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MiToBo - A microscope image analysis toolbox

What is MiToBo?
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. MiToBo is implemented as extension for the widely used image processing application ImageJ/Fiji and its new release ImageJ 2.0. All functions, operators and plugins of MiToBo are ready to be directly used as plugins in ImageJ and Fiji.

Highlight operators and tools in MiToBo

MiToBo logo CytoskeletonAnalyzer2D.png
CytoskeletonAnalyzer2D for the quantification of cytoskeleton structural patterns in microscopy images with texture measures
MiToBo logo PaCeQuant.png
PaCeQuant for quantifying the morphology and shape characteristics of cells
Neuron Analyzer for the segmentation of neurons in microscope images
Cell Migration Analyzer for analyzing single cell migration from time lapse image sequences
GFP U2OS overlay.png
Scratch Assay Analyzer for analyzing microscope images from collective cell migration experiments

MiToBo for developers 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 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.