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Quick Start

The easiest and fastest way to install and run MiToBo is to activate MiToBo's update site in Fiji:

To enable this site in your Fiji installation refer to the Fiji documentation.

For installing MiToBo this way you need to activate the following site:

  • MiToBo

For some operators additional sites are required:

  • Biomedgroup (e.g., for PaCeQuant)

More details how to install and run MiToBo can be found on our Installation page.

Downloads and Releases

The current release of the MiToBo core distribution and also of the extended MiToBo-Plugins distribution is 2.3.1.

Since release 1.3 we support Maven for managing MiToBo's resources.
You can download the MiToBo distributions as well as the Maven artifacts from our Maven server:

There are two MiToBo distributions available:

  • MiToBo:
    this package contains the core of MiToBo, i.e. all operators, the MiToBo runners for operator execution and also Grappa;
    not included are the plugins to run MiToBo from within ImageJ 1.x, hence, this distribution is mainly for stand-alone usage of MiToBo and development purposes
  • MiToBo-Plugins:
    this package contains the complete MiToBo distribution, some special plugins like the MTB Cell Counter, and in addition some ImageJ plugins to run MiToBo operators from within ImageJ; you should download the MiToBo-Plugins distribution if you like to use MiToBo with ImageJ

Since release 1.8 MiToBo's implementation requires at least Java 1.8.

At the bottom of this page additional files are available for download:

  • Old distributions: complete distributions including all dependencies, scripts, documentation, etc.
  • Binaries only: only the jar archives, no dependencies neither documentation
  • APIs: Javadoc APIs

Maven Project Template

Using MiToBo as a library for own developments can best be done by making use of Maven.
Particularly, Maven automatically resolves all dependencies which otherwise would have to be installed manually.

For getting started with MiToBo and Maven a project template is provided:

Maven project template [zip]

The project is readily configured and you can immediately start with own developments.
It also contains a demo operator showing the basic usage of MiToBo data types and operators on the code level.

Make sure that you have installed Maven and a Java Develpoment Kit (JDK) in version 1.8 or higher.
You can check the Java version by running 'mvn --version' from command line.
If an older Java version is used, let the 'JAVA_HOME' environment variable point to a folder containing a more recent JDK.

You can run Maven directly from within the extracted folder. Alternatively the Maven template project can easily be imported into an IDE like Eclipse.
The zip file contains a README file containing more information about installing and configuring the project template.


Detailed information about MiToBo, its API and usage, can be found in MiToBo's User and Programmer Guide.

  • MiToBo-Guide, Version 1.0 pdf

Additional resources

  • Chipory - a graph visualization tool for displaying MiToBo history graphs
    Chipory is an extended version of the Chisio software developed at the Bilkent University in Turkey.

The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.

  • To use Chipory on a Linux system with 32-bit architecture just type './'.
  • In case that your machine has a 64-bit architecture running Linux, call './'.
  • For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.

Download the current release:

Source code for Chipory is available upon request.

Earlier releases of MiToBo (< 1.5)

Since release 1.3 MiToBo's resources are available from our Maven archive server: [1]
Binaries, sources and documentation for versions older than the current release, but at least of version 1.3 or newer can be found there.
All other releases can be accessed via the list below.

Version Binaries Sources API Date
1.4.3 zip jar jar March 31st, 2015 (Support for callbacks)
1.4.2 zip jar jar Jan 7th, 2015
1.4.1 zip jar jar Dec 1st, 2014
1.2 zip zip zip May 17th, 2013
1.1 zip zip zip March 1st, 2013
1.0.5 zip zip zip October 23rd, 2012
1.0.1 zip zip zip July 6th, 2012
1.0.0 zip zip zip April 26th, 2012
0.96 zip zip zip September 01, 2011
0.95 zip zip zip June 08, 2011 (updated June 22nd, 2011)
0.9 zip tar.gz zip tar.gz zip tar.gz October 26, 2010

Requirements (for MiToBo < 1.3)

MiToBo requires Java 1.6 or later.

Note: Java 1.7 is currently not fully supported!

The following external jars are needed to run MiToBo plugins and use the code.
Note that the binary zip file already includes all jars required, there is no need for explicit download!

MiToBo depends on the following external jars:

  • JAI ImageIO, Version 1.1 (only required for MiToBo 0.9)

Project internal libraries

MiToBo also relies on some libraries provided by the MiToBo project itself.
In particular XML schemes for representing the history graphs and MiToBo's online help are included in separate jar archives.

You do not need to download these libraries explicitly. If you download the binary zip file all jars and libraries are already included.

The MiToBo internal archive files included in the zip file are the following ones:

  • ALDGraphml, Version 1.0.0 (Alida extensions for graphML):
  • MTBXml, Version 1.0.0 (MiToBo XML I/O for several datatypes, based on XMLBeans):
  • MiToBo-Help, Version 1.0.0 (MiToBo JavaHelp pages):

The following library is only required for MiToBo-0.9:

  • MTBImageIO-Ext, Version 0.9 (improved image I/O based on ImageIO-Ext):
    • Binary jar
    • Source code zip
    • Alternatively, the ImageIO-Ext library can be used, which depends on the JAI ImageIO library and the JAI library.
      MTBImageIO-Ext is simply the TIFF part of ImageIO-Ext with slight adjustments to remove dependency on the JAI library.