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'''What is MiToBo?'''<br>
'''What is MiToBo?'''<br>
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].<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/>
MiToBo ships with a set of operators ready to be used as plugins in ImageJ. They focus on the analysis of biomedical images acquired by various
 
types of microscopes.<br />
'''Highlight operators and tools in MiToBo'''
Some of MiToBo's operators are for example these ones:
{|style="background-color:#f8f8ff"
<ul>
|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]]
<li> ''ActinAnalyzer'' for the quantification of actin filament structures in microscopy images
|style="text-align:left;width:80%|'''''[[Applications/CytoskeletonAnalyzer2D|CytoskeletonAnalyzer2D]]''''' for the quantification of cytoskeleton structural patterns in microscopy images with texture measures;<br>
<li> ''Cell Migration Analyzer'' for analyzing single cell migration from time lapse image sequences
to ease cell boundary extraction in data preparation we additionally provide the '''''[[Applications/CellBoundaryExtractor2D|CellBoundaryExtractor2D]]''''' and a handy '''''[[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]]'''''
<li> ''Neuron Analyzer'' for the segmentation of neurons in microscope images
|-
<li> ''Scratch Assay Analyzer'' for analyzing microscope images from collective cell migration experiments
|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]]
<li> ''Snake Optimizer'' for performing image segmentation based on explicit active contours
|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
</ul>
|-
Furthermore, MiToBo offers a user- and programmer friendly framework for developing algorithms that have properties not available in ImageJ, <br />
|style="text-align:left;width:10%|[[File:NeuronAnalyzer2D.png|border|72px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/NeuronAnalyzer2D]]
however, still provides full compatibility to all ImageJ features. <br />
|style="text-align:left;width:80%|'''''[[Applications/NeuronAnalyzer2D|Neuron Analyzer]]''''' for the segmentation of neurons in microscope images
<p>
|-
MiToBo completely separates the implementation of image processing algorithms from potential user interfaces.<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]]
Moreover, MiToBo builds on top of [http://www.informatik.uni-halle.de/alida/ Alida] which is a library for easing the development of data analysis
|style="text-align:left;width:80%|'''''[[Applications/CellMigrationAnalyzer|Cell Migration Analyzer]]''''' for analyzing single cell migration from time lapse image sequences
algorithms and tools.<br> The main concept of Alida are operators as the core units for implementing data analysis algorithms. <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]]
|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  
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>
<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 MiToBo also at...'''<br>
'''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: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.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%"|[[file:logo-blue.png|90px|link=https://omictools.com/microscope-image-analysis-toolbox-tool]]
|style="text-align:center;width:10%"|[[file:Git.png|90px|link=https://github.com/mitobo-hub]]
|-
|-
|style="text-align:center;width:10%"|[http://imagej.net/MiToBo ImageJ.net]
|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%"|[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]
|style="text-align:center;width:10%"|[https://omictools.com/microscope-image-analysis-toolbox-tool OMIC Tools]
|style="text-align:center;width:10%"|[https://github.com/mitobo-hub GitHub]
|}
|}
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'''Latest News'''<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]].
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'''How to get MiToBo?'''<br>
'''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/1.8.3/mitobo-plugins-1.8.3-bin.zip MiToBo-Plugins package] and follow the installation instructions to be found [[Installation | here]].  
* 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 add MiToBo's update site [http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo] to your Fiji installation
* 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/>  
* use in general:<br> you can download MiToBo and the MiToBo plugins package [[Downloads | here]]. <br/>  


You can find the API documentation for this release [http://www.informatik.uni-halle.de/mitobo/api/index.html here].<br/>  
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<br> which you can download [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual.pdf here].
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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'''Latest News'''<br>
'''Support, Bug reports & Feature requests'''
* 12/2016: 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.
{|style="background-color:#f8f8ff"
* 11/2016: MiToBo 1.8.3 has been released.
|style="text-align:left;width:20%|[[File:forum-image-sc.png|border|64px|left|link=https://forum.image.sc/]]
* 05/2016: MiToBo 1.8.2 has been released.
|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].
* 05/2016: 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].  
|-
* 03/2016: MiToBo 1.8 has been released. From now on MiToBo builds upon Java 1.8.
|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].
The news archive can be found [[News Archive | here]].
|-
|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].
|}
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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'''Bug reports & Feature requests'''<br>
'''Gnu PGP Public Key'''<br>
Bug reports and feature requests can be submitted as issues on [https://github.com/mitobo-hub/mitobo/issues Github] or by mail to [mailto:mitobo@informatik.uni-halle.de mitobo@informatik.uni-halle.de]. Before reporting a new bug or requesting a new feature, please check if that bug has already been submitted.
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 15:55, 1 December 2020

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

  • 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/.