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MiToBo - A microscope image analysis toolbox

The Microscope Image Analysis Toolbox MiToBo is an extension for the widely used image processing application ImageJ.
MiToBo ships with a set of ready-to-use plugins that focus on the analysis of biomedical images acquired by various
types of microscopes.
Furthermore, MiToBo offers a framework for developing plugins that have properties not available in ImageJ.
Especially, MiToBo completely separates the implementation of image processing algorithms from the user interface, but
still offers full compatibility to all ImageJ features.
The underlying concept of operators which link the processing steps to a directed graph structure, allows, for example
the automatic documentation of the whole analysis process that lead from the input image to the analysis results.

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.
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.
The new release ships with new quick start plugins for the SnakeOptimizer and ScratchAssayAnalyzer operators.
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 download page for jars and sources.

New release of chipory ready for download

April 2012

Version 1.0.0 of MiToBo has been released.
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 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.
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 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:

• ImageJ, Version 1.46g
• XMLBeans, Version 2.5.0
• XStream, Version 1.3.1
• Loci Tools, Version 4.3.3
• Jama, Version 1.0.2
• JavaHelp, Version 2.0_05
• LIBSVM, Version 3.1

Finally some MiToBo internal jars are required (have a look at the download page for more details):

• ALDGraphml
• mtbxml
• MiToBo-Help
• Alida-SezPoz.

... and for the snakes you require C++ native libs:

• 32-bit Linux lib, 64-bit Linux lib, 32-bit Windows 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.
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 download page for jars and sources.

June 2011

Version 0.9.5 of MiToBo has just been released!
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 GNU General Public License version 3 or (at your option) any later version as published by the Free Software Foundation.

Current release

You can download MiToBo version 0.9.6 here.
You can find the API documentation for this release here.
Furthermore MiToBo offers you a user and programmer manual you can download here.

Bug reports & Feature requests

Bug reports and feature requests can be submitted via the MiToBo bugtracking system or by mail to mitobo@informatik.uni-halle.de.
Before reporting a new bug, please check if that bug has already been submitted in the report list.