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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/>


=== September 2011 ===
'''Highlight operators and tools in MiToBo'''
Version 0.9.6 of MiToBo has been released. <br/>
{|style="background-color:#f8f8ff"
Most interesting new features are:
|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.


* more user-friendly I/O interfaces
<br>
* MiCA, the 2D microscope cell image analyzer
'''MiToBo for developers'''<br>
* several bugfixes and internal enhancements
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>


Check the [[Downloads | download page]] for jars and sources.
<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.


=== June 2010 ===
The news archive can be found [[News Archive | here]].
Version 0.9.5 of MiToBo has just been released! <br/>
</div>
Most interesting new features are:
</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/>


* scratch assay analysis with levelsets
You can find the API documentation for the current release [http://www.informatik.uni-halle.de/mitobo/api/index.html here].<br/>
* enhanced image I/O
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].
* easy operator development with annotations
</div>
 
</div>
== Licensing information ==
<br>
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;">
<div style="padding: 0.3em 1em 0.7em 1em;">
'''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].
|-
|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].
|-
|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.
</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;">
'''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].
 
</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/.