GDSC ImageJ Plugins

The GDSC ImageJ plugins are a collection of analysis programs for microscopy images including colocalisation analysis and peak finding (FindFoci).

All the plugins are distributed using an ImageJ2/Fiji update site. See the installation notes below.

Find Foci

The Find Foci plugins allow the identification of peak intensity regions within 2D and 3D images. The tools provide: the automated and semi-automated labelling of peaks; comparison of marked points between images; optimisation of algorithm parameters; batch analysis of images; and alignment of manually marked points to peak maxima.

Colocalisation Analysis

The GDSC Colocalisation plugins provide various tools to perform colocalisation analysis. The tools provide: thresholding for N-dimensional images for signal identification; correlation and overlap coefficient analysis; and colocalisation significance testing.

Utility Plugins

The GDSC plugins provide various utility tools for image analysis. The tools include: thresholding and mask generation; difference of Gaussians for contrast enhancement; stack synchronisation for simultaneous image viewing; and image alignment.

Single Molecule Localisation Microscopy plugins

The GDSC Single Molecule Localisation Microscopy (SMLM) plugins provide various tools for use in super-resolution microscopy (STORM; PALM). The tools include spot fitting; image reconstruction; and clustering.

Installation Notes

Using ImageJ2/Fiji

The GDSC and SMLM plugins are distributed using an ImageJ2/Fiji update site.

To install the plugins using Fiji (an ImageJ distribution) just follow the instructions How_to_follow_a_3rd_party_update_site and add the GDSC and/or the GDSC SMLM2 update site.

All the plugins will appear under the 'Plugins > GDSC' or 'Plugins > GDSC SMLM' menus.


  1. The GDSC SMLM update site is for the previous version. It cannot be installed concurrently with either the GDSC or the GDSC SMLM2 plugins.
  2. The Edge Mask Creator plugin in the GDSC plugins depends on the Image Science library. If you wish to use this 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.

Using ImageJ (version 1)

If you do not want to use ImageJ2/Fiji to get the plugins then 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 should download the latest Jar files in the 'jars' and 'plugins' directories.

Note: The files will have a suffix that includes the timestamp when it was uploaded (e.g. .jar-20140619121126). You must change this file suffix to .jar otherwise ImageJ will not recognise the file. You can do this by right-clicking the file link and choosing 'Save as...' or you can rename the file after it has downloaded.

You will also need to install the additional dependencies (which are already included in Fiji). Use the 'Download' links below to obtain the packages:

Package Description GDSC SMLM
Apache Commons Math 3 Contains Maths routines
Apache Licence, V2
Download Y Y
Image Science support library A Java library for image analysis
© Erik Meijering
Required for the Edge Mask Creator plugin
Download Optional

Remember to put all the files in the ImageJ plugins directory.

Source Code

The source code for the GDSC plugins can be found on GitHub:

There is also a super-project that includes all the other projects as modules:

For further details on GDSC ImageJ plugins please contact Alex Herbert.