FunGal Finder
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Fiji/ImageJ macro code to analyse Coccidioides fungal spherules. Macro was developed by Cameron J Nowell of Monash University (cameron.nowell@monash.edu) in collaboration with Ben Croker (bcroker@uscd.edu) This code relies on a trained from scratch CellPose model that was trained to recognise spherules and reject other surrounding cells Code will take individual single channel TIFF files (ideally 16-bit) captured on an Incucyte Imaging System using autofluorescence and analyse the following parameters - The number of Spherules - The area of each spherule, logged as a per well avergae an indivudual objects - The standard deviation of spherule areas in a well Requirements to run - Standard install of the Fiji distribution of ImageJ (www.fiji.sc) - The BIOP plugins to run the CellPose wrapper (https://wiki-biop.epfl.ch/en/ipa/fiji/update-site) - CellPose enviroment installed and configured to work in Fiji Assumptions - Data is captured as a single 16-bit grey scale TIFF - Each well is captured as a single field or stiched highpower fields to show the whole well. Code is able to work with multiple wells in a plate Demo data for two wells and an CellPose modelsare linked to be able to test run the code.
