MiToBo - User contributions [en]

Main Page

2019-01-02T08:50:05Z

Posch: /* MiToBo - A microscope image analysis toolbox */

= 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 =

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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|64px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/CytoskeletonAnalyzer2D]]
|style="text-align:left;width:80%|'''''CytoskeletonAnalyzer2D''''' for the quantification of cytoskeleton structural patterns in microscopy images with texture measures
|-
|style="text-align:left;width:10%|[[File:MiToBo_logo_PaCeQuant.png|border|64px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/PaCeQuant]]
|style="text-align:left;width:80%|'''''PaCeQuant''''' for quantifying the morphology and shape characteristics of cells
|-
|style="text-align:left;width:10%|[[File:NeuronAnalyzer2D.png|border|64px|left|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/NeuronAnalyzer2D]]
|style="text-align:left;width:80%|'''''Neuron Analyzer''''' for the segmentation of neurons in microscope images
|-
|style="text-align:left;width:10%|[[File:Track-small.gif|64px|left|border|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/CellMigrationAnalyzer]]
|style="text-align:left;width:80%|'''''Cell Migration Analyzer''''' for analyzing single cell migration from time lapse image sequences
|-
|style="text-align:left;width:10%|[[File:GFP_U2OS_overlay.png|64px|left|border|link=http://mitobo.informatik.uni-halle.de/index.php/Applications/ScratchAssayAnalyzer]]
|style="text-align:left;width:80%|'''''Scratch Assay Analyzer''''' for analyzing microscope images from collective cell migration experiments
|}

'''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>
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<br>
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'''Visit 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: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: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://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://github.com/mitobo-hub GitHub]
|}
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|
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<div style="padding: 0.3em 1em 0.7em 1em;">
'''Latest News'''<br>
* 12/2018: MiToBo 1.8.13 has been released including the CytoskeletonAnalyzer2D.
* 07/2018: We have added a new page [[Tips_and_Tricks| Tips and Tricks]] here in the Wiki where you can find information on how to accomplish common tasks like manually labeling images.

The news archive can be found [[News Archive | here]].
</div>
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<br>
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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/>

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>
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<br>
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<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.
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<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].
</div>
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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/.
</div>
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|}

Main Page

2012-10-11T09:15:30Z

Posch:

== 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 ==

=== October 2012 ===
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.

=== 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].

== Current release ==
You can download MiToBo version 0.9.6 [[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 manual you can download [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual.pdf here].

== Bug reports & Feature requests ==
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 />
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 />

Main Page

2012-07-12T14:32:40Z

Posch: /* July 2012 - Release 1.0.1 */

== 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==
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 ==

=== 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.

=== 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].

== Current release ==
You can download MiToBo version 0.9.6 [[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 manual you can download [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual.pdf here].

== Bug reports & Feature requests ==
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 />
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 />

Downloads

2012-04-25T15:49:00Z

Posch: /* Additional resources */

__NOTOC__

Here you can find the current release of MiToBo for download. Likewise older versions and additional libraries required to run MiToBo can be found here.

For detailed information on the installation process take a look at the [[Installation]] page.

== Current release (v1.0.0)==
* the new release is coming very soon...


== All versions of MiToBo ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Binaries
! Sources
! API
! Date
|-
| 1.0.0
| 
| 
| 
| April 26th, 2012
|-
| 0.96
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.6.zip zip]
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.6.zip zip]
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-0.9.6.zip zip]
| September 01, 2011
|-
| 0.95
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.5.zip zip]
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.5.zip zip]
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-0.9.5.zip zip]
| June 08, 2011 (updated June 22nd, 2011)
|-
| 0.9
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.tar.gz tar.gz]
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.tar.gz tar.gz]
| [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.tar.gz tar.gz]
| October 26, 2010
|}
<br/>

== Manual ==

Detailed information about MiToBo, its API and usage, can be found in the user and programmer manual.

* MiToBo-Manual, Version 0.9.6 [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual.pdf pdf]
<br/>

== Requirements ==
MiToBo requires Java 1.6 or later.

The following external jars are needed to run MiToBo plugins and use the code.<br/>
<b>Note that the binary zip file already includes all jars required, there is no need for explicit download!</b>

MiToBo depends on the following external 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.csie.ntu.edu.tw/~cjlin/libsvm/ LIBSVM], Version 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://sezpoz.java.net/ SezPoz], Version 1.9

* [https://jai-imageio.dev.java.net/ JAI ImageIO], Version 1.1 (only required for MiToBo 0.9)

=== Project internal libraries ===

MiToBo also relies on some libraries provided by the MiToBo project itself.<br>
In particular XML schemes for representing the history graphs and MiToBo's online help are included in separate jar archives.

'''[[Note]]:''' <br/>
''' You do not need to download these libraries explicitly. If you download the binary zip file all jars and libraries are already included.''' <br/>

The MiToBo internal archive files included in the zip file are the following ones:

* ALDGraphml, Version 1.0.0 (Alida extensions for [http://graphml.graphdrawing.org/ graphML]):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/aldgraphml/aldgraphml.jar jar]
* MTBXml, Version 1.0.0 (MiToBo XML I/O for several datatypes, based on XMLBeans):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbxml/mtbxml.jar jar]
* MiToBo-Help, Version 1.0.0 (MiToBo JavaHelp pages):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mitoboHelp/MiToBo-Help.jar jar]

The following library is only required for MiToBo-0.9:

* MTBImageIO-Ext, Version 0.9 (improved image I/O based on ImageIO-Ext):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff-0.9.jar jar]
** Source code [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff_src-0.9.zip zip]
** Alternatively, the [https://imageio-ext.dev.java.net/ ImageIO-Ext] library can be used, which depends on the [https://jai-imageio.dev.java.net/ JAI ImageIO] library and the [https://jai.dev.java.net/ JAI] library.<br/>MTBImageIO-Ext is simply the TIFF part of ImageIO-Ext with slight adjustments to remove dependency on the JAI library.
<br/>

== Additional resources ==

* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.
<br/>
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.

* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR>
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR>
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.
<br/>
Download the current release:
* Chipory binary [http://www.informatik.uni-halle.de/mitobo/downloads/Chipory.zip zip]
* self extracting installer for Windows [http://www.informatik.uni-halle.de/mitobo/downloads/chipory-setup.exe chipory-setup.exe]
Source code for Chipory is available upon request.
<br/>

'''Example images'''<br/>
* [http://www.informatik.uni-halle.de/mitobo/downloads/scratch_examples.zip Scratch assay images]

== Logo ==

* MiToBo logo as [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.pdf PDF] or [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.png PNG]

Downloads

2011-05-05T09:14:58Z

Posch: /* Additional resources */

__NOTOC__
== Requirements ==
MiToBo requires Java 1.6 or later.

The following external jars are needed to run MiToBo plugins and use the code:

* [http://rsbweb.nih.gov/ij/ ImageJ], Version 1.43
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
* [http://xstream.codehaus.org/ XStream], Version 1.3.1
* [https://jai-imageio.dev.java.net/ JAI ImageIO], Version 1.1

MiToBo relies on some libraries provided by the MiToBo project itself.<br>
If you download the MiToBo binaries you will find them included in the zip file.<br/>

The zip file contains the following jars:

* MTBImageIO-Ext, Version 0.9 (improved image I/O based on ImageIO-Ext):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff-0.9.jar jar]
** Source code [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff_src-0.9.zip zip]
** Alternatively, the [https://imageio-ext.dev.java.net/ ImageIO-Ext] library can be used, which depends on the [https://jai-imageio.dev.java.net/ JAI ImageIO] library and the [https://jai.dev.java.net/ JAI] library.<br/>MTBImageIO-Ext is simply the TIFF part of ImageIO-Ext with slight adjustments to remove dependency on the JAI library.
* MTBGraphml, Version 0.9 (MiToBo extensions for [http://graphml.graphdrawing.org/ graphML]):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbgraphml/mtbgraphml-0.9.jar jar]
* MTBXml, Version 0.9 (MiToBo XML I/O for several datatypes, based on XMLBeans):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbxml/mtbxml-0.9.jar jar]
<br/>

== Current release (v0.9)==
* MiToBo Binaries [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.tar.gz tar.gz] (includes MiToBo binaries, license information and additional jars provided by the MiToBo project)
* MiToBo Sources [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.tar.gz tar.gz] (includes only the MiToBo sources)
* MiToBo API [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.tar.gz tar.gz]
<br/>

== All versions of MiToBo ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Binaries
! Sources
! API
! Date
|-
| 0.9
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.tar.gz tar.gz]
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.tar.gz tar.gz]
| [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.tar.gz tar.gz]
| October 26, 2010
|}
<br/>

== Manual ==

Detailed information about MiToBo, its API and usage, can be found in the user and programmer manual.

* MiToBo-Manual, Version 0.9 [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual-0.9.pdf pdf]
<br/>

== Additional resources ==

* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.
<br/>
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.

* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR>
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR>
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.
<br/>
Download the current release:
[http
* Chipory binary [http://www.informatik.uni-halle.de/mitobo/downloads/Chipory.zip zip]
* self extracting installer for Windows [http://www.informatik.uni-halle.de/mitobo/downloads/chipory-setup.exe chipory-setup.exe]
Source code for Chipory is available upon request.
<br/>

== Logo ==

* MiToBo logo as [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.pdf PDF] or [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.png PNG]

Downloads

2010-10-28T14:08:04Z

Posch: /* Additional resources */

__NOTOC__
== Requirements ==
MiToBo requires Java 1.6 or later.

The following external jars are needed to run MiToBo plugins and use the code:

* [http://rsbweb.nih.gov/ij/ ImageJ], Version 1.43
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
* [http://xstream.codehaus.org/ XStream], Version 1.3.1
* [https://jai-imageio.dev.java.net/ JAI ImageIO], Version 1.1

MiToBo relies on some libraries provided by the MiToBo project itself.<br>
If you download the MiToBo binaries you will find them included in the zip file.

The zip file contains the following jars:

* MTBImageIO-Ext, Version 0.9 (improved image I/O based on ImageIO-Ext):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff-0.9.jar jar]
** Source code [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff_src-0.9.zip zip]
** Alternatively, the [https://imageio-ext.dev.java.net/ ImageIO-Ext] library can be used, which depends on the [https://jai-imageio.dev.java.net/ JAI ImageIO] library and the [https://jai.dev.java.net/ JAI] library.<br/>MTBImageIO-Ext is simply the TIFF part of ImageIO-Ext with slight adjustments to remove dependency on the JAI library.
* MTBGraphml, Version 0.9 (MiToBo extensions for [http://graphml.graphdrawing.org/ graphML]):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbgraphml/mtbgraphml-0.9.jar jar]
* MTBXml, Version 0.9 (MiToBo XML I/O for several datatypes, based on XMLBeans):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbxml/mtbxml-0.9.jar jar]

== Current release (v0.9)==
* MiToBo Binaries [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.tar.gz tar.gz] (includes MiToBo binaries, license information and additional jars provided by the MiToBo project)
* MiToBo Sources [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.tar.gz tar.gz] (includes only the MiToBo sources)
* MiToBo API [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.tar.gz tar.gz]

== All versions of MiToBo ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Binaries
! Sources
! API
! Date
|-
| 0.9
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.tar.gz tar.gz]
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.tar.gz tar.gz]
| [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.tar.gz tar.gz]
| October 26, 2010
|}

== Manual ==

Detailed information about MiToBo, its API and usage, can be found in the user and programmer manual.

* MiToBo-Manual, Version 0.9 [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual-0.9.pdf pdf]

== Additional resources ==

* '''MTBChisio''' - a graph visualization tool for displaying MiToBo history graphs

MTBChisio is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.

The zip or the tgz file below contains all necessary files. Download one of these and unpack it into a folder of your choice.

* To use MTBChisio on a Linux system with 32-bit architecture just type './MTBChisio.sh'.<BR>
* In case that your machine has a 64-bit architecture running Linux, call './MTBChisio_64.sh'.<BR>
* For Windows with 32-bit architecture a self extracting installer including an executable of mtbchisio is available.

Download the current release:
* MTBChisio binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbchisio/mtbchisio.tar.gz tar.gz] [http://www.informatik.uni-halle.de/mitobo/downloads/mtbchisio/mtbchisio.zip zip]
* self extracting installer for Windows [http://www.informatik.uni-halle.de/mitobo/downloads/mtbchisio-installer.exe mtbchisio-installer.exe]
Source code for MTBChisio is available upon request.

== Logo ==

* MiToBo logo as [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.pdf PDF] or [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.png PNG]

Downloads

2010-10-28T14:07:44Z

Posch: /* Additional resources */

__NOTOC__
== Requirements ==
MiToBo requires Java 1.6 or later.

The following external jars are needed to run MiToBo plugins and use the code:

* [http://rsbweb.nih.gov/ij/ ImageJ], Version 1.43
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
* [http://xstream.codehaus.org/ XStream], Version 1.3.1
* [https://jai-imageio.dev.java.net/ JAI ImageIO], Version 1.1

MiToBo relies on some libraries provided by the MiToBo project itself.<br>
If you download the MiToBo binaries you will find them included in the zip file.

The zip file contains the following jars:

* MTBImageIO-Ext, Version 0.9 (improved image I/O based on ImageIO-Ext):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff-0.9.jar jar]
** Source code [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff_src-0.9.zip zip]
** Alternatively, the [https://imageio-ext.dev.java.net/ ImageIO-Ext] library can be used, which depends on the [https://jai-imageio.dev.java.net/ JAI ImageIO] library and the [https://jai.dev.java.net/ JAI] library.<br/>MTBImageIO-Ext is simply the TIFF part of ImageIO-Ext with slight adjustments to remove dependency on the JAI library.
* MTBGraphml, Version 0.9 (MiToBo extensions for [http://graphml.graphdrawing.org/ graphML]):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbgraphml/mtbgraphml-0.9.jar jar]
* MTBXml, Version 0.9 (MiToBo XML I/O for several datatypes, based on XMLBeans):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbxml/mtbxml-0.9.jar jar]

== Current release (v0.9)==
* MiToBo Binaries [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.tar.gz tar.gz] (includes MiToBo binaries, license information and additional jars provided by the MiToBo project)
* MiToBo Sources [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.tar.gz tar.gz] (includes only the MiToBo sources)
* MiToBo API [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.tar.gz tar.gz]

== All versions of MiToBo ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Binaries
! Sources
! API
! Date
|-
| 0.9
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.tar.gz tar.gz]
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.tar.gz tar.gz]
| [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.tar.gz tar.gz]
| October 26, 2010
|}

== Manual ==

Detailed information about MiToBo, its API and usage, can be found in the user and programmer manual.

* MiToBo-Manual, Version 0.9 [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual-0.9.pdf pdf]

== Additional resources ==

* '''MTBChisio''' - a graph visualization tool for displaying MiToBo history graphs

MTBChisio is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.

The zip or the tgz file below contains all necessary files. Download one of these and unpack it into a folder of your choice.

* To use MTBChisio on a Linux system with 32-bit architecture just type './MTBChisio.sh'.<BR>
* In case that your machine has a 64-bit architecture running Linux, call './MTBChisio_64.sh'.<BR>
* For Windows with 32-bit architecture a self extracting installer including an executable of mtbchisio is available.

Download the current release:
* MTBChisio binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbchisio/mtbchisio.tar.gz tar.gz] [http://www.informatik.uni-halle.de/mitobo/downloads/mtbchisio/mtbchisio.zip zip]
* self extracting installer for Windows [http://www.informatik.uni-halle.de/mitobo/downloads/mtbchisio-windows.exe mtbchisio-installer.exe]
Source code for MTBChisio is available upon request.

== Logo ==

* MiToBo logo as [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.pdf PDF] or [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.png PNG]

Acknowledgements

2010-10-27T21:41:49Z

Posch:

__NOTOC__

* We thank the [http://www.eclipse.org Eclipse Foundation] for developing the Eclipse IDE, which greatly accelerates the development of MiToBo.<br/><br/>

* Many thanks to the workgroup of Prof. Dr. Stefan Hüttelmaier ([http://www.medizin.uni-halle.de/cfi/index.php?id=339 Department for Molecular and Cell Biology] of the<br/> Martin Luther University Halle-Wittenberg) for their scientific support and image acquisition.

== Contributors ==
* Stefan Posch
* Birgit Möller
* Oliver Greß
* Danny Misiak
* Markus Glaß

Acknowledgements

2010-10-27T21:41:20Z

Posch:

__NOTOC__

* We thank the [http://www.eclipse.org Eclipse Foundation] for developing the Eclipse IDE, which greatly accelerates the development of MiToBo.<br/><br/>

* Many thanks to the workgroup of Prof. Dr. Stefan Hüttelmaier ([http://www.medizin.uni-halle.de/cfi/index.php?id=339 Department for Molecular and Cell Biology]) of the<br/> Martin Luther University Halle-Wittenberg) for their scientific support and image acquisition.

== Contributors ==
* Stefan Posch
* Birgit Möller
* Oliver Greß
* Danny Misiak
* Markus Glaß

Downloads

2010-10-27T21:39:03Z

Posch: /* Additional resources */

__NOTOC__
== Requirements ==
MiToBo requires Java 1.6 or later.

The following external jars are needed to run MiToBo plugins and use the code:

* [http://rsbweb.nih.gov/ij/ ImageJ], Version 1.43
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
* [http://xstream.codehaus.org/ XStream], Version 1.3.1
* [https://jai-imageio.dev.java.net/ JAI ImageIO], Version 1.1

MiToBo relies on some libraries provided by the MiToBo project itself.<br>
If you download the MiToBo binaries you will find them included in the zip file.

The zip file contains the following jars:

* MTBImageIO-Ext, Version 0.9 (improved image I/O based on ImageIO-Ext):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff-0.9.jar jar]
** Source code [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff_src-0.9.zip zip]
** Alternatively, the [https://imageio-ext.dev.java.net/ ImageIO-Ext] library can be used, which depends on the [https://jai-imageio.dev.java.net/ JAI ImageIO] library and the [https://jai.dev.java.net/ JAI] library. MTBImageIO-Ext is simply the TIFF part of ImageIO-Ext with slight adjustments to remove dependency on the JAI library.
* MTBGraphml, Version 0.9 (MiToBo extensions for [http://graphml.graphdrawing.org/ graphML]):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbgraphml/mtbgraphml-0.9.jar jar]
* MTBXml, Version 0.9 (MiToBo XML I/O for several datatypes, based on XMLBeans):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbxml/mtbxml-0.9.jar jar]

== Current release (v0.9)==
* MiToBo Binaries [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.tar.gz tar.gz] (includes MiToBo binaries, license information and additional jars provided by the MiToBo project)
* MiToBo Sources [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.tar.gz tar.gz] (includes only the MiToBo sources)
* MiToBo API [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.tar.gz tar.gz]

== All versions of MiToBo ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Binaries
! Sources
! API
! Date
|-
| 0.9
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.tar.gz tar.gz]
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.tar.gz tar.gz]
| [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.tar.gz tar.gz]
| October 26, 2010
|}

== Manual ==

Detailed information about MiToBo, its API and usage, can be found in the user and programmer manual.

* MiToBo-Manual, Version 0.9 [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual-0.9.pdf pdf]

== Additional resources ==

* '''MTBChisio''' - a graph visualization tool for displaying MiToBo history graphs

MTBChisio is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.

The zip or the tgz file below contains all necessary files. Download one of these and unpack it into a folder of your choice.

* To use MTBChisio on a Linux system with 32-bit architecture just type './MTBChisio.sh'.<BR>
* In case that your machine has a 64-bit architecture running Linux, call './MTBChisio_64.sh'.<BR>
* For Windows with 32-bit architecture a self extracting installer including an executable of mtbchisio is available.

Download the current release:
* MTBChisio binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbchisio/mtbchisio.tar.gz tar.gz] [http://www.informatik.uni-halle.de/mitobo/downloads/mtbchisio/mtbchisio.zip zip]
* self extracting installer for Windows [http://www.informatik.uni-halle.de/mitobo/downloads/mtbchisio-windows.exe mtbchisio-windows.exe]
Source code for MTBChisio is available upon request.

== Logo ==

* MiToBo logo as [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.pdf PDF] or [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.png PNG]

Downloads

2010-10-27T16:23:55Z

Posch: /* Additional resources */

__NOTOC__
== Requirements ==
MiToBo requires Java 1.6 or later.

The following external jars are needed to run MiToBo plugins and use the code:

* [http://rsbweb.nih.gov/ij/ ImageJ], Version 1.43
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
* [http://xstream.codehaus.org/ XStream], Version 1.3.1
* [https://jai-imageio.dev.java.net/ JAI ImageIO], Version 1.1

MiToBo relies on some libraries provided by the MiToBo project itself.<br>
If you download the MiToBo binaries you will find them included in the zip file.

The zip file contains the following jars:

* MTBImageIO-Ext, Version 0.9 (improved image I/O based on ImageIO-Ext):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff-0.9.jar jar]
** Source code [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff_src-0.9.zip zip]
** Alternatively, the [https://imageio-ext.dev.java.net/ ImageIO-Ext] library can be used, which depends on the [https://jai-imageio.dev.java.net/ JAI ImageIO] library and the [https://jai.dev.java.net/ JAI] library. MTBImageIO-Ext is simply the TIFF part of ImageIO-Ext with slight adjustments to remove dependency on the JAI library.
* MTBGraphml, Version 0.9 (MiToBo extensions for [http://graphml.graphdrawing.org/ graphML]):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbgraphml/mtbgraphml-0.9.jar jar]
* MTBXml, Version 0.9 (MiToBo XML I/O for several datatypes, based on XMLBeans):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbxml/mtbxml-0.9.jar jar]

== Current release (v0.9)==
* MiToBo Binaries [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.tar.gz tar.gz] (includes MiToBo binaries, license information and additional jars provided by the MiToBo project)
* MiToBo Sources [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.tar.gz tar.gz] (includes only the MiToBo sources)
* MiToBo API [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.tar.gz tar.gz]

== All versions of MiToBo ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Binaries
! Sources
! API
! Date
|-
| 0.9
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.tar.gz tar.gz]
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.tar.gz tar.gz]
| [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.tar.gz tar.gz]
| October 26, 2010
|}

== Manual ==

Detailed information about MiToBo, its API and usage, can be found in the user and programmer manual.

* MiToBo-Manual, Version 0.9 [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual-0.9.pdf pdf]

== Additional resources ==

* '''MTBChisio''' - a graph visualization tool for displaying MiToBo history graphs

MTBChisio is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.

* To use MTBChisio just download the zip file, unpack it into a folder of your choice, enter the folder and type './MTBChisio.sh'.<BR>
* Note that MTBChisio relies on some architecture-depended code. In case that your machine has a 64-bit architecture, call './MTBChisio_64.sh'.<BR>
* For windows with 32-bit architecture a self extracting installer is available.

Download the current release:
* MTBChisio binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbchisio/mtbchisio.tar.gz tar.gz] [http://www.informatik.uni-halle.de/mitobo/downloads/mtbchisio/mtbchisio.zip zip]
* self extracting installer for windows [http://www.informatik.uni-halle.de/mitobo/downloads/mtbchisio-windows.exe mtbchisio-windows.exe]
Source code for MTBChisio is available upon request.

== Logo ==

* MiToBo logo as [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.pdf PDF] or [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.png PNG]

Downloads

2010-10-27T14:11:54Z

Posch: /* Additional resources */

__NOTOC__
== Requirements ==
MiToBo requires Java 1.6 or later.

The following external jars are needed to run MiToBo plugins and use the code:

* [http://rsbweb.nih.gov/ij/ ImageJ], Version 1.43
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
* [http://xstream.codehaus.org/ XStream], Version 1.3.1
* [https://jai-imageio.dev.java.net/ JAI ImageIO], Version 1.1

MiToBo relies on some libraries provided by the MiToBo project itself.<br>
If you download the MiToBo binaries you will find them included in the zip file.

The zip file contains the following jars:

* MTBImageIO-Ext, Version 0.9 (improved image I/O based on ImageIO-Ext):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff-0.9.jar jar]
** Source code [http://www.informatik.uni-halle.de/mitobo/downloads/mtbimageio/mtb-imageio-ext-tiff_src-0.9.zip zip]
** Alternatively, the [https://imageio-ext.dev.java.net/ ImageIO-Ext] library can be used, which depends on the [https://jai-imageio.dev.java.net/ JAI ImageIO] library and the [https://jai.dev.java.net/ JAI] library. MTBImageIO-Ext is simply the TIFF part of ImageIO-Ext with slight adjustments to remove dependency on the JAI library.
* MTBGraphml, Version 0.9 (MiToBo extensions for [http://graphml.graphdrawing.org/ graphML]):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbgraphml/mtbgraphml-0.9.jar jar]
* MTBXml, Version 0.9 (MiToBo XML I/O for several datatypes, based on XMLBeans):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbxml/mtbxml-0.9.jar jar]

== Current release (v0.9)==
* MiToBo Binaries [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.tar.gz tar.gz] (includes MiToBo binaries, license information and additional jars provided by the MiToBo project)
* MiToBo Sources [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.tar.gz tar.gz] (includes only the MiToBo sources)
* MiToBo API [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.tar.gz tar.gz]

== All versions of MiToBo ==

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
! Version
! Binaries
! Sources
! API
! Date
|-
| 0.9
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.tar.gz tar.gz]
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.tar.gz tar.gz]
| [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.zip zip] [http://www.informatik.uni-halle.de/mitobo/downloads/mitobo-api-0.9.tar.gz tar.gz]
| October 26, 2010
|}

== Manual ==

Detailed information about MiToBo, its API and usage, can be found in the user and programmer manual.

* MiToBo-Manual, Version 0.9 [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual-0.9.pdf pdf]

== Additional resources ==

* '''MTBChisio''' - a graph visualization tool for displaying MiToBo history graphs

MTBChisio is en extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.

To use MTBChisio just download the zip file, unpack it into a folder of your choice, enter the folder and type './MTBChisio.sh'.<BR>
Note that MTBChisio relies on some architecture-depended code. In case that your machine has a 64-bit architecture, call './MTBChisio_64.sh'.

Download the current release:
* MTBChisio binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbchisio/mtbchisio.tar.gz tar.gz] [http://www.informatik.uni-halle.de/mitobo/downloads/mtbchisio/mtbchisio.zip zip]
* self extracting installer for windows [http://www.informatik.uni-halle.de/mitobo/downloads/mtbchisio-windows.exe mtbchisio-windows.exe]
Source code for MTBChisio is available upon request.

== Logo ==

* MiToBo logo as [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.pdf PDF] or [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.png PNG]