Simple RGC: ImageJ Plugins for Counting Retinal Ganglion Cells and Determining the Transduction Efficiency of Viral Vectors in Retinal Wholemounts

Tiger Cross; Rasika Navarange; Joon-Ho Son; William Burr; Arjun Singh; Kelvin Zhang; Miruna Rusu; Konstantinos Gkoutzis; Andrew Osborne; Bart Nieuwenhuis

doi:10.5334/jors.342

Journal of Open Research Software (Jun 2021)

Simple RGC: ImageJ Plugins for Counting Retinal Ganglion Cells and Determining the Transduction Efficiency of Viral Vectors in Retinal Wholemounts

Tiger Cross,
Rasika Navarange,
Joon-Ho Son,
William Burr,
Arjun Singh,
Kelvin Zhang,
Miruna Rusu,
Konstantinos Gkoutzis,
Andrew Osborne,
Bart Nieuwenhuis

Affiliations

Tiger Cross: Department of Computing, Imperial College London, 180 Queen’s Gate, South Kensington, London, SW7 2AZ
Rasika Navarange: Department of Computing, Imperial College London, 180 Queen’s Gate, South Kensington, London, SW7 2AZ
Joon-Ho Son: Department of Computing, Imperial College London, 180 Queen’s Gate, South Kensington, London, SW7 2AZ
William Burr: Department of Computing, Imperial College London, 180 Queen’s Gate, South Kensington, London, SW7 2AZ
Arjun Singh: Department of Computing, Imperial College London, 180 Queen’s Gate, South Kensington, London, SW7 2AZ
Kelvin Zhang: Department of Computing, Imperial College London, 180 Queen’s Gate, South Kensington, London, SW7 2AZ
Miruna Rusu: Department of Computing, Imperial College London, 180 Queen’s Gate, South Kensington, London, SW7 2AZ
Konstantinos Gkoutzis: Department of Computing, Imperial College London, 180 Queen’s Gate, South Kensington, London, SW7 2AZ
Andrew Osborne: John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Forvie Site, Robinson Way, Cambridge, CB2 0PY
Bart Nieuwenhuis: John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Forvie Site, Robinson Way, Cambridge, CB2 0PY, UK; Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), Meibergdreef 47, 1105 BA, Amsterdam

DOI: https://doi.org/10.5334/jors.342
Journal volume & issue: Vol. 9, no. 1

Abstract

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‘Simple RGC’ consists of a collection of ImageJ plugins to assist researchers investigating retinal ganglion cell (RGC) injury models in addition to helping assess the effectiveness of treatments. The first plugin named ‘RGC Counter’ accurately calculates the total number of RGCs from retinal wholemount images. The second plugin named ‘RGC Transduction’ measures the co-localisation between two channels making it possible to determine the transduction efficiencies of viral vectors and transgene expression levels. The third plugin named ‘RGC Batch’ is a batch image processor to deliver fast analysis of large groups of microscope images. These ImageJ plugins make analysis of RGCs in retinal wholemounts quick, consistent, and less prone to unconscious bias by the investigator. The plugins are freely available from the ImageJ update site https://sites.imagej.net/Sonjoonho/.

Published in Journal of Open Research Software

ISSN: 2049-9647 (Online)
Publisher: Ubiquity Press
Country of publisher: United Kingdom
LCC subjects: Science: Mathematics: Instruments and machines: Electronic computers. Computer science: Computer software
Website: http://openresearchsoftware.metajnl.com/

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