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== 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==
= 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 =
The Microscope Image Analysis Toolbox MiToBo is an extension for the widely used image processing application [http://rsbweb.nih.gov/ij/ ImageJ].<br />
MiToBo ships with a set of ready-to-use plugins that focus on the analysis of biomedical images acquired by various<br/>
types of microscopes.<br />
Furthermore, MiToBo offers a framework for developing plugins that have properties not available in ImageJ. <br />
Especially, MiToBo completely separates the implementation of image processing algorithms from the user interface, but<br />
still offers full compatibility to all ImageJ features. <br />
The underlying concept of operators which link the processing steps to a directed graph structure, allows, for example<br />
the automatic documentation of the whole analysis process that lead from the input image to the analysis results.<br />


== Latest News ==
{|width="100%"
|-
|style="vertical-align:top" |
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;">
<div style="padding: 0.3em 1em 0.7em 1em;">
'''What is MiToBo?'''<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/>


=== October 2012 ===
'''Highlight operators and tools in MiToBo'''
Updated version of Chipory available for download.
{|style="background-color:#f8f8ff"
|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]]
|style="text-align:left;width:80%|'''''[[Applications/CytoskeletonAnalyzer2D|CytoskeletonAnalyzer2D]]''''' for the quantification of cytoskeleton structural patterns in microscopy images with texture measures;<br>
to ease cell boundary extraction in data preparation we additionally provide the '''''[[Applications/CellBoundaryExtractor2D|CellBoundaryExtractor2D]]''''' and a handy '''''[[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]]'''''
|-
|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]]
|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
|-
|style="text-align:left;width:10%|[[File:NeuronAnalyzer2D.png|border|72px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/NeuronAnalyzer2D]]
|style="text-align:left;width:80%|'''''[[Applications/NeuronAnalyzer2D|Neuron Analyzer]]''''' for the segmentation of neurons in microscope images
|-
|style="text-align:left;width:10%|[[File:tracking_ES-2.gif|72px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/CellMigrationAnalyzer]]
|style="text-align:left;width:80%|'''''[[Applications/CellMigrationAnalyzer|Cell Migration Analyzer]]''''' for analyzing single cell migration from time lapse image sequences
|-
|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]]
|style="text-align:left;width:80%|'''''[[Applications/ScratchAssayAnalyzer|Scratch Assay Analyzer]]''''' for analyzing microscope images from collective cell migration experiments
|}
For several other important operators and plugins documentation is available via the [[Operator_Documentation| Operator Documentation pages]] here in the Wiki.<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>
'''MiToBo for developers'''<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.
The MiToBo API completely separates the implementation of image processing algorithms from potential user interfaces based
on [http://www.informatik.uni-halle.de/alida/ Alida] which is a library for easing the development of data analysis
algorithms and tools. The main concept of Alida are <i>operators</i> as the core units for implementing data analysis algorithms. <br />
Alida defines unified interfaces and execution procedures for operators which yield the fundament for its nice features like
<ul>
<li> automatic documentation of complete analysis processes, e.g., leading from an input image to analysis results, in terms of processing graphs
<li> automatic generation of commandline and graphical user interfaces
<li> a graphical programming editor named '''''Grappa''''' automatically considering all implemented operators as potential processing nodes<br>
</ul>


<p>
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.
</p>
</div>
</div>
<br>
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;">
<div style="padding: 0.3em 1em 0.7em 1em;">
'''Visit and follow MiToBo also at...'''<br>
{|
|style="text-align:center;width:10%"|[[file:Imagej-128.png|90px|link=http://imagej.net/MiToBo]]
|style="text-align:center;width:10%"|[[file:Git.png|90px|link=https://github.com/mitobo-hub]]
|style="text-align:center;width:10%"|[[file:mtbtw.png|320px|link=https://twitter.com/MiToBo_Hal]]
|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]]
|style="text-align:center;width:10%"|[[file:logo-blue.png|90px|link=https://omictools.com/microscope-image-analysis-toolbox-tool]]
|-
|style="text-align:center;width:10%"|[http://imagej.net/MiToBo ImageJ.net]
|style="text-align:center;width:10%"|[https://github.com/mitobo-hub GitHub]
|style="text-align:center;width:10%"|[https://twitter.com/MiToBo_Hal Twitter]
|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]
|style="text-align:center;width:10%"|[https://omictools.com/microscope-image-analysis-toolbox-tool OMIC Tools]
|}
</div>
</div>
|
|style="vertical-align:top" |
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;">
<div style="padding: 0.3em 1em 0.7em 1em;">
'''Latest News'''<br>
* 08/2023: MiToBo 2.3.1 has been released which fixes serious incompatibilities to Bioformats.
* 07/2023: MiToBo 2.3 has been released.<br>
* 05/2021: MiToBo 2.2 has been released.<br>
* 12/2020: MiToBo 2.1 has been released.<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].
* 07/2019: MiToBo 1.8.15 has been released fixing several issues with handling images in MiToBo.
* 02/2019: MiToBo 1.8.14 has been released.


=== August 2012 ===
The news archive can be found [[News Archive | here]].
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/>
</div>
In particular, two plugins for ImageJ implemented in MiToBo will be presented and demonstrated in posters:
</div>
<br>
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;">
<div style="padding: 0.3em 1em 0.7em 1em;">
'''How to get MiToBo?'''<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]].  
* 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
* use in general:<br> you can download MiToBo and the MiToBo plugins package [[Downloads | here]]. <br/>


* B. Möller and D. Misiak, "SnakeOptimizer - Object Segmentation with Parametric Active Contours in ImageJ"
You can find the API documentation for the current release [http://www.informatik.uni-halle.de/mitobo/api/index.html here].<br/>  
* M. Glaß, B. Möller and S. Posch, "Scratch Assay Analysis in ImageJ"
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].
 
</div>
We are looking forward to meet you in Mondorf-les-Bains!
</div>
 
<br>
=== July 2012 - Release 1.0.1 ===
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;">
Version 1.0.1 of MiToBo has been released. <br/>
<div style="padding: 0.3em 1em 0.7em 1em;">
The new release ships with new quick start plugins for the SnakeOptimizer and ScratchAssayAnalyzer operators.<br/>
'''Support, Bug reports & Feature requests'''
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.
{|style="background-color:#f8f8ff"
 
|style="text-align:left;width:20%|[[File:forum-image-sc.png|border|64px|left|link=https://forum.image.sc/]]
Check the [[Downloads | download page]] for jars and sources.
|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].
 
|-
New release of chipory ready for download
|style="text-align:left;width:20%|[[file:Git.png|64px|link=https://github.com/mitobo-hub]]
 
|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].
=== April 2012 ===
|-
Version 1.0.0 of MiToBo has been released. <br/>
|style="text-align:left;width:20%|[[file:Email.png|center|36px|link=]]
Most interesting new features are:
|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].
 
|}
* automatic generation of graphical user interfaces for MiToBo operators
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.
* a flexible generic tool for running operators via command line
</div>
* operators performing level set segmentation on images
</div>
* support for saving/loading parameter settings from GUI
<br>
 
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;">
Check the [[Downloads | download page]] for jars and sources.
<div style="padding: 0.3em 1em 0.7em 1em;">
 
'''Licensing information'''<br>
=== March 2012 - Preview of Release 1.0 ===
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!
 
* Download the beta release [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-preview-1.0-beta.jar here]!
 
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:
 
* [http://rsbweb.nih.gov/ij/ ImageJ], Version 1.46g
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
* [http://xstream.codehaus.org/ XStream], Version 1.3.1
* [http://www.loci.wisc.edu/software/bio-formats/ Loci Tools], Version 4.3.3
* [http://math.nist.gov/javanumerics/jama/ Jama], Version 1.0.2
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05
* [http://www.csie.ntu.edu.tw/~cjlin/libsvm/ LIBSVM], Version 3.1
 
Finally some MiToBo internal jars are required (have a look at the download page for more details):
 
* [http://www.informatik.uni-halle.de/mitobo/downloads/aldgraphml/aldgraphml.jar ALDGraphml]
* [http://www.informatik.uni-halle.de/mitobo/downloads/mtbxml/mtbxml.jar mtbxml]  
* [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-Help.jar MiToBo-Help]
* [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/sezpoz-1.9-alida.jar Alida-SezPoz].
 
... and for the snakes you require C++ native libs:
* 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]
 
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!
 
=== September 2011 ===
Version 0.9.6 of MiToBo has been released. <br/>
Most interesting new features are:
 
* more user-friendly I/O interfaces
* MiCA, the 2D microscope cell image analyzer
* several bugfixes and internal enhancements
 
Check the [[Downloads | download page]] for jars and sources.
 
=== June 2011 ===
Version 0.9.5 of MiToBo has just been released! <br/>
Most interesting new features are:
 
* scratch assay analysis with levelsets
* enhanced image I/O
* easy operator development with annotations
 
== Licensing information ==
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].
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].
 
</div>
== Current release ==
</div>
You can download MiToBo version 0.9.6 [[Downloads | here]]. <br />
<br>
You can find the API documentation for this release [http://www.informatik.uni-halle.de/mitobo/api/index.html here].<br/>
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;">
Furthermore MiToBo offers you a user and programmer manual you can download [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual.pdf here].
<div style="padding: 0.3em 1em 0.7em 1em;">
 
'''Gnu PGP Public Key'''<br>
== Bug reports & Feature requests ==
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/.
Bug reports and feature requests can be submitted via the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php MiToBo bugtracking system] or by mail to [mailto:mitobo@informatik.uni-halle.de mitobo@informatik.uni-halle.de].<br />
</div>
Before reporting a new bug, please check if that bug has already been submitted in the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php report list].<br />
</div>
|}

Latest revision as of 12:04, 29 November 2023

MiToBo - A microscope image analysis toolbox

What is MiToBo?
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 page of features for an overview). MiToBo is implemented as extension for the widely used image processing application ImageJ/Fiji and its new release ImageJ 2.0. All functions, operators and plugins of MiToBo are ready to be directly used as plugins in ImageJ and Fiji.

Highlight operators and tools in MiToBo

MiToBo logo CytoskeletonAnalyzer2D.png
CytoskeletonAnalyzer2D for the quantification of cytoskeleton structural patterns in microscopy images with texture measures;

to ease cell boundary extraction in data preparation we additionally provide the CellBoundaryExtractor2D and a handy LabelImageEditor

MiToBo logo PaCeQuant.png
PaCeQuant and corresponding tools, i.e. the LabelImageEditor, the FeatureColorMapper and the R package PaCeQuantAna, for quantification, visualization and statistical analysis of the morphology and shape characteristics of cells
NeuronAnalyzer2D.png
Neuron Analyzer for the segmentation of neurons in microscope images
Tracking ES-2.gif
Cell Migration Analyzer for analyzing single cell migration from time lapse image sequences
GFP U2OS overlay.png
Scratch Assay Analyzer for analyzing microscope images from collective cell migration experiments

For several other important operators and plugins documentation is available via the Operator Documentation pages here in the Wiki.
The pages are structured according to the package structure of MiToBo which is also mirrored in the selection panel of MiToBo's operator runner.


MiToBo for developers
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. The MiToBo API completely separates the implementation of image processing algorithms from potential user interfaces based on Alida which is a library for easing the development of data analysis algorithms and tools. The main concept of Alida are operators as the core units for implementing data analysis algorithms.
Alida defines unified interfaces and execution procedures for operators which yield the fundament for its nice features like

  • automatic documentation of complete analysis processes, e.g., leading from an input image to analysis results, in terms of processing graphs
  • automatic generation of commandline and graphical user interfaces
  • a graphical programming editor named Grappa automatically considering all implemented operators as potential processing nodes

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.


Visit and follow MiToBo also at...

Imagej-128.png Git.png Mtbtw.png Logo.png Logo-blue.png
ImageJ.net GitHub Twitter ImageJ Docu Wiki OMIC Tools

Latest News

  • 08/2023: MiToBo 2.3.1 has been released which fixes serious incompatibilities to Bioformats.
  • 07/2023: MiToBo 2.3 has been released.
  • 05/2021: MiToBo 2.2 has been released.
  • 12/2020: MiToBo 2.1 has been released.
  • 05/2020: MiToBo 2.0 has been released.
    From now on the online help system relies on operator class annotations, and the release includes a PaCeQuant update with new shape features and improvements for supplemental tools like the FeatureColorMapper and the LabelImageEditor.
  • 07/2019: MiToBo 1.8.15 has been released fixing several issues with handling images in MiToBo.
  • 02/2019: MiToBo 1.8.14 has been released.

The news archive can be found here.


How to get MiToBo?

  • ImageJ-Users:
    download the MiToBo-Plugins package and follow the installation instructions to be found here.
  • Fiji-Users:
    simply select MiToBo's update site http://sites.imagej.net/MiToBo in FijiIs list of update sites in your installation
  • use in general:
    you can download MiToBo and the MiToBo plugins package here.

You can find the API documentation for the current release here.
Furthermore MiToBo offers you a user and programmer guide which you can download here.


Support, Bug reports & Feature requests

Forum-image-sc.png
To get help on your questions about MiToBo tools, plugins and operators you can use the forum at image.sc tagging your post with #mitobo.
Git.png Bug reports and feature requests can be submitted as issues on Github.
Email.png
Alternatively you can also write an email to mitobo@informatik.uni-halle.de.

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.


Licensing information
MiToBo is free software: you can redistribute it and/or modify under the terms of the GNU General Public License version 3 or (at your option) any later version as published by the Free Software Foundation.


Gnu PGP Public Key
Since version 1.8.7 MiToBo and MiToBo-Plugins releases are PGP signed. MiToBo's public key for verification can be found on public key servers, e.g., at https://pgp.mit.edu/.