aherbert / gdsc-super

Contains all the GDSC ImageJ repos as submodules

GDSC-Super

Contains all the GDSC ImageJ repos as submodules.

This project can be used to checkout and build all the code required to install the GDSC ImageJ and GDSC SMLM ImageJ plugins into a version of ImageJ.

Installation from source

The source code is accessed using git and built using Maven.

1. Clone the GDSC Super repository

    git clone --recursive https://github.com/aherbert/gdsc-super.git
   

2. Build the code and package using Maven

    cd gdsc-super
    git submodule update --remote
    mvn package -DskipTests -Djavadoc.skip
   

   This will create a jar file for each module into a directory named [module]/target. The dependencies will be put into the [module]/target/dependencies directory.

   Note that the Maven package routine puts all dependencies into the [module]/target/dependencies directory even if they are not required by the GDSC code (it does not check what functions are actually used by the code).

3. If you are using ImageJ the main jars and dependencies are copied to the plugins directory.

    export PREFIX=/usr/local/imagej
   
    cp gdsc/target/gdsc-ij_*jar ${PREFIX}/plugins
    cd gdsc/target/dependencies
    cp gdsc-analytics* gdsc-core* commons-rng* quickhull3d* fastutil-core* commons-math3* beansbinding* ${PREFIX}/plugins
    cd ../../..
   
    cp gdsc-smlm/gdsc-smlm-ij/target/gdsc-smlm-ij_*jar ${PREFIX}/plugins
    cd gdsc-smlm/gdsc-smlm-ij/target/dependencies
    cp gdsc-analytics* gdsc-core* commons-rng* quickhull3d* fastutil-core* commons-math3* JTransforms* JLargeArrays* ejml* xstream* mxparser* protobuf-java*  mfl-core* commons-lang3* gdsc-smlm* ${PREFIX}/plugins
    cd ../../../..
   

4. If you are using Fiji then use the scijava:populate-app goal to copy the main jars and dependencies. The main plugin jars containing an underscore (_) must be moved to the plugins directory as they are ImageJ v1 plugins.

    export PREFIX=/usr/local/fiji
   
    cd gdsc
    mvn scijava:populate-app -Dscijava.app.directory=${PREFIX}
    cd ..
   
    cd gdsc-smlm
    mvn scijava:populate-app -Dscijava.app.directory=${PREFIX}
    cd ..
   
    mv ${PREFIX}/jars/gdsc*_*jar ${PREFIX}/plugins/
   

5. The plugins will now appear under the 'Plugins > GDSC' and 'Plugins > GDSC SMLM' menus in ImageJ.

Developers

The code was developed using Eclipse. Each submodule contains an eclipse directory with notes on how to set-up the code within Eclipse including code formatting rules.

Import using 'Import...' then 'Maven > Existing Maven Projects' and select the root gdsc-super folder.

To download each of the submodule repositories then use the utility script, e.g.

    ./checkout.sh ../gdsc

Background

Developed at the Genome Damage and Stability Centre, University of Sussex.

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

The GDSC Single Molecule Light Microscopy (SMLM) ImageJ plugins provide various tools for single molecule localisation analysis. This includes PALM, STORM and other single molecule microscopy methods.

The code is split into several repositories. This super-project contains all the GDSC ImageJ repositories as submodules.