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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: ActinAnalyzer for the quantification of actin filament structures in microscopy images Cell Migration Analyzer for analyzing single cell migration from time lapse image sequences Neuron Analyzer for the segmentation of neurons in microscope images Scratch Assay Analyzer for analyzing microscope images from collective cell migration experiments 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.

Download You can download MiToBo version 1.5 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 June 2015: Version 1.5 of MiToBo has been released. This release ships with the new MTB Cell Counter plugin for semi-automatic segmentation and annotation of cell images. Details about the plugin (derived from the CellCounter plugin written by Kurt de Vos) can be found on the MTB Cell Counter wikipage and in the corresponding paper of Franke et al., "The 'MTB Cell Counter' a versatile tool for the semi-automated quantification of sub-cellular phenotypes in fluorescence microscopy images. A case study on plastids, nuclei and peroxisomes.", which just appeared in the Journal of Endocytobiosis and Cell Research, (26) 31-42, 2015, to be found here. March 2015: Version 1.4.3 of MiToBo has been released. The most important new feature is support for parameter callbacks. Based upon Alida in version 2.5 and its support for callbacks it is now possible to update the values of operator parameters depending on changes of other parameters. In addition, callbacks enable dynamic changes of the set of parameters an operator owns and dynamic re-configuration of the graphical interfaces, respectively. January 2015: Version 1.4.2 of MiToBo has been released. December 2014: Version 1.4.1 of MiToBo has been released. MiToBo and its base Alida will be presented at the OGRW 2014, which is the 9th Open German-Russian Workshop on Pattern Recognition and Image Understanding. The workshop is taking place from 1st to 5th December in Koblenz/Germany. The title of our contribution is Design and Implementation of the Alida Framework to Ease the Development of Image Analysis Algorithms. July 2014: Version 1.4 of MiToBo has been released. The new version ships with new tools for the quantification of actin structures in microscopy images of cells, the ActinAnalyzer2D, and a new operator for detecting Xylems in images of cross sections of wood. January 2014: Version 1.3 of MiToBo has been released. The project management of MiToBo switched to Maven, from now on you can download MiToBo releases from our Maven server. The new release ships with a new version of the Neuron Analyzer 2D and includes the first release of the CellMigrationAnalyzer, a tool for cell tracking and migration analysis. In addition, in the MiToBo core several bugs were fixed, an illumination correction and a top-hat based contrast enhancement were added.

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.