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MiToBo - A microscope image analysis toolbox

What is MiToBo?
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.

Visit MiToBo also at...

Imagej-128.png Logo.png Logo-blue.png Git.png ImageJ Docu Wiki OMIC Tools GitHub

How to get MiToBo?

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

  • 07/2018: We have added a new page Tips and Tricks here in the Wiki where you can find information on how to accomplish common tasks like manually labeling images.
  • 05/2018: MiToBo 1.8.10 and MiToBo-Plugins 1.8.10 have been released shipping with new operators for biofilm analysis.
  • 05/2018: MiToBo 1.8.9 and MiToBo-Plugins 1.8.9 have been released mainly featuring an update of our MTBCellCounter tool.
  • 01/2018: MiToBo 1.8.7 and MiToBo-Plugins have been released mainly featuring improved support for commandline data I/O of operators.
    Note that from now on MiToBo releases are PGP signed. MiToBo's public key for verification can be found on public key servers, e.g., at
  • 09/2017: MiToBo and MiToBo-Plugins 1.8.6 have been released! The new release includes PaCeQuant , our new tool for high-throughput quantification of pavement cell shape.

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.

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

Bug reports & Feature requests
Bug reports and feature requests can be submitted as issues on Github or by mail to Before reporting a new bug or requesting a new feature, please check if that bug has already been submitted.