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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 and its new release ImageJ 2.0.
MiToBo ships with a set of operators ready to be used as plugins in ImageJ. They focus on the analysis of biomedical images acquired by various types of microscopes.
Some of MiToBo's operators are for example these ones:

• Scratch Assay Analyzer for analyzing microscope images from cell migration experiments
• Neuron Analyzer for the segmentation of neurons in microscope images
• Snake Optimizer for performing image segmentation based on explicit active contours

Furthermore, MiToBo offers a user- and programmer friendly framework for developing algorithms that have properties not available in ImageJ,
however, still provides full compatibility to all ImageJ features.

MiToBo completely separates the implementation of image processing algorithms from potential user interfaces.
Moreover, MiToBo builds on top of 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.

Current release

You can download MiToBo version 1.2 here.
You can find the API documentation for this release here.
Furthermore MiToBo offers you a user and programmer guide which you can download here.

Latest News

March 2013

• Version 1.1 of MiToBo has been released.
  

MiToBo has undergone several internal enhancements mainly dedicated to the stability and usability of the core and its user interfaces.
In addition, MiToBo now includes the Neuron Analyzer which is an application for the analysis of 2D images of neuronal cells.
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.
  

Most important new feature is the graphical programming editor "Grappa" which is released in this new MiToBo version!
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.
Grappa is available as plugin for ImageJ. Note that the editor will be presented in a talk at the ImageJ User & Developer Conference 2012.
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.
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!

News Archive

The news archive can be found here.

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.

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.