The Genome Damage and Stability Centre (GDSC) plugins are a collection of analysis programs for microscopy images including colocalisation analysis and peak finding.
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; and alignment of manually marked points to peak maxima.
See the FindFoci User Manual for full details.
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.
See the Colocalisation User Manual for full details.
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.
The GDSC 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 update site. All the plugins will appear under the 'Plugins > GDSC' menu.
Some plugins require on the following 3rd party updates sites: ImageScience; TrackMate
The source code is accessed using git and built using Maven.
The code depends on the gdsc-test, gdsc-ij-parent and gdsc-core artifacts so you will have to install these to your local Maven repository before building:
-
Clone the required repositories
git clone https://github.com/aherbert/gdsc-test.git git clone https://github.com/aherbert/gdsc-ij-parent.git git clone https://github.com/aherbert/gdsc-core.git git clone https://github.com/aherbert/gdsc.git -
Build the code and install using Maven
cd ../gdsc-test mvn install cd ../gdsc-ij-parent mvn install cd ../gdsc-core mvn install cd ../gdsc mvn packageThis will produce a gdsc_-[VERSION].jar file in the target directory. Dependencies can be copied into the target/dependencies directory using:
mvn dependency:copy-dependencies -
Installation into a Fiji/ImageJ2 install can be performed using the scijava maven goal to populate the application:
cd gdsc-smlm-ij mvn scijava:populate-app -Dscijava.app.directory=/usr/local/fiji cd ..where
/usr/local/fijiis the root directory of the ImageJ install. -
Manual installation must copy the gdsc-smlm-ij_* jar into the plugins directory of ImageJ.
Copy the dependencies into the plugins directory (or onto the Java classpath). Note that the Maven package routine puts all dependencies into the target/dependencies directory even if they are not required by the SMLM code (it does not check what functions are actually used by the code). The libraries you will need are:
gdsc-core gdsc-core-ij beansbinding commons-math3 commons-lang3 commons-rng-client-api commons-rng-core commons-rng-simple commons-rng-sampling imagescience Image_5D fastutil-coreThis excludes the 3D_Viewer and TrackMate functionality. View the dependencies of these using:
mvn dependency:tree -
The plugins will now appear under the 'Plugins > GDSC' menu in ImageJ.
Maven can be used to run ImageJ using a profile defined in the gdsc-ij-parent POM:
mvn -P run-imagej
This profile compiles all classes and then executes ImageJ with the appropriate Java classpath. A default plugin can then be run from the ImageJ Plugins menu to load the plugins defined in the project's ImageJ plugins.config file.
Note: This file is normally detected by ImageJ when loading plugin jar files to identify the available plugins. The default plugin has been written to duplicate this functionality by reading the configuration and populating the ImageJ menu.
The gdsc-smlm code was developed using the Eclipse IDE.
Details of how to open the source code with Eclipse can be found in the eclipse folder.
See LICENSE
Alex Herbert