Main Page: Difference between revisions

From MiToBo
Jump to navigationJump to search
No edit summary
 
(95 intermediate revisions by 4 users not shown)
Line 1: Line 1:
== 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] and its new release [http://developer.imagej.net/ ImageJ 2.0].<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
{|width="100%"
types of microscopes.<br />
|-
Some of MiToBo's operators are for example these ones:
|style="vertical-align:top" |
<ul>
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;">
<li> ''Scratch Assay Analyzer'' for analyzing microscope images from cell migration experiments
<div style="padding: 0.3em 1em 0.7em 1em;">
<li> ''Neuron Analyzer'' for the segmentation of neurons in microscope images
'''What is MiToBo?'''<br>
<li> ''Snake Optimizer'' for performing image segmentation based on explicit active contours
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/>
</ul>
 
Furthermore, MiToBo offers a user- and programmer friendly framework for developing algorithms that have properties not available in ImageJ, <br />
'''Highlight operators and tools in MiToBo'''
however, still provides full compatibility to all ImageJ features. <br />
{|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.


<p>
<br>
MiToBo completely separates the implementation of image processing algorithms from potential user interfaces.<br />
'''MiToBo for developers'''<br>
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
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.<br> The main concept of Alida are operators as the core units for implementing data analysis algorithms. <br />
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.
</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.


== Current release ==
You can download MiToBo version 1.3 [[Downloads | here]]. <br />
You can find the API documentation for this 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].
== Latest News ==
=== January 2014 ===
* 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 ''SingleCellMigrationAnalyzer'',<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 was added, especially for gray value bright filed images.
=== May 2013 ===
* Version 1.2 of MiToBo has been released. <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>
Also Grappa has undergone some changes to improve usability, e.g. it now supports key shortcuts for the most important actions.
=== March 2013 ===
* Version 1.1 of MiToBo has been released. <br/>
MiToBo has undergone several internal enhancements mainly dedicated to the stability and usability of the core and its user interfaces.<br>
In addition, MiToBo now includes the ''Neuron Analyzer'' which is an application for the analysis of 2D images of neuronal cells.<br>
The analyzer is capable of extracting complete regions of neuronal cells (not only traces) and allows for extraction of protein
concentrations along the neurites.
=== October 2012 ===
* Version 1.0.5 of MiToBo has been released. <br/>
Most important new feature is the graphical programming editor "Grappa" which is released in this new MiToBo version!<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>
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>
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.
* Updated version of Chipory available for download.
=== August 2012 ===
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/>
In particular, two plugins for ImageJ implemented in MiToBo will be presented and demonstrated in posters:
* B. Möller and D. Misiak, "SnakeOptimizer - Object Segmentation with Parametric Active Contours in ImageJ"
* M. Glaß, B. Möller and S. Posch, "Scratch Assay Analysis in ImageJ"
We are looking forward to meet you in Mondorf-les-Bains!
=== July 2012 - Release 1.0.1 ===
Version 1.0.1 of MiToBo has been released. <br/>
The new release ships with new quick start plugins for the SnakeOptimizer and ScratchAssayAnalyzer operators.<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.
Check the [[Downloads | download page]] for jars and sources.
New release of chipory ready for download
=== April 2012 ===
Version 1.0.0 of MiToBo has been released. <br/>
Most interesting new features are:
* automatic generation of graphical user interfaces for MiToBo operators
* a flexible generic tool for running operators via command line
* operators performing level set segmentation on images
* support for saving/loading parameter settings from GUI
Check the [[Downloads | download page]] for jars and sources.
== News Archive ==
The news archive can be found [[News Archive | here]].
The news archive can be found [[News Archive | here]].
</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;">
'''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].
</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;">
'''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>
== Bug reports & Feature requests ==
</div>
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 />
<br>
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 style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;">
<div style="padding: 0.3em 1em 0.7em 1em;">
'''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/.
</div>
</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/.