Simple RGC (Retinal Ganglion Cells)

Overview

This repository contains the source code for Simple RGC — an ImageJ plugin that provides tools for cell counting, segmentation, and percentage colocalization calculation of retinal ganglion cells.

It was originally developed in collaboration with scientists at Cambridge Neuroscience for the third year software engineering project at Imperial College London.

Installation and Usage

The plugin can be added via the update site:

https://sites.imagej.net/Sonjoonho/

This will install the plugin itself, along with the Kotlin standard library which it depends upon. You must have the Fiji and Java 8 update sites enabled in order for this plugin to work. If you are using Fiji, these should be enabled by default, so don't worry.

Alternatively, the .jar can be compiled using Maven and installed in the jars/ directory under your ImageJ/Fiji installation. However, this requires manual installation of dependencies.

After installing, the plugin can be found in the ImageJ menu under Plugins > Simple RGC.

Developing

We have provided convenient entry points for running ImageJ and the plugin directly from your IDE in RGCCounter.kt, RGCTransduction.kt and RGCBatch.kt. If you need more advanced features of Fiji (e.g. opening LIF files), you can use Maven to install the plugin directly to your Fiji installation.

mvn install -Dscijava.app.directory=/home/joon/.local/share/Fiji.app -Dscijava.deleteOtherVersions=true

Caveats

Make sure your project is configured to JDK 1.8.
If you get an error like attempted duplicate class definition: "ij/ImagePlus", a workaround is to add the line -javaagent:/home/joon/.m2/repository/net/imagej/ij1-patcher/0.12.9/ij1-patcher-0.12.9.jar=init

to your JVM arguments — the exact path will be given in the error message.
If you get an error to do with the CellSegmentationService not being in the Context, this can often be solved by running mvn clean before re-building.

Citation

If you use this plugin or source code in your research paper, please use this BibTeX citation:

@article{SimpleRGC,
  doi = {10.5334/jors.342},
  url = {https://doi.org/10.5334/jors.342},
  year = {2021},
  publisher = {Ubiquity Press,  Ltd.},
  volume = {9},
  author = {Tiger Cross and Rasika Navarange and Joon-Ho Son and William Burr and Arjun Singh and Kelvin Zhang and Miruna Rusu and Konstantinos Gkoutzis and Andrew Osborne and Bart Nieuwenhuis},
  title = {Simple {RGC}: {ImageJ} Plugins for Counting Retinal Ganglion Cells and Determining the Transduction Efficiency of Viral Vectors in Retinal Wholemounts},
  journal = {Journal of Open Research Software}
}

or alternatively:

Cross T, Navarange R, Son J-H, Burr W, Singh A, Zhang K, Rusu M, Gkoutzis K, Osborne A, Nieuwenhuis B 2021 Simple RGC: ImageJ Plugins for Counting Retinal Ganglion Cells and Determining the Transduction Efficiency of Viral Vectors in Retinal Wholemounts. Journal of Open Research Software, 9: 15. DOI: https://doi.org/10.5334/jors.342

Status

Simple RGC is still under development, and many aspects of it are subject to change. Pull Requests and Issues are welcomed.