1. Installation

The plugin is designed to run within ImageJ. This can be the original ImageJ (version 1) or any modified version of ImageJ such as ImageJ2 or Fiji.

1.1. Install using ImageJ2/Fiji

The GDSC plugins are distributed using an ImageJ2/Fiji update site. This allows the plugins to be easily installed and kept up-to-date. To install the plugins using Fiji just follow the instructions here:

Add the GDSC update site. Fiji will automatically check for a new version during start-up and install it if desired.

All the plugins will appear under the Plugins > GDSC menu.

The Edge Mask and Laplacian of Gaussian plugins, and the Laplacian of Gaussian output of the Scale Space plugin, depend on the Image Science library. If you wish to use these then you must also enable the ImageScience update site. This was previously installed by default within Fiji but changed to an optional component in August 2016.

1.2. Install using ImageJ version 1

The plugin is designed to run within ImageJ. You can obtain the latest version of ImageJ from:

To get the plugins you can download the latest jar files from the update site and put them in your ImageJ plugins folder. The jars can be found here:

You will also need to install the additional libraries listed in the table below. These are already included in Fiji so are not on the update site. A few plugins require the Image Science 3 library. The libraries can be obtained from Maven Central; for example:

Place all of the following jar files into the ImageJ plugins directory:

Jar File

Description

beansbinding

Contains routines to bind Java bean properties (used by the FindFoci GUI).

commons-lang3

Contains Java language utility routines.

commons-math3

Contains math routines.

commons-numbers-*

Contains number routines.

commons-rng-*

Contains random number routines.

commons-statistics-*

Contains statistics routines.

gdsc-core

Contains the GDSC core library.

gdsc-core-ij

Contains the GDSC core ImageJ library.

fastutil-core

Library for type-specific Java collections.

guava, failureaccess

Contains Google core libraries for Java.

imagescience

Contains image analysis routines.

Image_5D

Contains routines for 5D images (used by imagescience).

quickhull3d

A java implementation of the QuickHull algorithm.

slf4j-api

Contains the Simple Logging Facade for Java (used by quickhull3d).

The plugins will be visible under the Plugins > GDSC menu.

1.3. Toolsets

The plugins jar contains ImageJ macro toolsets that add buttons to the ImageJ toolbar to run some of the plugins. The toolset files are not installed automatically. To use a toolset, extract the file from the plugins jar (using an archiving utility; the jar is a zip file) and place it in the ImageJ/macros/toolsets directory. The toolset can then be selected using the More Tools menu button (>>, the last button on the ImageJ toolbar).

The toolset files are located in the jar in the directory uk/ac/sussex/gdsc/ij/macros/toolsets:

Toolset

Description

Spot Distance Tools.txt

Buttons to run the Spot Distance plugin; run the plugin with extra options; redo the analysis using the same parameters; and undo the last analysis (delete the last result).

Translocation Finder Tools.txt

Buttons to run the Translocation Finder plugin; and to add the Translocation Finder (Tool) to the toolbar.