin: auto;"<br />
|style="color:black; background-color:#ffffcc; width:25%"|'''Output File Name'''<br />
|style="color:black; background-color:#ffffcc; width:20%"|'''Where to find it...'''<br />
|style="color:black; background-color:#ffffcc; width:45%"|'''Description'''<br />
|-<br />
|<imageID>-features.txt<br />
|folder ''results_features''<br />
|Feature data for single image file.<br />
|-<br />
|<imageID>-features.tif<br />
|folder ''results_features''<br />
|Image stack visualizing the feature data for single image.<br />
|-<br />
|<imageID>-clusterDistro.txt<br />
|folder ''results_features''<br />
|Cluster distributions for each cell individually and for all cells in total of the image.<br />
|-<br />
|<imageID>-clusters.tif<br />
|folder ''results_features''<br />
|Pseudo-colored image illustrating the cluster distribution per image.<br />
|-<br />
|<groupID>-distributionChart.png<br />
|folder ''results_features''<br />
|Stacked bar plot of the cluster distribution for each cell of the group.<br />
|-<br />
|AllCellsClusterStats.txt<br />
|top-level folder<br />
|Cluster distribution of raw data for all images and cells.<br />
|-<br />
|AllCellsPCASubspaceStats.txt<br />
|top-level folder<br />
|If PCA is applied to the cluster distribution vectors this file contains the subspace feature vectors for all cells.<br />
|-<br />
|AllCellsDistanceData.txt<br />
|top-level folder<br />
|Matrix of pairwise normalized Euclidean distances between cluster distribution vectors of all cells.<br />
|-<br />
|AllGroupsDistanceData.txt<br />
|top-level folder<br />
|Matrix of pairwise normalized Euclidean distances between average cluster distribution vectors of all groups.<br />
|-<br />
|AllGroupsSimilarityNetworkData.txt<br />
|top-level folder<br />
|Similarity network suitable for import and visualization in Cytoscape.<br />
|-<br />
|}<br />
<br />
<br><br><br />
<br />
* '''<u>Configuration Parameters:</u>'''<br><br />
<br />
{|class="wikitable" style="margin: auto;"<br />
|style="color:black; background-color:#ffffcc; width=15%"|'''Parameter Name'''<br />
|style="color:black; background-color:#ffffcc; width=15%"|'''Possible Values'''<br />
|style="color:black; background-color:#ffffcc; width=30%"|'''Description'''<br />
|-<br />
|''Image File Folder''<br />
|<br />
|Top-level folder containing data for all groups and experimental conditions of interest, respectively.<br />
|-<br />
|rowspan=2|''Boundary File Format''<br />
|LABEL_IMAGE<br />
|rowspan=2|Format of the segmentation data files with cell boundary information:<br> - LABEL_IMAGE: images with unique labels for each cell and a value of zero for the background <br> - IJ_ROIS: set of ImageJ 1.x ROIs, one ROI for each cell<br />
|-<br />
|IJ_ROIS<br />
|-<br />
|''Cytoskeleton Channel''<br />
|<br />
|Channel with the image data of the fluorescently labeled cytoskeleton.<br />
|-<br />
|''Calculate features''<br />
|<br />
|Activates the feature calculation, can be omitted if features have been extracted already.<br />
|-<br />
|''Feature Extractor''<br />
|<br />
|Feature operator to apply.<br />
|-<br />
|''Tile size''<br />
|<br />
|Tile size in x and y direction for the sliding window used for feature extraction.<br />
|-<br />
|''Tile shift''<br />
|<br />
|Tile shifts in x and y direction, i.e. pixel distance between subsequent positions of the sliding window.<br />
|-<br />
|''Number of feature clusters''<br />
|<br />
|Number of feature clusters applied in feature vector clustering.<br />
|-<br />
|''Do PCA in stage II?''<br />
|<br />
|Optionally, a principal component analysis (PCA) can be applied to the extracted cluster distribution vectors,<br> and subsequent distance calculations can be restricted to the most significant principal components only.<br />
|}<br />
<br />
===== Remarks and Important Notes =====<br />
* The ''CytoskeletonAnalyzer2D'' extracts group names from the directory names. Thereby underscores are interpreted as separators. Thus, do not name your groups with common prefixes before the first underscore. For example, instead of naming your groups 'mygroup' and 'mygroup_variant', name them 'mygroup' and 'mygroupVariant' or something similar. To be completely on the save side, avoid underscores completely.<br />
<br />
<!--<br />
===== Additional Tools ===== <br />
The hierarchical clustering in stage II of our approach as described in the paper has been done using the [http://deim.urv.cat/~sgomez/multidendrograms.php MultiDendrograms] software.<br> In principal every hierarchical clustering tool can be applied. <br><br />
The basis for the hierarchical cluster analysis is the file ''AllImagesPairwiseDistanceData.txt'' to be found in the output directory upon termination of an analysis run. It contains a matrix of pairwise Euclidean distances of the (optionally dimension-reduced) cluster distribution vectors of all cells. The file can directly be loaded by MultiDendrograms, for other tools format convertion might be necessary.<br><br />
<br />
You can download the latest version of MultiDendrograms from its webpage: [http://deim.urv.cat/~sgomez/multidendrograms.php]<br />
--><br />
<br />
<!--<br />
===== Sample data =====<br />
For testing the ''ActinAnalyzer2D'' operator we provide some sample data:<br />
* [http://www.informatik.uni-halle.de/mitobo/downloads/actin_examples_update.zip ActinAnalyzer2D sample data for MiToBo >= 1.8]<br />
* [http://www.informatik.uni-halle.de/mitobo/downloads/actin_examples.zip ActinAnalyzer2D sample data for MiToBo <= 1.7]<br />
<br />
(With release 1.8 the handling of file names and automatic deduction of mask file names changed, thus, image names in the sample data archive had to be updated.)<br />
<br />
The archive contains the following sub-folders:<br />
* ''imageData'': test images that were used in the ICPR publication mentioned above<br />
* ''maskData'': corresponding label images<br />
* ''featureData'': pre-calculated features for the cells (re-calculating the features may require up to an hour, depending on the machine used)<br />
* ''resultData'': sample results calculated on the given data<br />
<br />
In addition, in the archive a file with a sample parameter configuration for the operator can be found. The parameters are those used for producing the sample results. Once the operator has been started the file can be loaded via the '' 'File' '' menu and its entry '' 'Load Settings' ''. Note that you need to set the image and mask directories, and also the feature directory according to your local file system structure and the place to where you extracted the zip file.<br />
<br />
For more information on the data and the morphological analysis of the cells, see<br> <br><br />
''Anne Zirkel, Marcell Lederer, Nadine Stöhr, Nikolaos Pazaitis, and Stefan Hüttelmaier''<br><br />
'''''IGF2BP1 promotes mesenchymal cell properties and migration of tumor-derived cells by enhancing the expression of LEF1 and SNAI2 (SLUG)'''''<br><br />
''Nucleic Acids Res. Jul 2013; 41(13): 6618–6636. Published online May 15, 2013. doi: 10.1093/nar/gkt410'', [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711427/ Article]<br />
--><br />
<br />
=== Updates ===<br />
----<br><br />
<br />
'''December 2020'''<br />
* Released some improvements and small bug fixes with regard to handling ImageJ ROI files in MiToBo/MiToBo plugins 2.1.<br />
<br />
'''December 2018'''<br />
* Released first official version of Cytoskeleton Analyzer 2D in MiToBo/MiToBo plugins 1.8.13.<br />
<br />
<br><br />
<br><br />
<br />
== Visualization and Evaluation of Result Data in R ==<br />
One option for further analyzing the outcomes of the Cytoskeleton Analyzer 2D, particularly differences and similarities between pattern distribution vectors, is to generate heatmaps of the pairwise distances between cell or group distribution vectors, respectively.<br />
<br />
As a starting point you can use the following R script:<br />
<br />
* [https://mitobo.informatik.uni-halle.de/downloads/cytoskeletonAnalyzer/generateDistanceHeatmaps.R generateDistanceHeatmaps.R]<br />
<br />
The script generates two heatmap plots, one to compare individual cells against each other and one to compare the average distribution vectors of different groups.<br />
<br />
===== Usage =====<br />
<br />
* Download the script file to your local system.<br />
<br />
You can either use RStudio or R directly to execute the script.<br />
<br />
====== RStudio ======<br />
* Run [https://www.rstudio.com/ RStudio] and open the script file in the editor window.<br />
<br />
* Edit lines 8 and 10 and enter the paths to your distance data files resulting from analyzing your data with the Cytoskeleton Analyzer 2D (see above).<br />
<br />
* Enter the destinations of the output files in lines 15 and 17 of the script.<br />
<br />
* To run the script, click the "Source" button in the top right corner of the RStudio GUI.<br />
<br />
====== R ======<br />
If you prefer to use plain R you can specify the input and output data file names in the script using your favorite text editor, and then run the script directly in R.</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Citing&diff=985Citing2020-05-29T15:56:40Z<p>Moeller: </p>
<hr />
<div>__NOTOC__<br />
<br />
== How to cite MiToBo? ==<br />
If you use functionality provided by MiToBo in your research or if you use the MiToBo library as basis for your own projects, please cite one of our main papers in your publications:<br />
* B. Möller, M. Glaß, D. Misiak and S. Posch, '''''MiToBo - A Toolbox for Image Processing and Analysis''''',<br> Journal of Open Research Software, 2016, 4:e17, DOI: http://dx.doi.org/10.5334/jors.103.<br />
<br />
More publications related to MiToBo can be found on the [http://www2.informatik.uni-halle.de/agprbio/mitobo/index.php/Publications publications page].<br><br />
Additional publications about the underlying [http://www.informatik.uni-halle.de/alida Alida] framework are available from [http://www2.informatik.uni-halle.de/agprbio/alida/index.php/Projects Alida's publications page].<br />
<br />
<br><br />
Selected major release versions of MiToBo are also indexed and archived at [https://zenodo.org/ Zenodo].<br><br />
You can directly refer to these release versions by adding a reference to the corresponding Zenodo artifacts to your work:<br />
<br />
* [https://doi.org/10.5281/zenodo.3865650 MiToBo 2.0]: Moeller, B., Posch, S. (2020). MiToBo - A Microscope Image Analysis Toolbox: v2.0, Zenodo [[Image:Zenodo.3865650.svg.png|180px|link=https://doi.org/10.5281/zenodo.3865650]] <br />
<br />
* [https://zenodo.org/record/495534 MiToBo 1.8]: Moeller, B., Posch, S., Glass, M., & Misiak, D. (2016). MiToBo - A Microscope Image Analysis Toolbox: v1.8, Zenodo [[Image:Zenodo.495534.png|165px|link=https://doi.org/10.5281/zenodo.495534]]<br />
<br />
* [https://zenodo.org/record/31364 MiToBo 1.7]: Moeller, B., Posch, S., Glass, M., & Misiak, D. (2015). MiToBo - A Microscope Image Analysis Toolbox: v1.7, Zenodo [[Image:Zenodo.31364.svg.png|165px|link=https://doi.org/10.5281/zenodo.31364]]</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=File:Zenodo.495534.png&diff=984File:Zenodo.495534.png2020-05-29T15:55:13Z<p>Moeller: </p>
<hr />
<div></div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Citing&diff=983Citing2020-05-29T15:54:48Z<p>Moeller: </p>
<hr />
<div>__NOTOC__<br />
<br />
== How to cite MiToBo? ==<br />
If you use functionality provided by MiToBo in your research or if you use the MiToBo library as basis for your own projects, please cite one of our main papers in your publications:<br />
* B. Möller, M. Glaß, D. Misiak and S. Posch, '''''MiToBo - A Toolbox for Image Processing and Analysis''''',<br> Journal of Open Research Software, 2016, 4:e17, DOI: http://dx.doi.org/10.5334/jors.103.<br />
<br />
More publications related to MiToBo can be found on the [http://www2.informatik.uni-halle.de/agprbio/mitobo/index.php/Publications publications page].<br><br />
Additional publications about the underlying [http://www.informatik.uni-halle.de/alida Alida] framework are available from [http://www2.informatik.uni-halle.de/agprbio/alida/index.php/Projects Alida's publications page].<br />
<br />
Selected major release versions of MiToBo are also indexed and archived at [https://zenodo.org/ Zenodo].<br><br />
You can directly refer to these release versions by adding a reference to the corresponding Zenodo artifacts to your work:<br />
<br />
* [https://doi.org/10.5281/zenodo.3865650 MiToBo 2.0]: Moeller, B., Posch, S. (2020). MiToBo - A Microscope Image Analysis Toolbox: v2.0, Zenodo [[Image:Zenodo.3865650.svg.png|180px|link=https://doi.org/10.5281/zenodo.3865650]] <br />
<br />
* [https://zenodo.org/record/495534 MiToBo 1.8]: Moeller, B., Posch, S., Glass, M., & Misiak, D. (2016). MiToBo - A Microscope Image Analysis Toolbox: v1.8, Zenodo [[Image:Zenodo.31364.svg.png|180px|link=https://doi.org/10.5281/zenodo.3865650]]http://doi.org/10.5281/zenodo.495534<br />
<br />
* [https://zenodo.org/record/31364 MiToBo 1.7]: Moeller, B., Posch, S., Glass, M., & Misiak, D. (2015). MiToBo - A Microscope Image Analysis Toolbox: v1.7, Zenodo [[Image:Zenodo.31364.svg.png|165px|link=https://doi.org/10.5281/zenodo.31364]]</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=File:Zenodo.31364.svg.png&diff=982File:Zenodo.31364.svg.png2020-05-29T15:51:05Z<p>Moeller: </p>
<hr />
<div></div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Citing&diff=981Citing2020-05-29T15:50:49Z<p>Moeller: </p>
<hr />
<div>__NOTOC__<br />
<br />
== How to cite MiToBo? ==<br />
If you use functionality provided by MiToBo in your research or if you use the MiToBo library as basis for your own projects, please cite one of our main papers in your publications:<br />
* B. Möller, M. Glaß, D. Misiak and S. Posch, '''''MiToBo - A Toolbox for Image Processing and Analysis''''',<br> Journal of Open Research Software, 2016, 4:e17, DOI: http://dx.doi.org/10.5334/jors.103.<br />
<br />
More publications related to MiToBo can be found on the [http://www2.informatik.uni-halle.de/agprbio/mitobo/index.php/Publications publications page].<br><br />
Additional publications about the underlying [http://www.informatik.uni-halle.de/alida Alida] framework are available from [http://www2.informatik.uni-halle.de/agprbio/alida/index.php/Projects Alida's publications page].<br />
<br />
Selected major release versions of MiToBo are also indexed and archived at [https://zenodo.org/ Zenodo].<br><br />
You can directly refer to these release versions by adding a reference to the corresponding Zenodo artifacts to your work:<br />
<br />
* [https://doi.org/10.5281/zenodo.3865650 MiToBo 2.0]: Moeller, B., Posch, S. (2020). MiToBo - A Microscope Image Analysis Toolbox: v2.0, Zenodo [[Image:Zenodo.3865650.svg.png|180px|link=https://doi.org/10.5281/zenodo.3865650]] <br />
<br />
* [https://zenodo.org/record/495534 MiToBo 1.8]: Moeller, B., Posch, S., Glass, M., & Misiak, D. (2016). MiToBo - A Microscope Image Analysis Toolbox: v1.8 [Data set]. Zenodo. http://doi.org/10.5281/zenodo.495534<br />
<br />
* [https://zenodo.org/record/31364 MiToBo 1.7]: Moeller, B., Posch, S., Glass, M., & Misiak, D. (2015). MiToBo - A Microscope Image Analysis Toolbox: v1.7 [Data set]. Zenodo. http://doi.org/10.5281/zenodo.31364</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=File:Zenodo.3865650.svg.png&diff=980File:Zenodo.3865650.svg.png2020-05-29T15:45:43Z<p>Moeller: </p>
<hr />
<div></div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Citing&diff=979Citing2020-05-29T15:45:20Z<p>Moeller: /* How to cite MiToBo? */</p>
<hr />
<div>__NOTOC__<br />
<br />
== How to cite MiToBo? ==<br />
If you use functionality provided by MiToBo in your research or if you use the MiToBo library as basis for your own projects, please cite one of our main papers in your publications:<br />
* B. Möller, M. Glaß, D. Misiak and S. Posch, '''''MiToBo - A Toolbox for Image Processing and Analysis''''',<br> Journal of Open Research Software, 2016, 4:e17, DOI: http://dx.doi.org/10.5334/jors.103.<br />
<br />
More publications related to MiToBo can be found on the [http://www2.informatik.uni-halle.de/agprbio/mitobo/index.php/Publications publications page].<br><br />
Additional publications about the underlying [http://www.informatik.uni-halle.de/alida Alida] framework are available from [http://www2.informatik.uni-halle.de/agprbio/alida/index.php/Projects Alida's publications page].<br />
<br />
Selected major release versions of MiToBo are also indexed and archived at [https://zenodo.org/ Zenodo].<br><br />
You can directly refer to these release versions by adding a reference to the corresponding Zenodo artifacts to your work:<br />
<br />
* [https://doi.org/10.5281/zenodo.3865650 MiToBo 2.0]: Moeller, B., Posch, S. (2020). MiToBo - A Microscope Image Analysis Toolbox: v2.0 [Data set]. Zenodo. https://doi.org/10.5281/zenodo.3865650<br />
<br />
* [https://zenodo.org/record/495534 MiToBo 1.8]: Moeller, B., Posch, S., Glass, M., & Misiak, D. (2016). MiToBo - A Microscope Image Analysis Toolbox: v1.8 [Data set]. Zenodo. http://doi.org/10.5281/zenodo.495534<br />
<br />
* [https://zenodo.org/record/31364 MiToBo 1.7]: Moeller, B., Posch, S., Glass, M., & Misiak, D. (2015). MiToBo - A Microscope Image Analysis Toolbox: v1.7 [Data set]. Zenodo. http://doi.org/10.5281/zenodo.31364</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Imprint&diff=978Imprint2020-05-29T15:12:49Z<p>Moeller: </p>
<hr />
<div>MiToBo is a project of the Martin Luther University Halle-Wittenberg.<br/><br/><br />
<br />
'''Editors:'''<br/><br />
* Stefan Posch<br />
* Birgit Möller<br />
* Danny Misiak<br />
* Markus Glass<br/><br/><br />
<br />
'''Contact:'''<br /><br />
* [mailto:mitobo@informatik.uni-halle.de mitobo@informatik.uni-halle.de]<br/><br/><br />
<br />
'''Institution:'''<br /><br />
Institute of Computer Science<br /><br />
Faculty of Natural Science III<br /><br />
Martin Luther University Halle-Wittenberg<br /><br />
Von-Seckendorff-Platz 1, 06120 Halle, Germany<br /></div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Imprint&diff=977Imprint2020-05-29T15:11:55Z<p>Moeller: </p>
<hr />
<div>MiToBo is a project of the Martin Luther University Halle-Wittenberg.<br/><br/><br />
<br />
'''Editors:'''<br/><br />
* Stefan Posch<br />
* Birgit Möller<br/><br/><br />
<br />
'''Contact:'''<br /><br />
* [mailto:mitobo@informatik.uni-halle.de mitobo@informatik.uni-halle.de]<br/><br/><br />
<br />
'''Institution:'''<br /><br />
Institute of Computer Science<br /><br />
Faculty of Natural Science III<br /><br />
Martin Luther University Halle-Wittenberg<br /><br />
Von-Seckendorff-Platz 1, 06120 Halle, Germany<br /></div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Acknowledgements&diff=976Acknowledgements2020-05-29T15:11:37Z<p>Moeller: </p>
<hr />
<div>__NOTOC__<br />
<br />
* The development of [http://mitobo.informatik.uni-halle.de/index.php/Applications/PaCeQuant PaCeQuant], the [http://mitobo.informatik.uni-halle.de/index.php/Applications/CytoskeletonAnalyzer2D CytoskeletonAnalyzer2D] and several other tools and operators have greatly profited from the image acquisition and user feedback as well as the overall intense scientific support of the group of [https://www.ipb-halle.de/en/employee/katharina-buerstenbinder/ Dr. Katharina Bürstenbinder], [https://www.ipb-halle.de/en/research/molecular-signal-processing/ Department of Molecular Signal Processing], [https://www.ipb-halle.de/en/ Leibniz Institute of Plant Biochemistry], Halle (Saale), Germany.<br/><br/><br />
<br />
* We thank [https://www.idiv.de/de/gruppen_und_personen/mitarbeiterinnen/mitarbeiterdetails/eshow/poeschl_yvonne.html Dr. Yvonne Pöschl-Grau], member of the [https://www.idiv.de/en/groups_and_people/central_management/bioinformatics_unit_biu.html Bioinformatics Unit (BIU)] of the [https://www.idiv.de/en.html German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig], for close collaboration in developing [http://mitobo.informatik.uni-halle.de/index.php/Applications/PaCeQuant PaCeQuant].<br/><br/><br />
<br />
* We greatfully acknowledge [https://www.biologie.uni-halle.de/institutsbereich_pflanzenphys/ag_schattat/2678173_2678352/#anchor2691932 Dr. Martin Schattat], Plant Organelle Shape and Dynamics Lab, [https://www.biologie.uni-halle.de/institutsbereich_pflanzenphys/ Institute of Plant Physiology], Martin Luther University Halle-Wittenberg, for the close collaboration, scientific support, image acquisition and comprehensive user feedback during the development of the MTBCellCounter and various other plant cell related operators.<br/><br/><br />
<br />
* Many thanks to the workgroup of Prof. Dr. Stefan Hüttelmaier ([http://www.medizin.uni-halle.de/index.php?id=326&L=1 Division for Molecular Cell Biology]) of the Martin Luther University Halle-Wittenberg) for their scientific support and image acquisition.<br/><br/><br />
<br />
* MiToBo builds on top of [https://imagej.net/Welcome ImageJ] and [https://fiji.sc/ Fiji] and takes great benefit from the infrastructure and very active community of theses tools. Hence, a big thanks goes to the ImageJ/Fiji development team around Wayne Rasband, Curtis Rueden and all the others for their never ending efforts to steadily push forward the tools.<br/><br/><br />
<br />
* We thank the [http://www.eclipse.org Eclipse Foundation] for developing the Eclipse IDE, which greatly accelerates the development of MiToBo.<br/><br/><br />
<br />
== Active MiToBo maintainers and core developers ==<br />
* Stefan Posch<br />
* Birgit Möller<br />
<br><br />
<br />
== Former members of the development team ==<br />
* Markus Glaß<br />
* Oliver Greß<br />
* Danny Misiak</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Acknowledgements&diff=975Acknowledgements2020-05-29T15:03:58Z<p>Moeller: /* MiToBo maintainer and active core developers */</p>
<hr />
<div>__NOTOC__<br />
<br />
* The development of [http://mitobo.informatik.uni-halle.de/index.php/Applications/PaCeQuant PaCeQuant], the [http://mitobo.informatik.uni-halle.de/index.php/Applications/CytoskeletonAnalyzer2D CytoskeletonAnalyzer2D] and several other tools and operators have greatly profited from the image acquisition and user feedback as well as the overall intense scientific support of the group of [https://www.ipb-halle.de/en/employee/katharina-buerstenbinder/ Dr. Katharina Bürstenbinder], [https://www.ipb-halle.de/en/research/molecular-signal-processing/ Department of Molecular Signal Processing], [https://www.ipb-halle.de/en/ Leibniz Institute of Plant Biochemistry], Halle (Saale), Germany.<br/><br/><br />
<br />
* We thank [https://www.idiv.de/de/gruppen_und_personen/mitarbeiterinnen/mitarbeiterdetails/eshow/poeschl_yvonne.html Dr. Yvonne Pöschl-Grau], member of the [https://www.idiv.de/en/groups_and_people/central_management/bioinformatics_unit_biu.html Bioinformatics Unit (BIU)] of the [https://www.idiv.de/en.html German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig], for close collaboration in developing [http://mitobo.informatik.uni-halle.de/index.php/Applications/PaCeQuant PaCeQuant].<br/><br/><br />
<br />
* We greatfully acknowledge [https://www.biologie.uni-halle.de/institutsbereich_pflanzenphys/ag_schattat/2678173_2678352/#anchor2691932 Dr. Martin Schattat], Plant Organelle Shape and Dynamics Lab, [https://www.biologie.uni-halle.de/institutsbereich_pflanzenphys/ Institute of Plant Physiology], Martin Luther University Halle-Wittenberg, for the close collaboration, scientific support, image acquisition and comprehensive user feedback during the development of the MTBCellCounter and various other plant cell related operators.<br/><br/><br />
<br />
* Many thanks to the workgroup of Prof. Dr. Stefan Hüttelmaier ([http://www.medizin.uni-halle.de/index.php?id=326&L=1 Division for Molecular Cell Biology]) of the Martin Luther University Halle-Wittenberg) for their scientific support and image acquisition.<br/><br/><br />
<br />
* MiToBo builds on top of [https://imagej.net/Welcome ImageJ] and [https://fiji.sc/ Fiji] and takes great benefit from the infrastructure and very active community of theses tools. Hence, a big thanks goes to the ImageJ/Fiji development team around Wayne Rasband, Curtis Rueden and all the others for their never ending efforts to steadily push forward the tools.<br/><br/><br />
<br />
* We thank the [http://www.eclipse.org Eclipse Foundation] for developing the Eclipse IDE, which greatly accelerates the development of MiToBo.<br/><br/><br />
<br />
== MiToBo maintainers and active core developers ==<br />
* Stefan Posch<br />
* Birgit Möller<br />
<br />
== Former members of the development team ==<br />
* Markus Glaß<br />
* Oliver Greß<br />
* Danny Misiak</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Acknowledgements&diff=974Acknowledgements2020-05-29T15:03:47Z<p>Moeller: </p>
<hr />
<div>__NOTOC__<br />
<br />
* The development of [http://mitobo.informatik.uni-halle.de/index.php/Applications/PaCeQuant PaCeQuant], the [http://mitobo.informatik.uni-halle.de/index.php/Applications/CytoskeletonAnalyzer2D CytoskeletonAnalyzer2D] and several other tools and operators have greatly profited from the image acquisition and user feedback as well as the overall intense scientific support of the group of [https://www.ipb-halle.de/en/employee/katharina-buerstenbinder/ Dr. Katharina Bürstenbinder], [https://www.ipb-halle.de/en/research/molecular-signal-processing/ Department of Molecular Signal Processing], [https://www.ipb-halle.de/en/ Leibniz Institute of Plant Biochemistry], Halle (Saale), Germany.<br/><br/><br />
<br />
* We thank [https://www.idiv.de/de/gruppen_und_personen/mitarbeiterinnen/mitarbeiterdetails/eshow/poeschl_yvonne.html Dr. Yvonne Pöschl-Grau], member of the [https://www.idiv.de/en/groups_and_people/central_management/bioinformatics_unit_biu.html Bioinformatics Unit (BIU)] of the [https://www.idiv.de/en.html German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig], for close collaboration in developing [http://mitobo.informatik.uni-halle.de/index.php/Applications/PaCeQuant PaCeQuant].<br/><br/><br />
<br />
* We greatfully acknowledge [https://www.biologie.uni-halle.de/institutsbereich_pflanzenphys/ag_schattat/2678173_2678352/#anchor2691932 Dr. Martin Schattat], Plant Organelle Shape and Dynamics Lab, [https://www.biologie.uni-halle.de/institutsbereich_pflanzenphys/ Institute of Plant Physiology], Martin Luther University Halle-Wittenberg, for the close collaboration, scientific support, image acquisition and comprehensive user feedback during the development of the MTBCellCounter and various other plant cell related operators.<br/><br/><br />
<br />
* Many thanks to the workgroup of Prof. Dr. Stefan Hüttelmaier ([http://www.medizin.uni-halle.de/index.php?id=326&L=1 Division for Molecular Cell Biology]) of the Martin Luther University Halle-Wittenberg) for their scientific support and image acquisition.<br/><br/><br />
<br />
* MiToBo builds on top of [https://imagej.net/Welcome ImageJ] and [https://fiji.sc/ Fiji] and takes great benefit from the infrastructure and very active community of theses tools. Hence, a big thanks goes to the ImageJ/Fiji development team around Wayne Rasband, Curtis Rueden and all the others for their never ending efforts to steadily push forward the tools.<br/><br/><br />
<br />
* We thank the [http://www.eclipse.org Eclipse Foundation] for developing the Eclipse IDE, which greatly accelerates the development of MiToBo.<br/><br/><br />
<br />
== MiToBo maintainer and active core developers ==<br />
* Stefan Posch<br />
* Birgit Möller<br />
<br />
== Former members of the development team ==<br />
* Markus Glaß<br />
* Oliver Greß<br />
* Danny Misiak</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Applications/PaCeQuantAna&diff=973Applications/PaCeQuantAna2020-05-23T09:54:30Z<p>Moeller: /* PaCeQuantAna: R package for Visualization and Statistical Analysis of Cell Shape Featues */</p>
<hr />
<div>== PaCeQuantAna: R package for Visualization and Statistical Analysis of Cell Shape Featues ==<br />
We provide an R package for visualizing and analyzing features extracted by PaCeQuant.<br><br />
<br />
'''Please note:'''<br><br />
'''The new version compatible with PaCeQuant as released in MiToBo 2.0 in May 2020 will appear soon!'''<br><br />
'''Due to implications of the Corona pandemic the release of the package update had to be postponed.'''<br><br />
'''We apologize for the inconvenience and hope to be able to make the new PaCeQuantAna release available to you very soon.'''<br />
<br />
The old version of PaCeQuantAna compatible with PaCeQuant results generated with MiToBo 1.8.x can be downloaded here:<br />
<br />
* [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/paceQuantEval/PaCeQuantAna_1.0.0.tar.gz R package v1.0.0]<br />
<br />
=== Installation ===<br />
For installation in RStudio download the package and follow the instructions below:<br />
<br />
<ol><br />
<li> Install the following packages:<br />
<ul><br />
<li> '''caroline'''<br />
<li> '''gplots'''<br />
<li> '''dunn.test'''<br />
<li> '''RColorBrewer'''<br />
</ul><br />
To this end start RStudio, select<br />
<blockquote>“Tools” → “Install Packages…” </blockquote><br />
from the menu bar.<br> Choose <blockquote>“Install from: Repository (CRAN)”</blockquote> and enter the names of the packages.<br> Activate <blockquote>“Install dependencies”.</blockquote><br />
<li> The multtest package can be installed via the following Bioconductor installation script:<br><br />
<blockquote>source ("<nowiki>http://bioconductor.org/biocLite.R</nowiki>")</blockquote><br />
<blockquote>biocLite("multtest")</blockquote><br />
<li> Install the PaCeQuantAna package selecting <br />
<blockquote>“Tools” → “Install Packages…”</blockquote> <br />
from the menu bar.<br> <br />
Choose <blockquote>“Install from: Package Archive File (.tgz; .tar.gz)"</blockquote> <br />
and select the tar.gz file of PaCeQuantAna via <blockquote>"Browse...".</blockquote><br />
</ol><br />
<br />
=== Documentation ===<br />
<br />
Find more details of how to use the package and details about the general workflow in the vignette of the package by either navigating to the vignette in the Rstudio package manager tab or by typing <br />
<blockquote>vignette("PaCeQuantAna")</blockquote><br />
in the console.<br />
<br />
The vignette contains comprehensive documentation of the various functions and options of the package.<br><br />
In addition, a sample workflow R script is provided which shows all commands to load your data, configure the output and do the analysis.<br><br />
You can directly copy the script into a file and load this file into the Rstudio editor to run it completely or line-wise.<br />
<br />
You can test the package on these sample data: [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/time_series.zip sample data for PaCeQuantAna]<br><br />
<br />
=== Important notes ===<br />
<ul><br />
<li> By default the working directory (set with ''setpw(...)'') where the result folder will be created, and the data directory (set with ''setDataDir(...)'') must not be identical!<br> <br />
If you require these folders to be identical for whatever reason you need to manually edit the file ''data_description.csv'' in the output folder and delete the row referring to the output folder.<br />
<li> On Windows operating systems you may encounter problems with missing fonts, i.e., error messages like the following one:<br />
<blockquote>...</blockquote><br />
<blockquote>Error in pdf(file = paste0(outdir, fsep, base_file_name,</blockquote><br />
<blockquote>"_dunn_test_heatmap_adjusted_pvalues.pdf"),&nbsp; :</blockquote><br />
<blockquote>&nbsp; unknown family 'Arial'</blockquote> <br />
<blockquote>...</blockquote><br />
To circumvent these problems call once in Rstudio the following two commands,<br />
<blockquote>library(extrafont)</blockquote><br />
<blockquote>font_import()</blockquote><br />
Initialize each of your workflows using PaCeQuantAna with<br />
<blockquote>library(extrafont)</blockquote><br />
This will initialize the Windows font database and should solve the problems.<br />
</ul><br />
<br />
<!--<br />
== R script for Visualization and Statistical Analysis of Results ==<br />
We provide an R script for visualizing and analyzing results generated by PaCeQuant:<br />
<br />
* [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/paceQuantEval/PaCeQuantEval_version0.1.zip R script v0.1]<br />
* [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/paceQuantEval/README.PaCeQuantEval README]<br />
<br />
Before running the script you need to set some path variables in the header of the script file which, e.g., specify where to find the PaCeQuant result data and where to save the final plots. <br />
<br />
The script will include result data from the current directory and from all direct sub-directories of the current folder into its analysis.<br> Each folder is treated as one group of cells, and the analysis is designed to compare different groups of cells against each other.<br />
<br />
You can test the script on the sample data provided on this page.<br />
--></div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Applications/PaCeQuantAna&diff=972Applications/PaCeQuantAna2020-05-23T09:54:17Z<p>Moeller: /* PaCeQuantAna: R package for Visualization and Statistical Analysis of Cell Shape Featues */</p>
<hr />
<div>== PaCeQuantAna: R package for Visualization and Statistical Analysis of Cell Shape Featues ==<br />
We provide an R package for visualizing and analyzing features extracted by PaCeQuant.<br><br />
<br />
'''Please note:'''<br><br />
'''The new version compatible with PaCeQuant as released in MiToBo 2.0 in May 2020 will appear soon!'''<br><br />
'''Due to implications of the Corona pandemic the release of the package update had to be postponed.'''<br><br />
'''We apologize for the inconvenience and hope to be able to make the new PaCeQuantAna release available to you very soon.'''<br />
<br />
The old version of PaCeQuantAna compatible with PaCeQuant results generated with MiToBo 1.8.x can be downloaded here:<br />
<br />
* [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/paceQuantEval/PaCeQuantAna_1.0.0.tar.gz R package v1.0.0] ()<br />
<br />
=== Installation ===<br />
For installation in RStudio download the package and follow the instructions below:<br />
<br />
<ol><br />
<li> Install the following packages:<br />
<ul><br />
<li> '''caroline'''<br />
<li> '''gplots'''<br />
<li> '''dunn.test'''<br />
<li> '''RColorBrewer'''<br />
</ul><br />
To this end start RStudio, select<br />
<blockquote>“Tools” → “Install Packages…” </blockquote><br />
from the menu bar.<br> Choose <blockquote>“Install from: Repository (CRAN)”</blockquote> and enter the names of the packages.<br> Activate <blockquote>“Install dependencies”.</blockquote><br />
<li> The multtest package can be installed via the following Bioconductor installation script:<br><br />
<blockquote>source ("<nowiki>http://bioconductor.org/biocLite.R</nowiki>")</blockquote><br />
<blockquote>biocLite("multtest")</blockquote><br />
<li> Install the PaCeQuantAna package selecting <br />
<blockquote>“Tools” → “Install Packages…”</blockquote> <br />
from the menu bar.<br> <br />
Choose <blockquote>“Install from: Package Archive File (.tgz; .tar.gz)"</blockquote> <br />
and select the tar.gz file of PaCeQuantAna via <blockquote>"Browse...".</blockquote><br />
</ol><br />
<br />
=== Documentation ===<br />
<br />
Find more details of how to use the package and details about the general workflow in the vignette of the package by either navigating to the vignette in the Rstudio package manager tab or by typing <br />
<blockquote>vignette("PaCeQuantAna")</blockquote><br />
in the console.<br />
<br />
The vignette contains comprehensive documentation of the various functions and options of the package.<br><br />
In addition, a sample workflow R script is provided which shows all commands to load your data, configure the output and do the analysis.<br><br />
You can directly copy the script into a file and load this file into the Rstudio editor to run it completely or line-wise.<br />
<br />
You can test the package on these sample data: [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/time_series.zip sample data for PaCeQuantAna]<br><br />
<br />
=== Important notes ===<br />
<ul><br />
<li> By default the working directory (set with ''setpw(...)'') where the result folder will be created, and the data directory (set with ''setDataDir(...)'') must not be identical!<br> <br />
If you require these folders to be identical for whatever reason you need to manually edit the file ''data_description.csv'' in the output folder and delete the row referring to the output folder.<br />
<li> On Windows operating systems you may encounter problems with missing fonts, i.e., error messages like the following one:<br />
<blockquote>...</blockquote><br />
<blockquote>Error in pdf(file = paste0(outdir, fsep, base_file_name,</blockquote><br />
<blockquote>"_dunn_test_heatmap_adjusted_pvalues.pdf"),&nbsp; :</blockquote><br />
<blockquote>&nbsp; unknown family 'Arial'</blockquote> <br />
<blockquote>...</blockquote><br />
To circumvent these problems call once in Rstudio the following two commands,<br />
<blockquote>library(extrafont)</blockquote><br />
<blockquote>font_import()</blockquote><br />
Initialize each of your workflows using PaCeQuantAna with<br />
<blockquote>library(extrafont)</blockquote><br />
This will initialize the Windows font database and should solve the problems.<br />
</ul><br />
<br />
<!--<br />
== R script for Visualization and Statistical Analysis of Results ==<br />
We provide an R script for visualizing and analyzing results generated by PaCeQuant:<br />
<br />
* [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/paceQuantEval/PaCeQuantEval_version0.1.zip R script v0.1]<br />
* [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/paceQuantEval/README.PaCeQuantEval README]<br />
<br />
Before running the script you need to set some path variables in the header of the script file which, e.g., specify where to find the PaCeQuant result data and where to save the final plots. <br />
<br />
The script will include result data from the current directory and from all direct sub-directories of the current folder into its analysis.<br> Each folder is treated as one group of cells, and the analysis is designed to compare different groups of cells against each other.<br />
<br />
You can test the script on the sample data provided on this page.<br />
--></div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Downloads&diff=971Downloads2020-05-16T17:03:55Z<p>Moeller: </p>
<hr />
<div>Here you can find the current release of MiToBo for download. Likewise older versions and additional libraries required to run MiToBo can be found here.<br />
<br />
For detailed information on the installation process take a look at the [[Installation]] page.<br />
<br />
== Current release ==<br />
<br />
The current release of the MiToBo core distribution is 2.0 and of the extended MiToBo-Plugins distribution 2.0.<br />
<br />
Since release 1.3 we support Maven for managing MiToBo's resources.<br> You can download the MiToBo distributions as well as the Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/archiva/#browse/de.unihalle.informatik.MiToBo https://moon.informatik.uni-halle.de/archiva/#browse/de.unihalle.informatik.MiToBo]<br />
<br />
<blockquote style="background-color: lightgrey; border: solid thin grey;"><br />
'''[[Using MiToBo with ImageJ 1.x:]]'''<br><br />
For using MiToBo with ImageJ it is the easiest to download the distribution zipfile,<br><br />
<br />
[https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/1.8.15/mitobo-plugins-1.8.15-bin.zip https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/1.8.15/mitobo-plugins-1.8.15-bin.zip]<br><br />
<br />
which already includes '''''all''''' dependencies and ships with some scripts to run MiToBo's operators and plugins out of the box.<br> See the [http://www2.informatik.uni-halle.de/agprbio/mitobo/index.php/Installation installation instructions] for further information.<br />
</blockquote><br />
<br />
<blockquote style="background-color: lightgrey; border: solid thin grey;"><br />
'''[[Using MiToBo with Fiji:]]'''<br><br />
Since release 1.5 MiToBo is available via a Fiji update site:<br />
<br />
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br><br />
<br />
To enable this site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].<br />
</blockquote><br />
<br />
There are two MiToBo distributions available:<br />
* <b>MiToBo:</b><br> this package contains the core of MiToBo, i.e. all operators, the MiToBo runners for operator execution and also Grappa;<br> <b>not included</b> are the plugins to run MiToBo from within ImageJ 1.x, hence, this distribution is mainly for stand-alone usage of MiToBo and development purposes<br><br />
* <b>MiToBo-Plugins:</b><br> this package contains the complete MiToBo distribution, some special plugins like the [[Applications/MTBCellCounter | MTB Cell Counter]], and in addition some ImageJ plugins to run MiToBo operators from within ImageJ; you should download the MiToBo-Plugins distribution if you like to use MiToBo with ImageJ<br />
<br />
<br><br />
<br />
Since release 1.8 MiToBo's implementation requires at least Java 1.8.<br />
<br><br />
<br />
Below the following kinds of files are available for download:<br />
* Distribution: complete distributions including all dependencies, scripts, documentation, etc.<br />
* Binaries only: only the jar archives, no dependencies nor documentation<br />
* API: Javadoc API<br />
<br><br />
<br />
== Maven Project Template ==<br />
Using MiToBo as a library for own developments can best be done by making use of Maven.<br><br />
Particularly, Maven automatically resolves all dependencies which otherwise would have to be installed manually.<br />
<br />
For getting started with MiToBo and Maven a project template is provided: <br />
<br />
[http://www.informatik.uni-halle.de/mitobo/downloads/maven/mitobo-demo-project-1.2-src.zip Maven project template [zip]]<br />
<br />
The project is readily configured and you can immediately start with own developments.<br><br />
It also contains a demo operator showing the basic usage of MiToBo data types and operators on the code level.<br />
<br />
Make sure that you have installed Maven and a Java Develpoment Kit (JDK) in version 1.8 or higher.<br><br />
You can check the Java version by running 'mvn --version' from command line.<br> <br />
If an older Java version is used, let the 'JAVA_HOME' environment variable point to a folder containing a more recent JDK.<br />
<br />
You can run Maven directly from within the extracted folder. Alternatively the Maven template project can easily be imported into an IDE like Eclipse.<br><br />
The zip file contains a README file containing more information about installing and configuring the project template.<br />
<br/><br />
<br />
== Manual ==<br />
<br />
Detailed information about MiToBo, its API and usage, can be found in MiToBo's User and Programmer Guide.<br />
<br />
* MiToBo-Guide, Version 1.0 [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual.pdf pdf]<br />
<br/><br />
<br />
<br />
== Additional resources ==<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release:<br />
* Chipory binary [http://www.informatik.uni-halle.de/mitobo/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www.informatik.uni-halle.de/mitobo/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br/><br />
<br />
<br />
== Logo ==<br />
<br />
* MiToBo logo as [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.pdf PDF] or [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.png PNG]<br />
<br />
<br />
== Earlier releases of MiToBo (< 1.5) ==<br />
<br />
Since release 1.3 MiToBo's resources are available from our Maven archive server: [https://moon.informatik.uni-halle.de/archiva/]<br>Binaries, sources and documentation for versions older than the current release, but at least of version 1.3 or newer can be found there.<br> All other releases can be accessed via the list below.<br><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 1.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3-javadoc.jar jar]<br />
| March 31st, 2015 (Support for callbacks)<br />
|-<br />
| 1.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 1.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 1.2<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-bin-v1.2.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-v1.2.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-v1.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
|-<br />
| 1.1<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-bin-v1.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-v1.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-v1.1.zip zip]<br />
| March 1st, 2013<br />
|-<br />
| 1.0.5<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.5.zip zip]<br />
| October 23rd, 2012<br />
|-<br />
| 1.0.1<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.1.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.1.zip zip]<br />
| July 6th, 2012<br />
|-<br />
| 1.0.0<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.0.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.0.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.0.zip zip]<br />
| April 26th, 2012<br />
|-<br />
| 0.96<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.6.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.6.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-0.9.6.zip zip]<br />
| September 01, 2011<br />
|-<br />
| 0.95<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.5.zip zip]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-0.9.5.zip zip]<br />
| June 08, 2011 (updated June 22nd, 2011)<br />
|-<br />
| 0.9<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.tar.gz tar.gz]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.tar.gz tar.gz]<br />
| [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.tar.gz tar.gz]<br />
| October 26, 2010<br />
|}<br />
<br/><br />
<br />
=== Requirements (for MiToBo < 1.3) ===<br />
MiToBo requires Java 1.6 or later. <br />
<br />
'''Note''': Java 1.7 is currently not fully supported!<br />
<br />
The following external jars are needed to run MiToBo plugins and use the code.<br/><br />
<b>Note that the binary zip file already includes all jars required, there is no need for explicit download!</b><br />
<br />
MiToBo depends on the following external jars:<br />
<br />
* [http://rsbweb.nih.gov/ij/ ImageJ], >= Version 1.47d<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://www.csie.ntu.edu.tw/~cjlin/libsvm/ LIBSVM], Version 3.1<br />
* [http://www.loci.wisc.edu/software/bio-formats/ Loci Tools], Version 4.3.3<br />
* [http://math.nist.gov/javanumerics/jama/ Jama], Version 1.0.2 <br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
* [http://sezpoz.java.net/ SezPoz], Version 1.9<br />
* [http://www.jgraph.com/mxdownload.html JGraph], Version 1.7.1.8<br />
<br />
* [https://jai-imageio.dev.java.net/ JAI ImageIO], Version 1.1 (only required for MiToBo 0.9)<br />
<br />
=== Project internal libraries ===<br />
<br />
MiToBo also relies on some libraries provided by the MiToBo project itself.<br><br />
In particular XML schemes for representing the history graphs and MiToBo's online help are included in separate jar archives.<br />
<br />
'''[[Note]]:''' <br/><br />
''' You do not need to download these libraries explicitly. If you download the binary zip file all jars and libraries are already included.''' <br/><br />
<br />
The MiToBo internal archive files included in the zip file are the following ones:<br />
<br />
* ALDGraphml, Version 1.0.0 (Alida extensions for [http://graphml.graphdrawing.org/ graphML]):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/aldgraphml/aldgraphml.jar jar]<br />
* MTBXml, Version 1.0.0 (MiToBo XML I/O for several datatypes, based on XMLBeans):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbxml/mtbxml.jar jar] <br />
* MiToBo-Help, Version 1.0.0 (MiToBo JavaHelp pages):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mitoboHelp/MiToBo-Help.jar jar] <br />
<br />
The following library is only required for MiToBo-0.9: <br />
<br />
* MTBImageIO-Ext, Version 0.9 (improved image I/O based on ImageIO-Ext):<br />
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff-0.9.jar jar]<br />
** Source code [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff_src-0.9.zip zip]<br />
** Alternatively, the [https://imageio-ext.dev.java.net/ ImageIO-Ext] library can be used, which depends on the [https://jai-imageio.dev.java.net/ JAI ImageIO] library and the [https://jai.dev.java.net/ JAI] library.<br/>MTBImageIO-Ext is simply the TIFF part of ImageIO-Ext with slight adjustments to remove dependency on the JAI library.<br />
<br/></div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Publications&diff=970Publications2020-05-16T17:02:26Z<p>Moeller: </p>
<hr />
<div>MiToBo has been used in diverse research projects. Below you can find a selection of our publications about MiToBo itself and also several of our research papers in which MiToBo has successfully been applied to various tasks.<br/><br />
<br />
* Y. Poeschl, B. Möller, L. Müller, and K. Bürstenbinder,<br>'''''User-friendly assessment of pavement cell shape features with PaCeQuant: Novel functions and tools'''''.<br>In [https://doi.org/10.1016/bs.mcb.2020.04.010 Methods in Cell Biology], Academic Press, 2020.<br />
<br />
* B. Möller, L. Zergiebel, and K. Bürstenbinder,<br>'''''Quantitative and Comparative Analysis of Global Patterns of (Microtubule) Cytoskeleton Organization with CytoskeletonAnalyzer2D'''''.<br>In F. Cvrčková and V. Žárský, editors, [http://dx.doi.org/10.1007/978-1-4939-9469-4_10 Plant Cell Morphogenesis: Methods and Protocols, chapter 10, pp. 151-171], Springer New York, New York, NY, 2019.<br />
<br />
* B. Möller, Y. Poeschl, S. Klemm, and K. Bürstenbinder,<br>'''''Morphological Analysis of Leaf Epidermis Pavement Cells with PaCeQuant'''''.<br>In F. Cvrčková and V. Žárský, editors, [http://dx.doi.org/10.1007/978-1-4939-9469-4_22 Plant Cell Morphogenesis: Methods and Protocols, chapter 22, pages 329-349], Springer New York, New York, NY, 2019.<br />
<br />
* B. Möller and K. Bürstenbinder,<br>'''''Semi-automatic Cell Segmentation from Noisy Image Data for Quantification of Microtubule Organization on Single Cell Level'''''.<br>In Proc. of IEEE 16th International Symposium on Biomedical Imaging (ISBI '19), pp. 199-203, ISBN: 978-1-5386-3640-4, Venice, Italy, April 2019.<br />
<br />
* B. Möller and M. Schattat,<br>'''''Quantification of Stromule Frequencies in Microscope Images of Plastids combining Ridge Detection and Geometric Criteria'''''.<br>In Proc. of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 2: BIOIMAGING, pp. 38-48, ISBN: 978-989-758-353-7, INSTICC, SciTePress, Prague, Czech Republic, February 2019.<br />
<br />
* D. Mitra, S. Klemm, P. Kumari, J. Quegwer, B. Möller, Y. Poeschl, P. Pflug, G. Stamm, S. Abel, K. Bürstenbinder,<br>'''''Microtubule-associated protein IQ67 DOMAIN5 regulates morphogenesis of leaf pavement cells in Arabidopsis thaliana'''''.<br>In [https://academic.oup.com/jxb/article/70/2/529/5165408 Journal of Experimental Botany, 70(2):529-543, January 2019].<br />
<br />
* B. Möller, Y. Poeschl, R. Plötner, and K. Bürstenbinder,<br>'''''PaCeQuant: A Tool for High-Throughput Quantification of Pavement Cell Shape Characteristics'''''.<br>In [http://www.plantphysiol.org/content/early/2017/09/20/pp.17.00961 Plant Physiology, 175(1), September 2017].<br />
<br />
* K. Bürstenbinder, B. Möller, R. Plötner, G. Stamm, G. Hause, D. Mitra, and S. Abel,<br>'''''The IQD Family of Calmodulin-Binding Proteins Links Calcium Signaling to Microtubules, Membrane Subdomains, and the Nucleus'''''.<br>In [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5338658/# Plant Physiology, 173(3):1692-1708, March 2017].<br />
<br />
* B. Möller, M. Glaß, D. Misiak and S. Posch, '''''MiToBo – A Toolbox for Image Processing and Analysis''''',<br> In Journal of Open Research Software 4: e17, DOI: http://dx.doi.org/10.5334/jors.103, 2016.<br />
<br />
* L. Franke, B. Storbeck, J. L. Erickson, D. Rödel, D. Schröter, B. Möller, and M. H. Schattat, <br/> '''''The 'MTB Cell Counter' a versatile tool for the semi-automated quantification of sub-cellular phenotypes in fluorescence microscopy images. A case study on plastids, nuclei and peroxisomes''''', <br/>In [http://zs.thulb.uni-jena.de/receive/jportal_jparticle_00342296 Journal of Endocytobiosis and Cell Research, 26:31-42, 2015].<br />
<br />
* B. Möller, E. Piltz and N. Bley, '''''Quantification of Actin Structures using Unsupervised Pattern Analysis Techniques''''', <br/>In Proc. of Int. Conf. on Pattern Recognition (ICPR '14), IEEE, pp. 3251-3256, Stockholm, Sweden, August 2014. <br />
<br />
* D. Misiak, S. Posch, M. Lederer, C. Reinke, S. Hüttelmaier and B. Möller, '''''Extraction of Protein Profiles from Primary Neurons using Active Contour Models and Wavelets''''', <br/> In [http://www.sciencedirect.com/science/article/pii/S0165027013004330 Journal of Neuroscience Methods , vol. 225, pages 1-12, March 2014]. <br />
<br />
* M. Glaß, B. Möller and S. Posch, '''''Scratch Assay Analysis in ImageJ'''', <br/> In Proc. of ImageJ User & Developer Conference, pp. 211-214, ISBN 2-919941-18-6, Mondorf-les-Bains, Luxembourg, October 2012. <br />
<br />
* B. Möller and D. Misiak, '''''SnakeOptimizer - Object Segmentation with Parametric Active Contours in ImageJ''''', <br/> In Proc. of ImageJ User & Developer Conference, pp. 215-217/222, ISBN 2-919941-18-6, Mondorf-les-Bains, Luxembourg, October 2012.<br />
<br />
* M. Glaß, B. Möller, A. Zirkel, K. Wächter, S. Hüttelmaier and S. Posch, '''''Cell Migration Analysis: Segmenting Scratch Assay Images with Level Sets and Support Vector Machines''''',<br> In Pattern Recognition, vol. 45, no. 9, pp. 3154-3165, Elsevier, September 2012. <br />
<br />
* B. Möller and S. Posch, '''''Comparing Active Contours for the Segmentation of Biomedical Images''''',<br> In Proc. of IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI), pp. 736-739, IEEEXplore Digital Library, ISBN 978-1-4577-1856-4, Barcelona, Spain, May 2012.<br />
<br />
* B. Möller and S. Posch, '''''MiCA - Easy Cell Image Analysis with Normalized Snakes''''',<br> In Proc. of Workshop on Microscopic Image Analysis with Applications in Biology (MIAAB), Heidelberg, Germany, September 2011. <br />
<br />
* M. Glaß, B. Möller, A. Zirkel, K. Wächter, S. Hüttelmaier and S. Posch, '''''Scratch Assay Analysis with Topology-preserving Level Sets and Texture Measure''''',<br> In Proc. of 5th Iberian Conference on Pattern Recognition and Image Analysis (IbPRIA), Jordi Vitrià, João M. Sanches, and Mario Hernández, editors, Springer, LNCS 6669, pp. 100-108, Las Palmas de Gran Canaria, Spain, June 2011.</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Applications&diff=969Applications2020-05-16T16:59:19Z<p>Moeller: </p>
<hr />
<div>Several image processing pipelines have already been developed in MiToBo. <br/><br />
Below you can find selected example applications.<br />
<br />
* [[Applications/CellBoundaryExtractor2D | CellBoundaryExtractor2D]] (since MiToBo 1.8.13.1) <br/> extracts cell boundaries from microscopy images using vesselness enhancement filters.<br />
<br />
* [[Applications/CytoskeletonAnalyzer2D | Cytoskeleton Analyzer 2D]] (since MiToBo 1.8.13) <br/> is an advanced version of the [[Applications/ActinAnalyzer2D | Actin Analyzer 2D]] operator for quantifying and comparing structural patterns of the cytoskeleton in cells, e.g., of actin microfilament structures or microtubuli patterns.<br />
<br />
* [[Applications/PaCeQuantToolset | PaCeQuant]] (released with MiToBo 1.8.6, updated in 2.0), <br/> for quantifying pavement cell shape in a high-throughput manner; the main plugin is supplemented by corresponding tools, i.e. the '''''[[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]]''''' and the '''''[[Applications/FeatureColorMapper|FeatureColorMapper]]''''' <br />
<br />
* [[Applications/MTBCellCounter | MTB Cell Counter]] (since MiToBo 1.5), <br/> a tool for semi-automatic labeling and counting of spot-like structures like, e.g., plastides, stress granules or p-bodies<br />
<br />
* [[Applications/MiCa | MiCA - MiToBo Cell Image Analyzer]]<br/> for segmenting cell boundaries and sub-cellular particles in fluorescent microscopy images<br />
<br />
* [[Applications/NeuronAnalyzer2D | Neuron Analyzer 2D]]<br/> for segmenting the area of neurites and quantify protein concentrations within these neurites<br />
<br />
* [[Applications/ScratchAssayAnalyzer | Scratch Assay Analyzer]]<br/> for analysis of collective cell migration based on scratch/ wound closure assay images<br />
<br />
* [[Applications/CellMigrationAnalyzer | Cell Migration Analyzer]]<br/> for migration analysis based on single cell tracking</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Main_Page&diff=968Main Page2020-05-16T16:56:30Z<p>Moeller: </p>
<hr />
<div>= MiToBo - A <span style="color:#CC0000">m</span>icroscope <span style="color:#CC0000">i</span>mage analysis <span style="color:#CC0000">to</span>ol<span style="color:#CC0000">bo</span>x =<br />
<br />
{|width="100%"<br />
|-<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''What is MiToBo?'''<br><br />
The Microscope Image Analysis Toolbox MiToBo is a toolbox with a large collection of basic and advanced functions and algorithms for processing and analyzing digital images. Many tools in MiToBo target at the analysis of various kinds of microscopy data, however, most of the functionality within MiToBo is generic (see [[Features|page of features]] for an overview). MiToBo is implemented as extension for the widely used image processing application [http://rsbweb.nih.gov/ij/ ImageJ]/[https://fiji.sc/ Fiji] and its new release [http://developer.imagej.net/ ImageJ 2.0]. All functions, operators and plugins of MiToBo are ready to be directly used as plugins in ImageJ and Fiji.<br /><br/><br />
<br />
'''Highlight operators and tools in MiToBo'''<br />
{|style="background-color:#f8f8ff"<br />
|style="text-align:left;width:10%|[[File:MiToBo_logo_CytoskeletonAnalyzer2D.png|border|72px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/CytoskeletonAnalyzer2D]]<br />
|style="text-align:left;width:80%|'''''[[Applications/CytoskeletonAnalyzer2D|CytoskeletonAnalyzer2D]]''''' for the quantification of cytoskeleton structural patterns in microscopy images with texture measures;<br><br />
to ease cell boundary extraction in data preparation we additionally provide the '''''[[Applications/CellBoundaryExtractor2D|CellBoundaryExtractor2D]]''''' and a handy '''''[[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]]'''''<br />
|-<br />
|style="text-align:left;width:10%|[[File:MiToBo_logo_PaCeQuant.png|border|72px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/PaCeQuantToolset]]<br />
|style="text-align:left;width:80%|'''''[[Applications/PaCeQuantToolset|PaCeQuant]]''''' and corresponding tools, i.e. the '''''[[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]]''''', the '''''[[Applications/FeatureColorMapper|FeatureColorMapper]]''''' and the R package '''''[[Applications/PaCeQuantAna|PaCeQuantAna]]''''', for quantification, visualization and statistical analysis of the morphology and shape characteristics of cells<br />
|-<br />
|style="text-align:left;width:10%|[[File:NeuronAnalyzer2D.png|border|72px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/NeuronAnalyzer2D]]<br />
|style="text-align:left;width:80%|'''''[[Applications/NeuronAnalyzer2D|Neuron Analyzer]]''''' for the segmentation of neurons in microscope images<br />
|-<br />
|style="text-align:left;width:10%|[[File:tracking_ES-2.gif|72px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/CellMigrationAnalyzer]]<br />
|style="text-align:left;width:80%|'''''[[Applications/CellMigrationAnalyzer|Cell Migration Analyzer]]''''' for analyzing single cell migration from time lapse image sequences<br />
|-<br />
|style="text-align:left;width:10%|[[File:GFP_U2OS_overlay.png|72px|left|border|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/ScratchAssayAnalyzer]]<br />
|style="text-align:left;width:80%|'''''[[Applications/ScratchAssayAnalyzer|Scratch Assay Analyzer]]''''' for analyzing microscope images from collective cell migration experiments<br />
|}<br />
For several other important operators and plugins documentation is available via the [[Operator_Documentation| Operator Documentation pages]] here in the Wiki.<br> <br />
The pages are structured according to the package structure of MiToBo which is also mirrored in the selection panel of MiToBo's operator runner.<br />
<br />
<br><br />
'''MiToBo for developers'''<br><br />
MiToBo aims not only to support users in analyzing their images, but also targets at developers by offering a programmer-friendly software framework and API for developing new algorithms.<br />
The MiToBo API completely separates the implementation of image processing algorithms from potential user interfaces based <br />
on [http://www.informatik.uni-halle.de/alida/ Alida] which is a library for easing the development of data analysis<br />
algorithms and tools. The main concept of Alida are <i>operators</i> as the core units for implementing data analysis algorithms. <br /><br />
Alida defines unified interfaces and execution procedures for operators which yield the fundament for its nice features like <br />
<ul><br />
<li> automatic documentation of complete analysis processes, e.g., leading from an input image to analysis results, in terms of processing graphs<br />
<li> automatic generation of commandline and graphical user interfaces<br />
<li> a graphical programming editor named '''''Grappa''''' automatically considering all implemented operators as potential processing nodes<br><br />
</ul><br />
<br />
<p><br />
MiToBo takes full advantage of Alida's features, hence, provides a framework for implementing image analysis algorithms allowing for automatic documentation and automatic user interface generation, and includes the graphical programming editor Grappa for user-friendly design of more complex processing pipelines.<br />
</p><br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Visit and follow MiToBo also at...'''<br><br />
{|<br />
|style="text-align:center;width:10%"|[[file:Imagej-128.png|90px|link=http://imagej.net/MiToBo]]<br />
|style="text-align:center;width:10%"|[[file:Git.png|90px|link=https://github.com/mitobo-hub]]<br />
|style="text-align:center;width:10%"|[[file:mtbtw.png|320px|link=https://twitter.com/MiToBo_Hal]]<br />
|style="text-align:center;width:10%"|[[file:logo.png|90px|link=http://imagejdocu.tudor.lu/doku.php?id=plugin:collections:mitobo_-_a_microscope_image_analysis_toolbox:start]]<br />
|style="text-align:center;width:10%"|[[file:logo-blue.png|90px|link=https://omictools.com/microscope-image-analysis-toolbox-tool]]<br />
|-<br />
|style="text-align:center;width:10%"|[http://imagej.net/MiToBo ImageJ.net]<br />
|style="text-align:center;width:10%"|[https://github.com/mitobo-hub GitHub]<br />
|style="text-align:center;width:10%"|[https://twitter.com/MiToBo_Hal Twitter]<br />
|style="text-align:center;width:10%"|[http://imagejdocu.tudor.lu/doku.php?id=plugin:collections:mitobo_-_a_microscope_image_analysis_toolbox:start ImageJ Docu Wiki]<br />
|style="text-align:center;width:10%"|[https://omictools.com/microscope-image-analysis-toolbox-tool OMIC Tools]<br />
|}<br />
</div><br />
</div><br />
|<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Latest News'''<br><br />
* 05/2020: MiToBo 2.0 has been released.<br> From now on the online help system relies on operator class annotations, and the release includes a [https://mitobo.informatik.uni-halle.de/index.php/Applications/PaCeQuantToolset PaCeQuant] update with new shape features and improvements for supplemental tools like the [https://mitobo.informatik.uni-halle.de/index.php/Applications/FeatureColorMapper FeatureColorMapper] and the [https://mitobo.informatik.uni-halle.de/index.php/Operators/Tools/Interactive/LabelImageEditor LabelImageEditor].<br />
* 07/2019: MiToBo 1.8.15 has been released fixing several issues with handling images in MiToBo.<br />
* 02/2019: MiToBo 1.8.14 has been released.<br />
<br />
The news archive can be found [[News Archive | here]].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''How to get MiToBo?'''<br><br />
* ImageJ-Users:<br> download the [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/1.8.7.1/mitobo-plugins-1.8.7.1-bin.zip MiToBo-Plugins package] and follow the installation instructions to be found [[Installation | here]]. <br />
* Fiji-Users:<br> simply select MiToBo's update site [http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo] in FijiIs list of update sites in your installation<br />
* use in general:<br> you can download MiToBo and the MiToBo plugins package [[Downloads | here]]. <br/> <br />
<br />
You can find the API documentation for the current release [http://www.informatik.uni-halle.de/mitobo/api/index.html here].<br/> <br />
Furthermore MiToBo offers you a user and programmer guide which you can download [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual.pdf here].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Support, Bug reports & Feature requests'''<br />
{|style="background-color:#f8f8ff"<br />
|style="text-align:left;width:20%|[[File:forum-image-sc.png|border|64px|left|link=https://forum.image.sc/]]<br />
|style="text-align:left;width:60%|To get help on your questions about MiToBo tools, plugins and operators you can use the forum at [https://forum.image.sc/ image.sc] tagging your post with [https://forum.image.sc/tags/mitobo #mitobo].<br />
|-<br />
|style="text-align:left;width:20%|[[file:Git.png|64px|link=https://github.com/mitobo-hub]]<br />
|style="text-align:left;width:60%|Bug reports and feature requests can be submitted as issues on [https://github.com/mitobo-hub/mitobo/issues Github].<br />
|-<br />
|style="text-align:left;width:20%|[[file:Email.png|center|36px|link=]]<br />
|style="text-align:left;width:60%|Alternatively you can also write an email to [mailto:mitobo@informatik.uni-halle.de mitobo@informatik.uni-halle.de].<br />
|}<br />
Before reporting a new bug or requesting a new feature, please check if that bug has already been submitted in the forum or on Github.<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Licensing information'''<br><br />
MiToBo is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Gnu PGP Public Key'''<br><br />
Since version 1.8.7 MiToBo and MiToBo-Plugins releases are PGP signed. MiToBo's [https://pgp.mit.edu/pks/lookup?op=get&search=0x259F7DD171EFF7A9 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/.<br />
</div><br />
</div><br />
|}</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=News_Archive&diff=967News Archive2020-05-16T16:51:25Z<p>Moeller: </p>
<hr />
<div>=== December 2018 ===<br />
* MiToBo 1.8.13 has been released including the CytoskeletonAnalyzer2D.<br />
<br />
=== July 2018 ===<br />
* We have added a new page [[Tips_and_Tricks| Tips and Tricks]] here in the Wiki where you can find information on how to accomplish common tasks like manually labeling images.<br />
<br />
=== May 2018 ===<br />
* MiToBo 1.8.10 and MiToBo-Plugins 1.8.10 have been released shipping with new operators for biofilm analysis.<br />
* MiToBo 1.8.9 and MiToBo-Plugins 1.8.9 have been released mainly featuring an update of our MTBCellCounter tool.<br />
<br />
=== January 2018 ===<br />
* MiToBo 1.8.7 and MiToBo-Plugins 1.8.7.1 have been released mainly featuring improved support for commandline data I/O of operators.<br>Note that from now on MiToBo releases are PGP signed. MiToBo's [https://pgp.mit.edu/pks/lookup?op=get&search=0x259F7DD171EFF7A9 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/. <br />
<br />
=== September 2017 ===<br />
* MiToBo and MiToBo-Plugins 1.8.6 have been released! The new release includes [[Applications/PaCeQuant | PaCeQuant ]], our new tool for high-throughput quantification of pavement cell shape.<br />
<br />
=== March 2017 ===<br />
* MiToBo 1.8.5 and MiToBo-Plugins 1.8.4 have been released.<br />
<br />
=== December 2016 ===<br />
* MiToBo 1.8.4 and MiToBo-Plugins 1.8.3 have been released.<br> Also MiToBo's update site in Fiji now offers version 1.8.3.<br> Note that this requires the Java-8 update site to be activated as well.<br />
<br />
=== November 2016 ===<br />
* MiToBo 1.8.3 has been released.<br />
<br />
=== May 2016 ===<br />
* MiToBo 1.8.2 has been released.<br />
* A new article about MiToBo entitled '''''MiToBo - a toolbox for image processing and analysis''''' has just been published in the ''Journal of Open Research Software'', 4:e17, DOI:[http://dx.doi.org/10.5334/jors.103]. <br />
<br />
=== March 2016 ===<br />
* MiToBo 1.8 has been released. From now on MiToBo builds upon Java 1.8.<br />
<br />
=== September 2015 ===<br />
* MiToBo 1.7 has been released. The new version mainly fixes some bugs in the GUI. MiToBo 1.7 is available via [http://fiji.sc/Fiji Fiji], from our Maven server [https://moon.informatik.uni-halle.de/archiva/#browse/de.unihalle.informatik.MiToBo 'moon'] and on [https://zenodo.org/record/31364 Zenodo].<br />
<br />
=== June 2015 ===<br />
* MiToBo is now available via a Fiji update site: [http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo].<br> To enable the site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation]. <br />
<br />
* Version 1.5 of MiToBo has been released<br/> This release ships with the new [[Applications/MTBCellCounter | MTB Cell Counter]] plugin for semi-automatic segmentation and annotation of cell images. Details about the plugin (derived from the [http://fiji.sc/Cell_Counter CellCounter plugin] written by Kurt de Vos) can be found on the [[Applications/MTBCellCounter | MTB Cell Counter wikipage]].<br />
<br />
=== March 2015 ===<br />
* Version 1.4.3 of MiToBo has been released <br/> The most important new feature is support for parameter callbacks. Based upon Alida in version 2.5 and its support for callbacks it is now possible to update the values of operator parameters depending on changes of other parameters. In addition, callbacks enable dynamic changes of the set of parameters an operator owns and dynamic re-configuration of the graphical interfaces, respectively.<br />
<br />
=== January 2015 ===<br />
* Version 1.4.2 of MiToBo has been released<br />
<br />
=== December 2014 ===<br />
* Version 1.4.1 of MiToBo has been released <br/> MiToBo and its base Alida will be presented at the OGRW 2014, which is the 9th Open German-Russian Workshop on Pattern Recognition and Image Understanding. The workshop is taking place from 1st to 5th December in Koblenz/Germany. The title of our contribution is '''''Design and Implementation of the Alida Framework to Ease the Development of Image Analysis Algorithms.'''''<br />
<br />
=== July 2014 ===<br />
* Version 1.4 of MiToBo has been released <br/> The new version ships with new tools for the quantification of actin structures in microscopy images of cells, the ''[[Applications/ActinAnalyzer2D | ActinAnalyzer2D]]'', and a new operator for detecting Xylems in images of cross sections of wood.<br />
<br />
=== January 2014 ===<br />
* Version 1.3 of MiToBo has been released <br/> The project management of MiToBo switched to Maven, from now on you can download MiToBo releases from our [https://moon.informatik.uni-halle.de/archiva/browse/de.unihalle.informatik.MiToBo Maven server].<br> The new release ships with a new version of the ''[[Applications/NeuronAnalyzer2D | Neuron Analyzer 2D]]'' and includes the first release of the ''CellMigrationAnalyzer'',<br> a tool for cell tracking and migration analysis. In addition, in the MiToBo core several bugs were fixed, an illumination correction and a<br> top-hat based contrast enhancement were added.<br />
<br />
=== May 2013 ===<br />
* Version 1.2 of MiToBo has been released. <br/><br />
MiToBo now includes Alida 2.2.1 which comes with a new mechanism to save and load operator configurations based on XML Beans.<br><br />
Also Grappa has undergone some changes to improve usability, e.g. it now supports key shortcuts for the most important actions.<br />
<br />
=== March 2013 ===<br />
* Version 1.1 of MiToBo has been released. <br/><br />
MiToBo has undergone several internal enhancements mainly dedicated to the stability and usability of the core and its user interfaces.<br><br />
In addition, MiToBo now includes the ''Neuron Analyzer'' which is an application for the analysis of 2D images of neuronal cells.<br><br />
The analyzer is capable of extracting complete regions of neuronal cells (not only traces) and allows for extraction of protein <br />
concentrations along the neurites.<br />
<br />
=== October 2012 ===<br />
* Version 1.0.5 of MiToBo has been released. <br/><br />
Most important new feature is the graphical programming editor "Grappa" which is released in this new MiToBo version!<br><br />
The editor, although still in an early state, already provides a solid fundament for designing image analysis workflows in a graphical manner without need for programming.<br><br />
Grappa is available as plugin for ImageJ. Note that the editor will be presented in a talk at the '''ImageJ User & Developer Conference 2012'''.<br><br />
Besided the new editor other changes have mainly been done under the hood, e.g., online consistency checks within the graphical user interfaces have been integrated.<br />
* Updated version of Chipory available for download.<br />
<br />
=== August 2012 ===<br />
Some of the MiToBo developers will join the '''ImageJ User & Developer Conference 2012''' to be held at the end of October in Mondorf-les-Bains, Luxembourg.<br/><br />
In particular, two plugins for ImageJ implemented in MiToBo will be presented and demonstrated in posters:<br />
<br />
* B. Möller and D. Misiak, "SnakeOptimizer - Object Segmentation with Parametric Active Contours in ImageJ"<br />
* M. Glaß, B. Möller and S. Posch, "Scratch Assay Analysis in ImageJ"<br />
<br />
We are looking forward to meet you in Mondorf-les-Bains!<br />
<br />
=== July 2012 - Release 1.0.1 ===<br />
Version 1.0.1 of MiToBo has been released. <br/><br />
The new release ships with new quick start plugins for the SnakeOptimizer and ScratchAssayAnalyzer operators.<br/><br />
In addition a lot of bugs have been fixed in the core of Alida/MiToBo improving robustness and usability of the operators and their automatically generated user interfaces.<br />
<br />
Check the [[Downloads | download page]] for jars and sources.<br />
<br />
New release of chipory ready for download<br />
<br />
=== April 2012 ===<br />
Version 1.0.0 of MiToBo has been released. <br/><br />
Most interesting new features are:<br />
<br />
* automatic generation of graphical user interfaces for MiToBo operators<br />
* a flexible generic tool for running operators via command line<br />
* operators performing level set segmentation on images<br />
* support for saving/loading parameter settings from GUI<br />
<br />
Check the [[Downloads | download page]] for jars and sources.<br />
<br />
=== March 2012 - Preview of Release 1.0 ===<br />
Very soon a new version of MiToBo will be released! Amongst others one of the main features will be the automatic user interface generation for implemented operators.<br/> In particular, MiToBo will include mature (automatically generated!) graphical user interfaces for several of its operators, e.g. for the scratch assay analyzer or the snake segmentation. To get a first impression on these interfaces take a look at the beta release. This beta release does not contain MiToBo as a whole, but just selected operators. It is also not fully functional, but allows you to get a first impression of what MiToBo's next release is going to offer you, and especially how easy it will be even for non-experts to use MiToBo's functionality!<br />
<br />
* Download the beta release [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-preview-1.0-beta.jar here]!<br />
<br />
Just put the jar archive into your ImageJ plugins folder and make sure that it is also part of your classpath! In addition you will also need the following jars:<br />
<br />
* [http://rsbweb.nih.gov/ij/ ImageJ], Version 1.46g<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://www.loci.wisc.edu/software/bio-formats/ Loci Tools], Version 4.3.3<br />
* [http://math.nist.gov/javanumerics/jama/ Jama], Version 1.0.2 <br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
* [http://www.csie.ntu.edu.tw/~cjlin/libsvm/ LIBSVM], Version 3.1<br />
<br />
Finally some MiToBo internal jars are required (have a look at the download page for more details):<br />
<br />
* [http://www.informatik.uni-halle.de/mitobo/downloads/aldgraphml/aldgraphml.jar ALDGraphml]<br />
* [http://www.informatik.uni-halle.de/mitobo/downloads/mtbxml/mtbxml.jar mtbxml] <br />
* [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-Help.jar MiToBo-Help] <br />
* [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/sezpoz-1.9-alida.jar Alida-SezPoz].<br />
<br />
... and for the snakes you require C++ native libs:<br />
* 32-bit Linux [http://www.informatik.uni-halle.de/mitobo/downloads/native/libJNI_Cgal_Polygon2D-64-betaRelease.so lib], 64-bit Linux [http://www.informatik.uni-halle.de/mitobo/downloads/native/libJNI_Cgal_Polygon2D-64-betaRelease.so lib], 32-bit Windows [http://www.informatik.uni-halle.de/mitobo/downloads/native/libJNI_Cgal_Polygon2D-win32-betaRelease.dll lib]<br />
<br />
On running ImageJ you will find an entry "MiToBo->mitoboRunner->MiToBo Runner" in the plugins menu. By selecting the item the operator choser window will pop-up and allow you to browse and execute some of the MiToBo operators. We hope that you enjoy MiToBo! If you have questions or comments, please do not hesitate to contact us, we are pleased with any feedback to further improve MiToBo!<br />
<br />
=== September 2011 ===<br />
Version 0.9.6 of MiToBo has been released. <br/><br />
It will be presented at the Workshop ''Microscopic Image Analysis with Applications in Biology''<br />
in Heidelberg, Germany, September 2, 2011<br><br />
Most interesting new features are:<br />
<br />
* more user-friendly I/O interfaces<br />
* MiCA, the 2D microscope cell image analyzer<br />
* several bugfixes and internal enhancements<br />
<br />
Check the [[Downloads | download page]] for jars and sources.<br />
<br />
=== June 2011 ===<br />
Version 0.9.5 of MiToBo has just been released! <br/><br />
Most interesting new features are:<br />
<br />
* scratch assay analysis with levelsets<br />
* enhanced image I/O<br />
* easy operator development with annotations<br />
<br />
=== October 2010 ===<br />
The first version (v0.9) of MiToBo has been released.</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Applications/PaCeQuant&diff=966Applications/PaCeQuant2020-05-16T16:24:21Z<p>Moeller: /* PaCeQuant Plugin */</p>
<hr />
<div><br/><br />
<br/><br />
<br />
== PaCeQuant Plugin ==<br />
[[File:MiToBo_logo_PaCeQuant.png|border|150px|left|link=]]<br />
<br />
PaCeQuant is available since release version 1.8.6 of MiToBo.<br />
<br/><br />
<br />
In MiToBo version 2.0 released in May 2020 it got an update which added the largest empty circle as shape criterion to PaCeQuant's feature set.<br />
<br><br />
<br />
The PaCeQuant plugin as part of MiToBo as well as the R script for the visualization of result data are published under the terms of [https://www.gnu.org/licenses/gpl-3.0.en.html GNU General Public License v3.0].<br />
<br />
[[File:sampleImage-inverse.png|300px|right|link=]]<br />
[[File:sampleImage-colorResult-inverse.png|300px|right|link=]]<br />
[[File:sampleImage-features-white.png|300px|right|link=]]<br />
<br />
==== Name of Plugin/Operator ====<br />
<code><br />
de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant<br />
</code><br />
<br><br />
(available since MiToBo version 1.8.6)<br />
<br><br><br />
<br />
==== Related Publications ====<br />
<br />
When using PaCeQuant, please cite us:<br />
* Y. Poeschl, B. Möller, L. Müller, and K. Bürstenbinder,<br>'''''User-friendly assessment of pavement cell shape features with PaCeQuant: Novel functions and tools'''''.<br>In [https://www.sciencedirect.com/science/article/pii/S0091679X20300741?via%3Dihub Methods in Cell Biology], Academic Press, 2020.<br />
* B. Möller, Y. Poeschl, S. Klemm, and K. Bürstenbinder,<br>'''''Morphological Analysis of Leaf Epidermis Pavement Cells with PaCeQuant'''''.<br>In F. Cvrčková and V. Žárský, editors, [https://link.springer.com/protocol/10.1007%2F978-1-4939-9469-4_22 Plant Cell Morphogenesis: Methods and Protocols, chapter 22, pages 329-349], Springer New York, New York, NY, 2019.<br />
* B. Möller, Y. Poeschl, R. Plötner, and K. Bürstenbinder,<br> '''''PaCeQuant: A Tool for High-Throughput Quantification of Pavement Cell Shape Characteristics'''''.<br> [http://www.plantphysiol.org/content/early/2017/09/20/pp.17.00961 Plant Physiology, 175(1), September 2017].<br />
<br><br />
<br />
<br />
==== Main Features ==== <br />
* extraction of 28 characteristic shape features to quantify pavement cell shape<br />
* fully automatic segmentation of cell regions from input images<br />
* optional import of external/manual cell segmentation data<br />
* classification of lobes into type I (2-cell contact) and type II (3-cell contact)<br />
* additional R scripts for feature visualization<br />
<br />
<br />
==== Supplemental Tools ====<br />
The core PaCeQuant plugin has been supplemented by additional tools to ease feature visualization and analysis:<br />
* the [[Applications/FeatureColorMapper|FeatureColorMapper]] plugin for creating heatmap visualizations of cell features<br />
<p><p><br />
* the [[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]] for handy manual post-processing of segmentation results<br />
<p><p><br />
* the R package [[Applications/PaCeQuantAna|PaCeQuantAna]] for statistical analysis of feature data and creation of publication-ready plots of feature distributions and statistical analysis results<br><br><br />
<br />
<br />
==== Usage - Parameters ====<br />
To run PaCeQuant perform the following steps:<br />
* install MiToBo by following the instructions on the [[Installation]] page<br />
* run MiToBo and start the operator runner by selecting the menu item '''''PaCeQuant''''' from '''''Plugins -> MiToBo''''' <br />
This will bring up the operator window of PaCeQuant.<br />
<br />
===== Phases and Operation modes ===== <br />
PaCeQuant supports three different options for running listed below:<br />
* ''SEGMENTATION_AND_FEATURES:''<br> expects images as input, segments the images and extracts features<br />
* ''SEGMENTATION_ONLY:''<br> expects images as input, just segments the cell regions, no feature extraction<br />
* ''FEATURES_ONLY:''<br> works on binary or label images or ImageJ regions, extracts features for the given regions<br />
<br />
In addition PaCeQuant can be run in either of two modes:<br />
* ''INTERACTIVE:''<br> PaCeQuant processes the data provided directly within the graphical environment of ImageJ, i.e. reads regions from the ROI manager, and directly shows results<br />
* ''BATCH:''<br> PaCeQuant processes all files (images or ROI files) in a given folder and writes results to disk<br />
For batch mode the user can specify an input directory, in interactive mode PaCeQuant expects an input image or regions to be available in ImageJ.<br />
<br />
Depending on the chosen phase and operation mode the graphical user interface is dynamically re-configured to show only the options relevant for the selected options.<br />
<br />
===== Input Image/Directory =====<br />
Depending on the chosen phases and operation modes here you need to specify either input data already loaded in ImageJ/Fiji or a directory where PaCeQuant can find the data to process. In detail, you have to provide the following information for the various configurations:<br />
{|class="wikitable"<br />
|style="width:20%;"|Operation Mode <br />
| Phase(s) to Run <br />
| Input Data <br />
|-<br />
|''INTERACTIVE'' <br />
|''SEGMENTATION_ONLY'' <br />
|Gray-scale input image already opened in ImageJ/Fiji.<br />
|-<br />
| <br />
|''SEGMENTATION_AND_FEATURES'' <br />
|Gray-scale input image already opened in ImageJ/Fiji.<br />
|-<br />
| <br />
|''FEATURES_ONLY'' <br />
|Binary or label image already opened in ImageJ/Fiji, or ImageJ ROI set from ROI manager.<br />
|-<br />
|''BATCH'' <br />
|''SEGMENTATION_ONLY'' <br />
|Directory containing gray-scale input images.<br> First-level sub-folders are also processed.<br />
|-<br />
| <br />
|''SEGMENTATION_AND_FEATURES'' <br />
|Directory containing gray-scale input images.<br> First-level sub-folders are also processed.<br />
|-<br />
| <br />
|''FEATURES_ONLY'' <br />
|Directory containing either binary or label images to process, a collection of ImageJ ROI files (with ending '.roi'), or an archive of multiple ImageJ ROIs (with ending '.zip').<br />
|}<br />
<span style="color:#ff0000">'''Important notice''':</span><br> In ''BATCH'' mode PaCeQuant tries to analyze ''all'' image files present in the given folder or any of its direct sub-folders. In particular, PaCeQuant will also analyze data from a potential result folder of a previous run, if it is present in the given folder. To avoid problems resulting from analyzing wrong data you should ensure that the provided directory only contains native input images or segmentation data and no other image data not suitable for processing with PaCeQuant.<br />
<br />
===== Calibration =====<br />
As PaCeQuant measures lengths and areas from the given data it is important that the tool is properly calibrated, i.e. the physical size of a pixel is known. PaCeQuant supports two calibration modes:<br />
* AUTO:<br> here PaCeQuant seeks to extract calibration information from the given input data<br />
* MANUAL:<br> the user can enter calibration data, i.e. the physical size of a pixel and the units to use<br />
<span style="color:#ff0000">'''Important notice''':</span><br> Please note that in ImageJ ROI files no calibration data is stored. Thus, when using PaCeQuant to extract features from external segmentation data provided as ImageJ ROIs, you always need to manually provide calibration data. And this also holds when manually post-processing segmentation data extracted with PaCeQuant as all calibration data of the original images will get lost.<br />
<br />
===== Configuration of Segmentation Phase =====<br />
For detailed configuration of the algorithms applied during the segmentation phase the following parameters are available:<br />
{|class="wikitable"<br />
|style="width:20%;"|Name<br />
|Description<br />
|-<br />
|''Border Contrast''<br />
|Allows to select whether the boundaries of the cells are darker or brighter than the background.<br />
|-<br />
|''Heuristic for Gap Closing''<br />
|During segmentation sometimes small gaps in the boundaries remain which can be closed by PaCeQuant applying one of the following heuristics:<br />
* WATERSHED (recommended): calculates a distance image from the binary boundary image extracted so far and then applies a watershed transformation to find additional boundaries<br />
* NAIVE_HEURISTIC: just calculates the distance between two end-points and links them if the distance is below a threshold<br />
|-<br />
|''Unit for Size Thresholds''<br />
|Unit in which the size thresholds for filtering valid regions (see next two parameters) are specified, i.e. either PIXELS or MICRONS.<br />
|-<br />
|''Minimal Size of Cells''<br />
|Segmented cells being too small can automatically be excluded by specifying a minimal size for valid cells.<br />
|-<br />
|''Maximal Size of Cells''<br />
|Segmented cells being too large can also automatically be excluded by specifying a maximal size for valid cells.<br />
|}<br />
<br />
===== Configuration of Feature Extraction Phase =====<br />
{|class="wikitable"<br />
|style="width:20%;"|Name<br />
|Description<br />
|-<br />
|''Feature Extraction''<br />
|For changing various parameters used in feature extraction the [[Operators/Features/MorphologyAnalyzer2D | MorphologyAnalyzer2D]] operator of MiToBo is used and can be configured here. Note that changing parameters might hamper comparison of PaCeQuant results among different work groups or laboratories.<br />
|-<br />
|''Analyze lobe types?''<br />
|Activates the optional classification of individual lobes into type I (2-cell contact) or type II (3-cell contact) lobes.<br />
|}<br />
<br />
===== Additional Configuration Parameters =====<br />
{|class="wikitable"<br />
|style="width:20%;"|Name<br />
|Description<br />
|-<br />
|''Niblack threshold''<br />
|Allows to configure the binarization step in the segmentation phase, i.e., to increase or decrease the sensitivity of PaCeQuant for cell boundaries. The lower the threshold the more potential boundary candidate pixels will be extracted which might add to an improved segmentation in case of low contrast.<br />
|-<br />
|''Draw region IDs to output image?''<br />
|If the segmentation phase is run PaCeQuant outputs a label image showing segmented cell regions. If this option is activated region IDs are drawn to that image for easier interpretation. But note that this renders the image unsuitable for any further automatic analysis.<br />
|-<br />
|''Verbose''<br />
|If enabled additional log messages will be printed to console.<br />
|-<br />
|''Show/save additional results?''<br />
|If enabled an additional image stack with a collection of intermediate images will be generated. The images in this stack might help to get a deeper insight into PaCeQuant and might help to identify problems in case that the segmentation of input images fails.<br />
|-<br />
|''Show/save feature stack?''<br />
|If enabled a stack of images is generated where each image visualizes the values of a specific feature. For most images in this stack the feature values of individual cells are mapped to the intensity value of the corresponding cell (e.g., for features like area, solidity, width, length, branch count, etc.). <br />
|}<br />
<br />
==== Usage - Output data ====<br />
If PaCeQuant is run in ''INTERACTIVE'' mode all results are directly shown in ImageJ/Fiji, while in ''BATCH'' mode all result data is saved to a folder named ''results'' in the input folder. Which kinds of output data are resulting from running PaCeQuant depends on the selected phases:<br />
<br />
* list of result files from '''''SEGMENTATION''''' phase:<br />
** *-allRois.zip: ImageJ ROI archive containing all ROIs extracted from a single image<br />
** *_<number>.roi: ROI file containing only ROI with ID ''number''extracted from single image<br />
** *-grayscale-result.tif: gray-scale label image of extracted cell regions <br />
** *-color-result.tif: overlay of extracted cell regions (in pseudo-color) over input image<br />
** *-intermediate-result-stack.tif: (optional) stack of intermediate result images<br />
* list of result files from '''''FEATURES''''' phase:<br />
** *-allRois-table.txt: extracted feature values for all cells in a given image<br />
** *-allRois-grayscale-result.tif: gray-scale label image showing analyzed regions<br />
** *-intermediate-result-stack.tif: (optional) stack of intermediate result images<br />
** *-feature-stack.tif: (optional) stack of images visualizing feature values for cells<br />
** *-allRois-lobe-types.tif: (if lobe type classification is enabled) image visualizing the type of each lobe of all cells analyzed<br />
** *-allRois-cell-<number>-lobe-table.txt: (if lobe type classification is enabled) file containing features for lobes of cell with ID ''number'' <br />
<br />
Note that the asterisk in the above file names represents a single image, i.e. the set of files exists for each image present in the given folder.<br> All files with ending ''*.ald'' are internal MiToBo log files in XML format where, e.g., parameter settings are stored and which usually can be ignored or just preserved for later reference.<br />
<br />
==== Sample data ====<br />
Here we provide some sample data with which you can test your local PaCeQuant installation:<br />
<br />
* [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/sampleData/sampleData.zip sample data]<br />
* [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/sampleData/sampleDataResults.zip reference results extracted with PaCeQuant]<br />
<br />
To apply PaCeQuant to the test data simply unpack the data archive to a folder of your choice and set the input directory parameter of PaCeQuant to the sample data folder.<br />
<br />
The second archive contains result data extracted with PaCeQuant for validating if your local PaCeQuant installation yields correct results.<br><br><br />
<br />
<p><br />
<br />
== Complementary Tools: FeatureColorMapper, LabelImageEditor and PaCeQuantAna ==<br />
Over the time several complementary tools for PaCeQuant have been developed which ease manual correction of segmentation results and simplify analysis and exploration of extracted shape features:<br />
<br><br />
* the [[Applications/FeatureColorMapper|FeatureColorMapper]] plugin for creating heatmap visualizations of cell features<br />
<p><p><br />
* the [[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]] for handy manual post-processing of segmentation results<br />
<p><p><br />
* the R package [[Applications/PaCeQuantAna|PaCeQuantAna]] for statistical analysis of feature data and creation of publication-ready plots of feature distributions and statistical analysis results<br><br><br />
<br />
<br />
<p><br />
== Notes on manual or semi-automatic segmentation of cells ==<br />
PaCeQuant supports extracting features from externally provided segmentation data.<br> This can be helpful in cases where the original input images are not suitable for automatic segmentation by PaCeQuant,<br> e.g., due to a general low image quality or image acquisition techniques for which PaCeQuant is not optimized.<br />
<br />
The segmentation data can be provided in different formats:<br />
* an 8-bit binary image where all cell regions are labeled white (intensity = 255)<br />
* an 8-bit gray-scale image where each cell region is marked with an individual label (intensity larger than zero) and the background in black (intensity = 0)<br />
* ImageJ ROI files<br />
Note that when providing binary images neighboring regions must not touch each other. Optimally the margins between neighboring cell regions will have a width of at least 3 pixels.<br />
<br />
=== ImageJ ROI files ===<br />
For providing segmentation data in terms of ImageJ ROI files the easiest way to do this is to segment regions directly in ImageJ/Fiji.<br />
<br />
Use the [https://imagej.nih.gov/ij/docs/guide/146-19.html#sub:Polygon-Selection-Tool Polygon Section Tool] for segmenting individual cells, add each of the polygons to the <br />
[https://imagej.nih.gov/ij/docs/guide/146-30.html#sub:ROI-Manager... ROI manager], and finally save all ROIs to a file.<br />
<br />
In case that you aim to improve an initial segmentation result of PaCeQuant, open the ROI files generated by PaCeQuant during the segmentation phase with ImageJ's ROI manager and edit the ROIs. <br />
<br />
For editing polygon selections ImageJ offers a large variety of possibilities, e.g.:<br />
* single points can be removed (Ctrl + click)<br />
* new points can be added by splitting segments (Shift + click)<br />
* the complete region can be moved<br />
* the polygon can be interpolated, i.e. sub-sampled<br />
More information on the various options can be found in the ImageJ documentation:<br />
* [https://imagej.nih.gov/ij/docs/guide/146-19.html#sub:Polygon-Selection-Tool Polygon Section Tool]<br />
* [https://imagej.nih.gov/ij/docs/guide/146-30.html#sub:ROI-Manager... ROI manager]<br />
Probably of interest might also be the macro [http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Modify_Polygon_Selection 'Modifying Polygon Selections'].</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Applications/PaCeQuant&diff=965Applications/PaCeQuant2020-05-16T16:17:27Z<p>Moeller: /* Main features */</p>
<hr />
<div><br/><br />
<br/><br />
<br />
== PaCeQuant Plugin ==<br />
[[File:MiToBo_logo_PaCeQuant.png|border|150px|left|link=]]<br />
<br />
PaCeQuant is available since release version 1.8.6 of MiToBo.<br />
<br/><br />
<br />
In MiToBo version 2.0 released in May 2020 it got an update which added the largest empty circle as shape criterion to PaCeQuant's feature set.<br />
<br><br />
<br />
The PaCeQuant plugin as part of MiToBo as well as the R script for the visualization of result data are published under the terms of [https://www.gnu.org/licenses/gpl-3.0.en.html GNU General Public License v3.0].<br />
<br />
[[File:sampleImage-inverse.png|300px|right|link=]]<br />
[[File:sampleImage-colorResult-inverse.png|300px|right|link=]]<br />
[[File:sampleImage-features-white.png|300px|right|link=]]<br />
<br />
==== Name of Plugin/Operator ====<br />
<code><br />
de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant<br />
</code><br />
<br><br />
(available since MiToBo version 1.8.6)<br />
<br><br><br />
<br />
==== Related Publications ====<br />
<br />
When using PaCeQuant, please cite us:<br />
* Y. Poeschl, B. Möller, L. Müller, and K. Bürstenbinder,<br>'''''User-friendly assessment of pavement cell shape features with PaCeQuant: Novel functions and tools'''''.<br>In [https://www.sciencedirect.com/science/article/pii/S0091679X20300741?via%3Dihub Methods in Cell Biology], Academic Press, 2020.<br />
* B. Möller, Y. Poeschl, S. Klemm, and K. Bürstenbinder,<br>'''''Morphological Analysis of Leaf Epidermis Pavement Cells with PaCeQuant'''''.<br>In F. Cvrčková and V. Žárský, editors, [https://link.springer.com/protocol/10.1007%2F978-1-4939-9469-4_22 Plant Cell Morphogenesis: Methods and Protocols, chapter 22, pages 329-349], Springer New York, New York, NY, 2019.<br />
* B. Möller, Y. Poeschl, R. Plötner, and K. Bürstenbinder,<br> '''''PaCeQuant: A Tool for High-Throughput Quantification of Pavement Cell Shape Characteristics'''''.<br> [http://www.plantphysiol.org/content/early/2017/09/20/pp.17.00961 Plant Physiology, 175(1), September 2017].<br />
<br><br />
<br />
==== Main features ==== <br />
* extraction of 28 characteristic shape features to quantify pavement cell shape<br />
* fully automatic segmentation of cell regions from input images<br />
* optional import of external/manual cell segmentation data<br />
* classification of lobes into type I (2-cell contact) and type II (3-cell contact)<br />
* additional R scripts for feature visualization<br />
<br />
==== Usage - Parameters ====<br />
To run PaCeQuant perform the following steps:<br />
* install MiToBo by following the instructions on the [[Installation]] page<br />
* run MiToBo and start the operator runner by selecting the menu item '''''PaCeQuant''''' from '''''Plugins -> MiToBo''''' <br />
This will bring up the operator window of PaCeQuant.<br />
<br />
===== Phases and Operation modes ===== <br />
PaCeQuant supports three different options for running listed below:<br />
* ''SEGMENTATION_AND_FEATURES:''<br> expects images as input, segments the images and extracts features<br />
* ''SEGMENTATION_ONLY:''<br> expects images as input, just segments the cell regions, no feature extraction<br />
* ''FEATURES_ONLY:''<br> works on binary or label images or ImageJ regions, extracts features for the given regions<br />
<br />
In addition PaCeQuant can be run in either of two modes:<br />
* ''INTERACTIVE:''<br> PaCeQuant processes the data provided directly within the graphical environment of ImageJ, i.e. reads regions from the ROI manager, and directly shows results<br />
* ''BATCH:''<br> PaCeQuant processes all files (images or ROI files) in a given folder and writes results to disk<br />
For batch mode the user can specify an input directory, in interactive mode PaCeQuant expects an input image or regions to be available in ImageJ.<br />
<br />
Depending on the chosen phase and operation mode the graphical user interface is dynamically re-configured to show only the options relevant for the selected options.<br />
<br />
===== Input Image/Directory =====<br />
Depending on the chosen phases and operation modes here you need to specify either input data already loaded in ImageJ/Fiji or a directory where PaCeQuant can find the data to process. In detail, you have to provide the following information for the various configurations:<br />
{|class="wikitable"<br />
|style="width:20%;"|Operation Mode <br />
| Phase(s) to Run <br />
| Input Data <br />
|-<br />
|''INTERACTIVE'' <br />
|''SEGMENTATION_ONLY'' <br />
|Gray-scale input image already opened in ImageJ/Fiji.<br />
|-<br />
| <br />
|''SEGMENTATION_AND_FEATURES'' <br />
|Gray-scale input image already opened in ImageJ/Fiji.<br />
|-<br />
| <br />
|''FEATURES_ONLY'' <br />
|Binary or label image already opened in ImageJ/Fiji, or ImageJ ROI set from ROI manager.<br />
|-<br />
|''BATCH'' <br />
|''SEGMENTATION_ONLY'' <br />
|Directory containing gray-scale input images.<br> First-level sub-folders are also processed.<br />
|-<br />
| <br />
|''SEGMENTATION_AND_FEATURES'' <br />
|Directory containing gray-scale input images.<br> First-level sub-folders are also processed.<br />
|-<br />
| <br />
|''FEATURES_ONLY'' <br />
|Directory containing either binary or label images to process, a collection of ImageJ ROI files (with ending '.roi'), or an archive of multiple ImageJ ROIs (with ending '.zip').<br />
|}<br />
<span style="color:#ff0000">'''Important notice''':</span><br> In ''BATCH'' mode PaCeQuant tries to analyze ''all'' image files present in the given folder or any of its direct sub-folders. In particular, PaCeQuant will also analyze data from a potential result folder of a previous run, if it is present in the given folder. To avoid problems resulting from analyzing wrong data you should ensure that the provided directory only contains native input images or segmentation data and no other image data not suitable for processing with PaCeQuant.<br />
<br />
===== Calibration =====<br />
As PaCeQuant measures lengths and areas from the given data it is important that the tool is properly calibrated, i.e. the physical size of a pixel is known. PaCeQuant supports two calibration modes:<br />
* AUTO:<br> here PaCeQuant seeks to extract calibration information from the given input data<br />
* MANUAL:<br> the user can enter calibration data, i.e. the physical size of a pixel and the units to use<br />
<span style="color:#ff0000">'''Important notice''':</span><br> Please note that in ImageJ ROI files no calibration data is stored. Thus, when using PaCeQuant to extract features from external segmentation data provided as ImageJ ROIs, you always need to manually provide calibration data. And this also holds when manually post-processing segmentation data extracted with PaCeQuant as all calibration data of the original images will get lost.<br />
<br />
===== Configuration of Segmentation Phase =====<br />
For detailed configuration of the algorithms applied during the segmentation phase the following parameters are available:<br />
{|class="wikitable"<br />
|style="width:20%;"|Name<br />
|Description<br />
|-<br />
|''Border Contrast''<br />
|Allows to select whether the boundaries of the cells are darker or brighter than the background.<br />
|-<br />
|''Heuristic for Gap Closing''<br />
|During segmentation sometimes small gaps in the boundaries remain which can be closed by PaCeQuant applying one of the following heuristics:<br />
* WATERSHED (recommended): calculates a distance image from the binary boundary image extracted so far and then applies a watershed transformation to find additional boundaries<br />
* NAIVE_HEURISTIC: just calculates the distance between two end-points and links them if the distance is below a threshold<br />
|-<br />
|''Unit for Size Thresholds''<br />
|Unit in which the size thresholds for filtering valid regions (see next two parameters) are specified, i.e. either PIXELS or MICRONS.<br />
|-<br />
|''Minimal Size of Cells''<br />
|Segmented cells being too small can automatically be excluded by specifying a minimal size for valid cells.<br />
|-<br />
|''Maximal Size of Cells''<br />
|Segmented cells being too large can also automatically be excluded by specifying a maximal size for valid cells.<br />
|}<br />
<br />
===== Configuration of Feature Extraction Phase =====<br />
{|class="wikitable"<br />
|style="width:20%;"|Name<br />
|Description<br />
|-<br />
|''Feature Extraction''<br />
|For changing various parameters used in feature extraction the [[Operators/Features/MorphologyAnalyzer2D | MorphologyAnalyzer2D]] operator of MiToBo is used and can be configured here. Note that changing parameters might hamper comparison of PaCeQuant results among different work groups or laboratories.<br />
|-<br />
|''Analyze lobe types?''<br />
|Activates the optional classification of individual lobes into type I (2-cell contact) or type II (3-cell contact) lobes.<br />
|}<br />
<br />
===== Additional Configuration Parameters =====<br />
{|class="wikitable"<br />
|style="width:20%;"|Name<br />
|Description<br />
|-<br />
|''Niblack threshold''<br />
|Allows to configure the binarization step in the segmentation phase, i.e., to increase or decrease the sensitivity of PaCeQuant for cell boundaries. The lower the threshold the more potential boundary candidate pixels will be extracted which might add to an improved segmentation in case of low contrast.<br />
|-<br />
|''Draw region IDs to output image?''<br />
|If the segmentation phase is run PaCeQuant outputs a label image showing segmented cell regions. If this option is activated region IDs are drawn to that image for easier interpretation. But note that this renders the image unsuitable for any further automatic analysis.<br />
|-<br />
|''Verbose''<br />
|If enabled additional log messages will be printed to console.<br />
|-<br />
|''Show/save additional results?''<br />
|If enabled an additional image stack with a collection of intermediate images will be generated. The images in this stack might help to get a deeper insight into PaCeQuant and might help to identify problems in case that the segmentation of input images fails.<br />
|-<br />
|''Show/save feature stack?''<br />
|If enabled a stack of images is generated where each image visualizes the values of a specific feature. For most images in this stack the feature values of individual cells are mapped to the intensity value of the corresponding cell (e.g., for features like area, solidity, width, length, branch count, etc.). <br />
|}<br />
<br />
==== Usage - Output data ====<br />
If PaCeQuant is run in ''INTERACTIVE'' mode all results are directly shown in ImageJ/Fiji, while in ''BATCH'' mode all result data is saved to a folder named ''results'' in the input folder. Which kinds of output data are resulting from running PaCeQuant depends on the selected phases:<br />
<br />
* list of result files from '''''SEGMENTATION''''' phase:<br />
** *-allRois.zip: ImageJ ROI archive containing all ROIs extracted from a single image<br />
** *_<number>.roi: ROI file containing only ROI with ID ''number''extracted from single image<br />
** *-grayscale-result.tif: gray-scale label image of extracted cell regions <br />
** *-color-result.tif: overlay of extracted cell regions (in pseudo-color) over input image<br />
** *-intermediate-result-stack.tif: (optional) stack of intermediate result images<br />
* list of result files from '''''FEATURES''''' phase:<br />
** *-allRois-table.txt: extracted feature values for all cells in a given image<br />
** *-allRois-grayscale-result.tif: gray-scale label image showing analyzed regions<br />
** *-intermediate-result-stack.tif: (optional) stack of intermediate result images<br />
** *-feature-stack.tif: (optional) stack of images visualizing feature values for cells<br />
** *-allRois-lobe-types.tif: (if lobe type classification is enabled) image visualizing the type of each lobe of all cells analyzed<br />
** *-allRois-cell-<number>-lobe-table.txt: (if lobe type classification is enabled) file containing features for lobes of cell with ID ''number'' <br />
<br />
Note that the asterisk in the above file names represents a single image, i.e. the set of files exists for each image present in the given folder.<br> All files with ending ''*.ald'' are internal MiToBo log files in XML format where, e.g., parameter settings are stored and which usually can be ignored or just preserved for later reference.<br />
<br />
==== Sample data ====<br />
Here we provide some sample data with which you can test your local PaCeQuant installation:<br />
<br />
* [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/sampleData/sampleData.zip sample data]<br />
* [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/sampleData/sampleDataResults.zip reference results extracted with PaCeQuant]<br />
<br />
To apply PaCeQuant to the test data simply unpack the data archive to a folder of your choice and set the input directory parameter of PaCeQuant to the sample data folder.<br />
<br />
The second archive contains result data extracted with PaCeQuant for validating if your local PaCeQuant installation yields correct results.<br><br><br />
<br />
<p><br />
== Complementary Tools: FeatureColorMapper, LabelImageEditor and PaCeQuantAna ==<br />
Over the time several complementary tools for PaCeQuant have been developed which ease manual correction of segmentation results and simplify analysis and exploration of extracted shape features:<br />
<br><br />
* the [[Applications/FeatureColorMapper|FeatureColorMapper]] plugin for creating heatmap visualizations of cell features<br />
<p><p><br />
* the [[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]] for handy manual post-processing of segmentation results<br />
<p><p><br />
* the R package [[Applications/PaCeQuantAna|PaCeQuantAna]] for statistical analysis of feature data and creation of publication-ready plots of feature distributions and statistical analysis results<br><br><br />
<br />
<br />
<p><br />
== Notes on manual or semi-automatic segmentation of cells ==<br />
PaCeQuant supports extracting features from externally provided segmentation data.<br> This can be helpful in cases where the original input images are not suitable for automatic segmentation by PaCeQuant,<br> e.g., due to a general low image quality or image acquisition techniques for which PaCeQuant is not optimized.<br />
<br />
The segmentation data can be provided in different formats:<br />
* an 8-bit binary image where all cell regions are labeled white (intensity = 255)<br />
* an 8-bit gray-scale image where each cell region is marked with an individual label (intensity larger than zero) and the background in black (intensity = 0)<br />
* ImageJ ROI files<br />
Note that when providing binary images neighboring regions must not touch each other. Optimally the margins between neighboring cell regions will have a width of at least 3 pixels.<br />
<br />
=== ImageJ ROI files ===<br />
For providing segmentation data in terms of ImageJ ROI files the easiest way to do this is to segment regions directly in ImageJ/Fiji.<br />
<br />
Use the [https://imagej.nih.gov/ij/docs/guide/146-19.html#sub:Polygon-Selection-Tool Polygon Section Tool] for segmenting individual cells, add each of the polygons to the <br />
[https://imagej.nih.gov/ij/docs/guide/146-30.html#sub:ROI-Manager... ROI manager], and finally save all ROIs to a file.<br />
<br />
In case that you aim to improve an initial segmentation result of PaCeQuant, open the ROI files generated by PaCeQuant during the segmentation phase with ImageJ's ROI manager and edit the ROIs. <br />
<br />
For editing polygon selections ImageJ offers a large variety of possibilities, e.g.:<br />
* single points can be removed (Ctrl + click)<br />
* new points can be added by splitting segments (Shift + click)<br />
* the complete region can be moved<br />
* the polygon can be interpolated, i.e. sub-sampled<br />
More information on the various options can be found in the ImageJ documentation:<br />
* [https://imagej.nih.gov/ij/docs/guide/146-19.html#sub:Polygon-Selection-Tool Polygon Section Tool]<br />
* [https://imagej.nih.gov/ij/docs/guide/146-30.html#sub:ROI-Manager... ROI manager]<br />
Probably of interest might also be the macro [http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Modify_Polygon_Selection 'Modifying Polygon Selections'].</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Applications/PaCeQuant&diff=964Applications/PaCeQuant2020-05-16T16:16:58Z<p>Moeller: </p>
<hr />
<div><br/><br />
<br/><br />
<br />
== PaCeQuant Plugin ==<br />
[[File:MiToBo_logo_PaCeQuant.png|border|150px|left|link=]]<br />
<br />
PaCeQuant is available since release version 1.8.6 of MiToBo.<br />
<br/><br />
<br />
In MiToBo version 2.0 released in May 2020 it got an update which added the largest empty circle as shape criterion to PaCeQuant's feature set.<br />
<br><br />
<br />
The PaCeQuant plugin as part of MiToBo as well as the R script for the visualization of result data are published under the terms of [https://www.gnu.org/licenses/gpl-3.0.en.html GNU General Public License v3.0].<br />
<br />
[[File:sampleImage-inverse.png|300px|right|link=]]<br />
[[File:sampleImage-colorResult-inverse.png|300px|right|link=]]<br />
[[File:sampleImage-features-white.png|300px|right|link=]]<br />
<br />
==== Name of Plugin/Operator ====<br />
<code><br />
de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant<br />
</code><br />
<br><br />
(available since MiToBo version 1.8.6)<br />
<br><br><br />
<br />
==== Related Publications ====<br />
<br />
When using PaCeQuant, please cite us:<br />
* Y. Poeschl, B. Möller, L. Müller, and K. Bürstenbinder,<br>'''''User-friendly assessment of pavement cell shape features with PaCeQuant: Novel functions and tools'''''.<br>In [https://www.sciencedirect.com/science/article/pii/S0091679X20300741?via%3Dihub Methods in Cell Biology], Academic Press, 2020.<br />
* B. Möller, Y. Poeschl, S. Klemm, and K. Bürstenbinder,<br>'''''Morphological Analysis of Leaf Epidermis Pavement Cells with PaCeQuant'''''.<br>In F. Cvrčková and V. Žárský, editors, [https://link.springer.com/protocol/10.1007%2F978-1-4939-9469-4_22 Plant Cell Morphogenesis: Methods and Protocols, chapter 22, pages 329-349], Springer New York, New York, NY, 2019.<br />
* B. Möller, Y. Poeschl, R. Plötner, and K. Bürstenbinder,<br> '''''PaCeQuant: A Tool for High-Throughput Quantification of Pavement Cell Shape Characteristics'''''.<br> [http://www.plantphysiol.org/content/early/2017/09/20/pp.17.00961 Plant Physiology, 175(1), September 2017].<br />
<br><br />
<br />
==== Main features ==== <br />
* extraction of 27 characteristic shape features to quantify pavement cell shape<br />
* fully automatic segmentation of cell regions from input images<br />
* optional import of external/manual cell segmentation data<br />
* classification of lobes into type I (2-cell contact) and type II (3-cell contact)<br />
* additional R scripts for feature visualization<br />
<br />
==== Usage - Parameters ====<br />
To run PaCeQuant perform the following steps:<br />
* install MiToBo by following the instructions on the [[Installation]] page<br />
* run MiToBo and start the operator runner by selecting the menu item '''''PaCeQuant''''' from '''''Plugins -> MiToBo''''' <br />
This will bring up the operator window of PaCeQuant.<br />
<br />
===== Phases and Operation modes ===== <br />
PaCeQuant supports three different options for running listed below:<br />
* ''SEGMENTATION_AND_FEATURES:''<br> expects images as input, segments the images and extracts features<br />
* ''SEGMENTATION_ONLY:''<br> expects images as input, just segments the cell regions, no feature extraction<br />
* ''FEATURES_ONLY:''<br> works on binary or label images or ImageJ regions, extracts features for the given regions<br />
<br />
In addition PaCeQuant can be run in either of two modes:<br />
* ''INTERACTIVE:''<br> PaCeQuant processes the data provided directly within the graphical environment of ImageJ, i.e. reads regions from the ROI manager, and directly shows results<br />
* ''BATCH:''<br> PaCeQuant processes all files (images or ROI files) in a given folder and writes results to disk<br />
For batch mode the user can specify an input directory, in interactive mode PaCeQuant expects an input image or regions to be available in ImageJ.<br />
<br />
Depending on the chosen phase and operation mode the graphical user interface is dynamically re-configured to show only the options relevant for the selected options.<br />
<br />
===== Input Image/Directory =====<br />
Depending on the chosen phases and operation modes here you need to specify either input data already loaded in ImageJ/Fiji or a directory where PaCeQuant can find the data to process. In detail, you have to provide the following information for the various configurations:<br />
{|class="wikitable"<br />
|style="width:20%;"|Operation Mode <br />
| Phase(s) to Run <br />
| Input Data <br />
|-<br />
|''INTERACTIVE'' <br />
|''SEGMENTATION_ONLY'' <br />
|Gray-scale input image already opened in ImageJ/Fiji.<br />
|-<br />
| <br />
|''SEGMENTATION_AND_FEATURES'' <br />
|Gray-scale input image already opened in ImageJ/Fiji.<br />
|-<br />
| <br />
|''FEATURES_ONLY'' <br />
|Binary or label image already opened in ImageJ/Fiji, or ImageJ ROI set from ROI manager.<br />
|-<br />
|''BATCH'' <br />
|''SEGMENTATION_ONLY'' <br />
|Directory containing gray-scale input images.<br> First-level sub-folders are also processed.<br />
|-<br />
| <br />
|''SEGMENTATION_AND_FEATURES'' <br />
|Directory containing gray-scale input images.<br> First-level sub-folders are also processed.<br />
|-<br />
| <br />
|''FEATURES_ONLY'' <br />
|Directory containing either binary or label images to process, a collection of ImageJ ROI files (with ending '.roi'), or an archive of multiple ImageJ ROIs (with ending '.zip').<br />
|}<br />
<span style="color:#ff0000">'''Important notice''':</span><br> In ''BATCH'' mode PaCeQuant tries to analyze ''all'' image files present in the given folder or any of its direct sub-folders. In particular, PaCeQuant will also analyze data from a potential result folder of a previous run, if it is present in the given folder. To avoid problems resulting from analyzing wrong data you should ensure that the provided directory only contains native input images or segmentation data and no other image data not suitable for processing with PaCeQuant.<br />
<br />
===== Calibration =====<br />
As PaCeQuant measures lengths and areas from the given data it is important that the tool is properly calibrated, i.e. the physical size of a pixel is known. PaCeQuant supports two calibration modes:<br />
* AUTO:<br> here PaCeQuant seeks to extract calibration information from the given input data<br />
* MANUAL:<br> the user can enter calibration data, i.e. the physical size of a pixel and the units to use<br />
<span style="color:#ff0000">'''Important notice''':</span><br> Please note that in ImageJ ROI files no calibration data is stored. Thus, when using PaCeQuant to extract features from external segmentation data provided as ImageJ ROIs, you always need to manually provide calibration data. And this also holds when manually post-processing segmentation data extracted with PaCeQuant as all calibration data of the original images will get lost.<br />
<br />
===== Configuration of Segmentation Phase =====<br />
For detailed configuration of the algorithms applied during the segmentation phase the following parameters are available:<br />
{|class="wikitable"<br />
|style="width:20%;"|Name<br />
|Description<br />
|-<br />
|''Border Contrast''<br />
|Allows to select whether the boundaries of the cells are darker or brighter than the background.<br />
|-<br />
|''Heuristic for Gap Closing''<br />
|During segmentation sometimes small gaps in the boundaries remain which can be closed by PaCeQuant applying one of the following heuristics:<br />
* WATERSHED (recommended): calculates a distance image from the binary boundary image extracted so far and then applies a watershed transformation to find additional boundaries<br />
* NAIVE_HEURISTIC: just calculates the distance between two end-points and links them if the distance is below a threshold<br />
|-<br />
|''Unit for Size Thresholds''<br />
|Unit in which the size thresholds for filtering valid regions (see next two parameters) are specified, i.e. either PIXELS or MICRONS.<br />
|-<br />
|''Minimal Size of Cells''<br />
|Segmented cells being too small can automatically be excluded by specifying a minimal size for valid cells.<br />
|-<br />
|''Maximal Size of Cells''<br />
|Segmented cells being too large can also automatically be excluded by specifying a maximal size for valid cells.<br />
|}<br />
<br />
===== Configuration of Feature Extraction Phase =====<br />
{|class="wikitable"<br />
|style="width:20%;"|Name<br />
|Description<br />
|-<br />
|''Feature Extraction''<br />
|For changing various parameters used in feature extraction the [[Operators/Features/MorphologyAnalyzer2D | MorphologyAnalyzer2D]] operator of MiToBo is used and can be configured here. Note that changing parameters might hamper comparison of PaCeQuant results among different work groups or laboratories.<br />
|-<br />
|''Analyze lobe types?''<br />
|Activates the optional classification of individual lobes into type I (2-cell contact) or type II (3-cell contact) lobes.<br />
|}<br />
<br />
===== Additional Configuration Parameters =====<br />
{|class="wikitable"<br />
|style="width:20%;"|Name<br />
|Description<br />
|-<br />
|''Niblack threshold''<br />
|Allows to configure the binarization step in the segmentation phase, i.e., to increase or decrease the sensitivity of PaCeQuant for cell boundaries. The lower the threshold the more potential boundary candidate pixels will be extracted which might add to an improved segmentation in case of low contrast.<br />
|-<br />
|''Draw region IDs to output image?''<br />
|If the segmentation phase is run PaCeQuant outputs a label image showing segmented cell regions. If this option is activated region IDs are drawn to that image for easier interpretation. But note that this renders the image unsuitable for any further automatic analysis.<br />
|-<br />
|''Verbose''<br />
|If enabled additional log messages will be printed to console.<br />
|-<br />
|''Show/save additional results?''<br />
|If enabled an additional image stack with a collection of intermediate images will be generated. The images in this stack might help to get a deeper insight into PaCeQuant and might help to identify problems in case that the segmentation of input images fails.<br />
|-<br />
|''Show/save feature stack?''<br />
|If enabled a stack of images is generated where each image visualizes the values of a specific feature. For most images in this stack the feature values of individual cells are mapped to the intensity value of the corresponding cell (e.g., for features like area, solidity, width, length, branch count, etc.). <br />
|}<br />
<br />
==== Usage - Output data ====<br />
If PaCeQuant is run in ''INTERACTIVE'' mode all results are directly shown in ImageJ/Fiji, while in ''BATCH'' mode all result data is saved to a folder named ''results'' in the input folder. Which kinds of output data are resulting from running PaCeQuant depends on the selected phases:<br />
<br />
* list of result files from '''''SEGMENTATION''''' phase:<br />
** *-allRois.zip: ImageJ ROI archive containing all ROIs extracted from a single image<br />
** *_<number>.roi: ROI file containing only ROI with ID ''number''extracted from single image<br />
** *-grayscale-result.tif: gray-scale label image of extracted cell regions <br />
** *-color-result.tif: overlay of extracted cell regions (in pseudo-color) over input image<br />
** *-intermediate-result-stack.tif: (optional) stack of intermediate result images<br />
* list of result files from '''''FEATURES''''' phase:<br />
** *-allRois-table.txt: extracted feature values for all cells in a given image<br />
** *-allRois-grayscale-result.tif: gray-scale label image showing analyzed regions<br />
** *-intermediate-result-stack.tif: (optional) stack of intermediate result images<br />
** *-feature-stack.tif: (optional) stack of images visualizing feature values for cells<br />
** *-allRois-lobe-types.tif: (if lobe type classification is enabled) image visualizing the type of each lobe of all cells analyzed<br />
** *-allRois-cell-<number>-lobe-table.txt: (if lobe type classification is enabled) file containing features for lobes of cell with ID ''number'' <br />
<br />
Note that the asterisk in the above file names represents a single image, i.e. the set of files exists for each image present in the given folder.<br> All files with ending ''*.ald'' are internal MiToBo log files in XML format where, e.g., parameter settings are stored and which usually can be ignored or just preserved for later reference.<br />
<br />
==== Sample data ====<br />
Here we provide some sample data with which you can test your local PaCeQuant installation:<br />
<br />
* [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/sampleData/sampleData.zip sample data]<br />
* [http://mitobo.informatik.uni-halle.de/downloads/paceQuant/sampleData/sampleDataResults.zip reference results extracted with PaCeQuant]<br />
<br />
To apply PaCeQuant to the test data simply unpack the data archive to a folder of your choice and set the input directory parameter of PaCeQuant to the sample data folder.<br />
<br />
The second archive contains result data extracted with PaCeQuant for validating if your local PaCeQuant installation yields correct results.<br><br><br />
<br />
<p><br />
== Complementary Tools: FeatureColorMapper, LabelImageEditor and PaCeQuantAna ==<br />
Over the time several complementary tools for PaCeQuant have been developed which ease manual correction of segmentation results and simplify analysis and exploration of extracted shape features:<br />
<br><br />
* the [[Applications/FeatureColorMapper|FeatureColorMapper]] plugin for creating heatmap visualizations of cell features<br />
<p><p><br />
* the [[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]] for handy manual post-processing of segmentation results<br />
<p><p><br />
* the R package [[Applications/PaCeQuantAna|PaCeQuantAna]] for statistical analysis of feature data and creation of publication-ready plots of feature distributions and statistical analysis results<br><br><br />
<br />
<br />
<p><br />
== Notes on manual or semi-automatic segmentation of cells ==<br />
PaCeQuant supports extracting features from externally provided segmentation data.<br> This can be helpful in cases where the original input images are not suitable for automatic segmentation by PaCeQuant,<br> e.g., due to a general low image quality or image acquisition techniques for which PaCeQuant is not optimized.<br />
<br />
The segmentation data can be provided in different formats:<br />
* an 8-bit binary image where all cell regions are labeled white (intensity = 255)<br />
* an 8-bit gray-scale image where each cell region is marked with an individual label (intensity larger than zero) and the background in black (intensity = 0)<br />
* ImageJ ROI files<br />
Note that when providing binary images neighboring regions must not touch each other. Optimally the margins between neighboring cell regions will have a width of at least 3 pixels.<br />
<br />
=== ImageJ ROI files ===<br />
For providing segmentation data in terms of ImageJ ROI files the easiest way to do this is to segment regions directly in ImageJ/Fiji.<br />
<br />
Use the [https://imagej.nih.gov/ij/docs/guide/146-19.html#sub:Polygon-Selection-Tool Polygon Section Tool] for segmenting individual cells, add each of the polygons to the <br />
[https://imagej.nih.gov/ij/docs/guide/146-30.html#sub:ROI-Manager... ROI manager], and finally save all ROIs to a file.<br />
<br />
In case that you aim to improve an initial segmentation result of PaCeQuant, open the ROI files generated by PaCeQuant during the segmentation phase with ImageJ's ROI manager and edit the ROIs. <br />
<br />
For editing polygon selections ImageJ offers a large variety of possibilities, e.g.:<br />
* single points can be removed (Ctrl + click)<br />
* new points can be added by splitting segments (Shift + click)<br />
* the complete region can be moved<br />
* the polygon can be interpolated, i.e. sub-sampled<br />
More information on the various options can be found in the ImageJ documentation:<br />
* [https://imagej.nih.gov/ij/docs/guide/146-19.html#sub:Polygon-Selection-Tool Polygon Section Tool]<br />
* [https://imagej.nih.gov/ij/docs/guide/146-30.html#sub:ROI-Manager... ROI manager]<br />
Probably of interest might also be the macro [http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Modify_Polygon_Selection 'Modifying Polygon Selections'].</div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Applications/PaCeQuantToolset&diff=963Applications/PaCeQuantToolset2020-05-16T16:13:35Z<p>Moeller: /* The PaCeQuant Plugin and Corresponding Tools */</p>
<hr />
<div>== The PaCeQuant Plugin and Corresponding Tools ==<br />
[[File:MiToBo_logo_PaCeQuant.png|border|150px|left|link=]]<br />
<br />
The [[Applications/PaCeQuant|PaCeQuant plugin]] for fully automatic cell segmentation and shape feature extraction is part of MiToBo since release 1.8.6. <br />
<br><br />
In MiToBo version 2.0 released in May 2020 it got an update which added the largest empty circle as shape criterion to PaCeQuant's feature set.<br />
<br><br />
<br />
More details about the plugin and its usage can be found on the [[Applications/PaCeQuant|PaCeQuant's website]].<br />
<br />
<br><br />
Main publication:<br />
* B. Möller, Y. Poeschl, R. Plötner, and K. Bürstenbinder,<br> '''''PaCeQuant: A Tool for High-Throughput Quantification of Pavement Cell Shape Characteristics'''''.<br> [http://www.plantphysiol.org/content/early/2017/09/20/pp.17.00961 Plant Physiology, 175(1), September 2017].<br />
<br />
<br><br />
<br><br />
<br />
Over the time the main plugin has been supplemented with several complementary tools to ease cell shape analysis and feature visualization:<br />
<br><br />
* the [[Applications/FeatureColorMapper|FeatureColorMapper]] plugin for creating heatmap visualizations of cell features<br />
<p><p><br />
* the [[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]] for handy manual post-processing of segmentation results<br />
<p><p><br />
* the R package [[Applications/PaCeQuantAna|PaCeQuantAna]] for statistical analysis of feature data and creation of publication-ready plots of feature distributions and statistical analysis results<br><br><br />
<br />
<p><br />
Further references where PaCeQuant and the tools are documented or have been used:<br />
<br />
* Y. Poeschl, B. Möller, L. Müller, and K. Bürstenbinder,<br>'''''User-friendly assessment of pavement cell shape features with PaCeQuant: Novel functions and tools'''''.<br>In [https://www.sciencedirect.com/science/article/pii/S0091679X20300741?via%3Dihub Methods in Cell Biology], Academic Press, 2020.<br />
<br />
* B. Möller, Y. Poeschl, S. Klemm, and K. Bürstenbinder,<br>'''''Morphological Analysis of Leaf Epidermis Pavement Cells with PaCeQuant'''''.<br>In F. Cvrčková and V. Žárský, editors, [https://link.springer.com/protocol/10.1007%2F978-1-4939-9469-4_22 Plant Cell Morphogenesis: Methods and Protocols, chapter 22, pages 329-349], Springer New York, New York, NY, 2019.<br />
<br />
* D. Mitra, S. Klemm, P. Kumari, J. Quegwer, B. Möller, Y. Poeschl, P. Pflug, G. Stamm, S. Abel, K. Bürstenbinder,<br>'''''Microtubule-associated protein IQ67 DOMAIN5 regulates morphogenesis of leaf pavement cells in Arabidopsis thaliana'''''.<br>In [https://academic.oup.com/jxb/article/70/2/529/5165408 Journal of Experimental Botany, 70(2):529-543, January 2019].<br><br><br />
<br />
<p><br />
PaCeQuant and the different tools have been developed in close collaboration with...<br />
<br />
* the group of [https://www.ipb-halle.de/en/employee/katharina-buerstenbinder/ Dr. Katharina Bürstenbinder], [https://www.ipb-halle.de/en/research/molecular-signal-processing/ Department of Molecular Signal Processing], [https://www.ipb-halle.de/en/ Leibniz Institute of Plant Biochemistry], Halle (Saale), Germany.<br/><br />
<br />
* [https://www.idiv.de/de/gruppen_und_personen/mitarbeiterinnen/mitarbeiterdetails/eshow/poeschl_yvonne.html Dr. Yvonne Pöschl-Grau], member of the [https://www.idiv.de/en/groups_and_people/central_management/bioinformatics_unit_biu.html Bioinformatics Unit (BIU)] of the [https://www.idiv.de/en.html German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig]<br/><br/></div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Applications/PaCeQuantToolset&diff=962Applications/PaCeQuantToolset2020-05-16T16:10:50Z<p>Moeller: /* The PaCeQuant Plugin and Corresponding Tools */</p>
<hr />
<div>== The PaCeQuant Plugin and Corresponding Tools ==<br />
[[File:MiToBo_logo_PaCeQuant.png|border|150px|left|link=]]<br />
<br />
The [[Applications/PaCeQuant|PaCeQuant plugin]] for fully automatic cell segmentation and shape feature extraction is part of MiToBo since release 1.8.6. <br />
<br><br />
<br />
More details about the plugin and its usage can be found on the [[Applications/PaCeQuant|PaCeQuant's website]].<br />
<br />
<br><br />
Main publication:<br />
* B. Möller, Y. Poeschl, R. Plötner, and K. Bürstenbinder,<br> '''''PaCeQuant: A Tool for High-Throughput Quantification of Pavement Cell Shape Characteristics'''''.<br> [http://www.plantphysiol.org/content/early/2017/09/20/pp.17.00961 Plant Physiology, 175(1), September 2017].<br />
<br />
<br><br />
<br><br />
<br />
Over the time the main plugin has been supplemented with several complementary tools to ease cell shape analysis and feature visualization:<br />
<br><br />
* the [[Applications/FeatureColorMapper|FeatureColorMapper]] plugin for creating heatmap visualizations of cell features<br />
<p><p><br />
* the [[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]] for handy manual post-processing of segmentation results<br />
<p><p><br />
* the R package [[Applications/PaCeQuantAna|PaCeQuantAna]] for statistical analysis of feature data and creation of publication-ready plots of feature distributions and statistical analysis results<br><br><br />
<br />
<p><br />
Further references where PaCeQuant and the tools are documented or have been used:<br />
<br />
* Y. Poeschl, B. Möller, L. Müller, and K. Bürstenbinder,<br>'''''User-friendly assessment of pavement cell shape features with PaCeQuant: Novel functions and tools'''''.<br>In [https://www.sciencedirect.com/science/article/pii/S0091679X20300741?via%3Dihub Methods in Cell Biology], Academic Press, 2020.<br />
<br />
* B. Möller, Y. Poeschl, S. Klemm, and K. Bürstenbinder,<br>'''''Morphological Analysis of Leaf Epidermis Pavement Cells with PaCeQuant'''''.<br>In F. Cvrčková and V. Žárský, editors, [https://link.springer.com/protocol/10.1007%2F978-1-4939-9469-4_22 Plant Cell Morphogenesis: Methods and Protocols, chapter 22, pages 329-349], Springer New York, New York, NY, 2019.<br />
<br />
* D. Mitra, S. Klemm, P. Kumari, J. Quegwer, B. Möller, Y. Poeschl, P. Pflug, G. Stamm, S. Abel, K. Bürstenbinder,<br>'''''Microtubule-associated protein IQ67 DOMAIN5 regulates morphogenesis of leaf pavement cells in Arabidopsis thaliana'''''.<br>In [https://academic.oup.com/jxb/article/70/2/529/5165408 Journal of Experimental Botany, 70(2):529-543, January 2019].<br><br><br />
<br />
<p><br />
PaCeQuant and the different tools have been developed in close collaboration with...<br />
<br />
* the group of [https://www.ipb-halle.de/en/employee/katharina-buerstenbinder/ Dr. Katharina Bürstenbinder], [https://www.ipb-halle.de/en/research/molecular-signal-processing/ Department of Molecular Signal Processing], [https://www.ipb-halle.de/en/ Leibniz Institute of Plant Biochemistry], Halle (Saale), Germany.<br/><br />
<br />
* [https://www.idiv.de/de/gruppen_und_personen/mitarbeiterinnen/mitarbeiterdetails/eshow/poeschl_yvonne.html Dr. Yvonne Pöschl-Grau], member of the [https://www.idiv.de/en/groups_and_people/central_management/bioinformatics_unit_biu.html Bioinformatics Unit (BIU)] of the [https://www.idiv.de/en.html German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig]<br/><br/></div>Moellerhttps://mitobo.informatik.uni-halle.de/index.php?title=Operators/Tools/Interactive/LabelImageEditor&diff=961Operators/Tools/Interactive/LabelImageEditor2020-02-19T07:57:36Z<p>Moeller: </p>
<hr />
<div><br/><br />
<br/><br />
<br />
== Label Image Editor ==<br />
[[File:LabelImageEditor-MTBOperatorControlFrame.png|400px|right|link=]]<br />
<br />
The ''Label Image Editor'' is available since release version 1.8.8 of MiToBo.<br/><br />
In MiToBo/MiToBo plugins release 1.8.13.1 it got a rich feature update.<br />
<br />
===== Latest News =====<br />
The editor got latest updates in MiToBo/MiToBo plugins 1.9.<br />
<br />
===== Name of Plugin/Operator =====<br />
<code><br />
de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor<br />
</code><br />
<br><br />
(available since MiToBo version 1.8.8)<br />
<br><br />
<br />
===== Main features ===== <br />
* images provided in an input folder are subsequently displayed to the user<br />
* regions, i.e. connected components, can be removed and joined by simple mouse-clicks<br />
* additional boundaries can be added by drawing free-hand lines<br />
* region labels can be adjusted to enhance visibility <br />
* region re-labeling is supported to guarantee unique labels<br />
* holes within regions can be filled <br />
<br />
===== Usage =====<br />
The editor is dedicated to the analysis of label images. In a label image each region or connected component, respectively, is assumed to be marked with a unique intensity or color value, i.e. all of its pixels should share this value.<br />
The editor provides various editing functions to remove or join regions within such images.<br><br><br />
Note that the editor can also handle label images with one-pixel wide black boundaries between regions.<br><br><br />
The editor takes as input a directory from where the images are loaded one after the other.<br><br />
Once an image is displayed to the user edit operations can be performed. Afterwards the changes are saved to a new image file and the next label image is read from the given input directory. <br />
<br />
<br><br />
To run the LabelImageEditor perform the following steps:<br />
* install MiToBo by following the instructions on the [[Installation]] page<br />
* run MiToBo and start the operator runner by selecting the menu item '''''MiToBo Runner''''' from '''''Plugins -> MiToBo''''' <br />
* in the selection menu navigate to '''de.unihalle.informatik.MiToBo.tool.interactive''' and select the operator '''''LabelImageEditor'''''<br />
This will bring up the operator window of the LabelImageEditor (see figure on the right, top) where the basic configuration parameters can be added. Clicking the "Run" button will open the editor window with the first image loaded (figure on the right, bottom).<br />
<br />
<br><br />
* Input data:<br>The operator reads the contents of a given input image directory and displays all images one after the other to the user. <br>The user can edit the images, i.e. remove labeled regions, by clicking with the left mouse button somewhere into the region to remove.<br> Clicking the "Next" button at the top of the editor window will save the current image to disk and proceed with the next image in the folder. <br><br><br />
* Output data:<br>For each input image the operator will save a corresponding output image, either in the same folder or a specific output folder if provided.<br> Output images will share the name of the corresponding input image extended with substring "-edited".<br> Note, all images are relabeled automatically before saving to ensure consecutive labels in the resulting edited images. <br> Consecutive labels are a pre-requisite for some other MiToBo tools which can be used in further processing steps, like the [[Applications/FeatureColorMapper|FeatureColorMapper]].<br />
<br />
<br><br />
* Parameters:<br />
{|class="wikitable"<br />
|Name<br />
|Description<br />
|-<br />
|''Input Directory''<br />
|directory from where the images to process will be loaded<br />
|-<br />
|''File Filter''<br />
|Optional string to filter image files to be processed. If the string is empty all files are processed. <br>If a non-empty string is provided, files with names not containing the pattern will be skipped.<br> For example, if the string ".tif" is provided, only images ending with ".tif", i.e. in TIFF format, will be considered.<br> The string "cell" would select only images containing the word "cell" somewhere in their names.<br> Note that as string any valid Java regular expression is admissible. See for example [http://www.vogella.com/tutorials/JavaRegularExpressions/article.html this website] for more details on regular expressions.<br />
|-<br />
|''Output directory''<br />
|optional; edited result label images will be saved to this directory; if not provided the result images will be stored in the input folder<br />
|}<br />
<br />
[[File:LabelImageEditor-EditorWindow.png|500px|right|link=]]<br />
<br />
<br><br />
The following table lists all available operations available in the editor window:<br />
{|class="wikitable"<br />
|Operation<br />
|How to do it<br />
|-<br />
|''remove a region''<br />
|click with left mouse button somewhere into the region to be removed;<br>the region will then be removed by setting all its pixels to a value of zero<br />
|-<br />
|''join two regions''<br />
|press 'Shift' and left-click into the first region to remember its label, then release 'Shift' and left-click into the second region;<br>the label of the first region will be transferred to the second region; black pixels between both parts can be removed afterwards using the "Fix borders" button<br />
|-<br />
|''draw a new boundary''<br />
|keep left mouse button pressed and drag the mouse; this will add a one-pixel wide free-hand line to the label image<br />
|}<br />
<br />
<br><br />
The buttons in the editor window have the following functions:<br />
{|class="wikitable"<br />
|Button<br />
|Function<br />
|Keyboard Shortcut<br />
|-<br />
|''Next''<br />
|save current changes and jump to next image<br />
|''Alt + n''<br />
|-<br />
|''Skip''<br />
|cancel current image, don't save anything and jump to next image<br />
|''Alt + s''<br />
|-<br />
|''Contrast''<br />
|adjust labels to optimize visibility, i.e., shift labels into upper third of gray-scale range with maximal distances between them<br />
|''Alt + c''<br />
|-<br />
|''Relabel''<br />
|relabel the image, i.e., make sure that every region gets a unique label<br />
|''Alt + r''<br />
|-<br />
|''Fix Borders''<br />
|remove all background pixels with more than one foreground label in their 3x3 neighborhood<br />
|''Alt + b''<br />
|-<br />
|''Fill Holes''<br />
|fill background regions enclosed by a single region with the region label<br />
|''Alt + h''<br />
|-<br />
|''Undo''<br />
|undo the last action; IMPORTANT: only the most recent action can be undone!<br />
|''Alt + u''<br />
|-<br />
|''Quit''<br />
|save current changes and quit the editor window<br />
|''Alt + q''<br />
|}<br />
<br />
<br><br><br />
'''Hint:''' The ''Undo'' function has currently only a history of length one. If you accidentally deleted too many regions or want to undo more than one action, either run the editor once again on the complete directory or copy the corresponding image to a separate folder and run the editor on that folder. Results of a former run will be overwritten without further inquiry.<br />
<br />
=== Updates ===<br />
----<br><br />
<br />
'''January 2019'''<br />
* The editor got a comprehensive update in MiToBo 1.8.13.1 and MiToBo-plugins 1.8.13.1, respectively. There is now much more editing functionality available, e.g., filling holes or drawing of free-hand lines.<br />
<br />
'''March 2018'''<br />
* The LabelImageEditor has been released in MiToBo 1.8.8 and MiToBo-plugins 1.8.8, respectively.<br><br><br />
<p><br />
<br />
=== Technical Details ===<br />
----<br><br />
The label editor relies on analyzing and manipulating the grayscale values of segmented regions in a given image.<br> In detail, the most important functions are implemented as follows:<br />
* deleting regions:<br> the grayscale value at the mouse-click position is determined and all pixels in the image sharing this value are set to black<br />
* joining regions:<br> upon clicking into the first region its grayscale value is internally stored;<br> when the user clicks into the second region which is to be merged with the first one<br> the grayscale value at the click position is extracted and all pixels with this value are relabeled with the formerly stored grayscale value of the first region;<br> important: after doing the join both joined regions share the same grayscale value, however, are not connected to each other; hence, to get a valid label image again you should run the "Fix Borders" function<br />
* relabel image:<br> the image is thresholded with a threshold of zero to get a binary image of background and labeled regions;<br> then a sequential component labeling is run on the image which assigns consecutive grayscale labels to all connected components in the foreground of the image<br />
* adjust contrast:<br> the image is relabeled, however, the target labels are equidistantly spread over just the upper two third of the available grayscale range;<br> the underlying motivation for this is given by the observation that low grayscale values are hard to distinguish from the background, thus, brighter labels improve visibility<br />
* fix borders:<br> this functions seeks to eliminate borders between regions with identical labels which may for example occur after joining two regions;<br> for removing borders for each background pixel in the image the grayscale values in a 7x7 neighborhood of the pixel are analyzed,<br> and if there is only a single grayscale value found and more than half of the analyzed neighborhood pixels share this value, the corresponding background pixel gets the value as well;<br> the neighborhood is currently fixed to 7x7, thus, borders which are wider cannot be closed, and it has to be noted that sometimes the function has to be run several times to remove all pixels belonging to a single border</div>Moeller