Installation

General remarks

There are two common ways to work with MiToBo:

• just using the operators included in MiToBo for improving your work and easing image processing tasks, e.g., via ImageJ or Fiji
• using the MiToBo API to write operators, plugins and other image analysis applications on your own

The functionality of MiToBo is best used from within ImageJ or Fiji. In case that you aim to use MiToBo for your own development, you need to download the binaries explicitly. The actual installation instructions differ in some parts depending on which way of using MiToBo you have in mind.
Below we will first outline more details about the installation steps required for simply using MiToBo's operators in ImageJ and Fiji, and then provide some notes regarding the binary zip file. Finally we will present some details for using MiToBo's API with your own code.

The recommended way to install and run MiToBo and its operators/plugins is via Fiji!
MiToBo has its own Fiji update site named "MiToBo".

http://sites.imagej.net/MiToBo

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

Note that for some plugins (e.g., PaCeQuant) also the "Biomedgroup" update site needs to be activated.

Using MiToBo with Fiji

Since release 1.5 MiToBo features a Fiji update site and the easiest way to use MiToBo's operators and plugins is to enable the update site in your Fiji installation.
The MiToBo update site is

http://sites.imagej.net/MiToBo

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

Important notices:

• Occasionally MiToBo operators crash when run from within Fiji. The reason for this behaviour are most of the time conflicting jar archives delivered with the Fiji distribution.
  We figured out that particularly the jar file
  • jars/bio-formats/formats-common-5.1.x.jar
  often causes such trouble. Thus, if you encounter problems running MiToBo operators, please try to locally delete or uninstall the abovementioned jar archive from your local Fiji installation and then re-run the MiToBo operator.
• For some of our operators special issues exist and require special treatment:
  • CellBoundaryExtractor2D: there are version conflicts with regard to the JGraphT library used by this operator and also by default included in every Fiji distribution; please refer to installation instructions on the webpage of the operator for a workaround

Using MiToBo with ImageJ

Important Note: These instructions refer to ImageJ 1.

General remarks:
For using MiToBo with ImageJ it is the easiest to download the latest distribution zipfile (*-bin.zip) from

https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/

which already includes all dependencies and ships with some scripts to run MiToBo's operators and plugins out of the box.

Linux

Using MiToBo with a Linux operating system.

Windows

Using MiToBo with a Windows operating system.

The MiToBo Binary Zip File

To get the current release of MiToBo (e.g. for using it as a library for your own developments) either download and extract the MiToBo Binary zip file from https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo/ or clone our Github repository https://github.com/mitobo-hub/mitobo.
You will find the following structure of directories and files:

• lib - includes nesessary libaries for Linux and Windows
• licences - includes MiToBo license and licences for other software used by MiToBo
• macros - includes the MiToBo macro toolset
• plugins - includes MiToBo jar and other jars used by MiToBo
• testimages - some sample images
• MiToBo-Guide-1.0.pdf - the user and programmer guide for MiToBo
• oprunner.sh - shell script to run MiToBo operators from commandline (Linux only)
• run.sh - shell script to run ImageJ with MiToBo (Linux only)
• README - with basic information

Using MiToBo's APIs

To use the API of MiToBo and benefit from MiToBo's functionality in your own code you just need to make the jar archive to be found in the zip file available on your classpath. In addition, make sure that all jar archives MiToBo depends on and which are listed on the Download page are also in your classpath.
Note that the jars are also included in the MiToBo's binary zip file, thus, you don't need to download them manually.