rhizoTrak

Installation

To install there are two options

1. Using Fiji and the MiToBo update site
   • Download Fiji and follow the installation instructions of Fiji.
   • Run Fiji by opening the application file provided in the Fiji directory (on Windows/MacOS) or by executing the available shell scripts (Linux).
   • Navigate to the update function via Help → Update... from the Fiji menu and click the button Manage update sites in the ImageJ Updater.
   • Find the update site MiToBo and check it active and click the button Close.
   • Fiji will now display a message that there are some new files to install:
     click the button Apply changes to install the files,
   • Restart Fiji and rhizoTrak will be available as a new plugin

2. From source code

   This is mainly of interest for those who want to modify the code

   • Clone the rhizoTrak git repository from github.
     (Note: this repository is a fork of the TrakEM2 repository)
   • Check out the branch rhizoTrak.
   • Execute the maven goal package which creates the rhizoTrak jar in the directory target.
     The name of the jar will be rhizoTrak_???.jar, where ??? depends on the version of the artefact.
   • This jar needs to be located in the plugins directory of a ImageJ or Fiji installation, and all dependencies of rhizoTrak in the corresponding jarsdirectory.
     The easiest way to achieve this is to install rhizoTrak using Fiji and the MiToBo update site (see above) and copy the rhizoTrak jar to its plugins directory.

Licence

rhizoTrak is free software: you can use, redistribute and/or modify it under the terms of the GNU General Public License version 3 as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.