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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 = | |||
The Microscope Image Analysis Toolbox MiToBo is an extension for the widely used image processing application [http://rsbweb.nih.gov/ij/ ImageJ] and its new release [http://developer.imagej.net/ ImageJ 2.0]. | |||
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< | '''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/> | |||
'''Highlight operators and tools in MiToBo''' | |||
{|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]]''''' | |||
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|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 | |||
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|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 | |||
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|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 | |||
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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 completely separates the implementation of image processing algorithms from potential user interfaces | '''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. | |||
algorithms and tools. | 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 | Alida defines unified interfaces and execution procedures for operators which yield the fundament for its nice features like | ||
<ul> | <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 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> automatic generation of commandline and graphical user interfaces | ||
<li> a graphical programming editor named '''''Grappa''''' automatically considering all implemented operators as potential processing nodes | <li> a graphical programming editor named '''''Grappa''''' automatically considering all implemented operators as potential processing nodes<br> | ||
</ul> | </ul> | ||
<p> | <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. | 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. | ||
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'''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]] | |||
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|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] | |||
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'''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. | |||
The news archive can be found [[News Archive | here]]. | The news archive can be found [[News Archive | here]]. | ||
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'''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/> | |||
== Licensing information | You can find the API documentation for the current release [http://www.informatik.uni-halle.de/mitobo/api/index.html here].<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]. | |||
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'''Support, Bug reports & Feature requests''' | |||
{|style="background-color:#f8f8ff" | |||
|style="text-align:left;width:20%|[[File:forum-image-sc.png|border|64px|left|link=https://forum.image.sc/]] | |||
|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]. | |||
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|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]. | |||
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|style="text-align:left;width:20%|[[file:Email.png|center|36px|link=]] | |||
|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]. | |||
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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. | |||
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'''Licensing information'''<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]. | 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]. | ||
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'''Gnu PGP Public Key'''<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/. | |||
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Latest revision as of 12:04, 29 November 2023
MiToBo - A microscope image analysis toolbox
What is MiToBo? Highlight operators and tools in MiToBo
For several other important operators and plugins documentation is available via the Operator Documentation pages here in the Wiki.
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...
|
Latest News
The news archive can be found here.
How to get MiToBo?
You can find the API documentation for the current release here.
Support, Bug reports & Feature requests
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
Gnu PGP Public Key |