Cardiomyocyte Analysis - H and E stain with Cellpose

Fiji/ImageJ macro code to analyse images, that had been previously marked, of cardiomyocytes in H and E stained mouse heart sections. Developed my Cameron J Nowell of Monash University ([e-mail]) in collaboration with Miles De Blasio ([e-mail]) This data set contains the Fiji/ImageJ macros, and example image and two custom trained Cellpose models (one for the cells and one for the nuclei). There is an intial macro for marking out areas of interest (right and left ventricle) and areas to exclude from the analysis. This code relies on two trained from scratch cellpose models. One for segmenting the nuclei and one for segemnting the cardiocyocytes. Images are expected to be RGB tiff images extracted from a whoel slide scans on something like an Aperio imager or similar Code will select only cardomyocytes that have an associated nucleus and output the following parameters as both summary (averages) and detailed (each individual cell) - Area (um^2) - Minor and major chord (um) adn the aspect ration between the two - Circulatiry, Roundness and Solidity - Minimum and maximum Feret's distances Requirements to run the anlaysis portion. To run the mark up only a standard install of Fiji is required - Standard install of the Fiji distrubution of ImageJ (www.fiji.sc) - The BIOP plugins to run the cellpose wrapper and work with cellpose label images - Cellpose environment installed and configured to work in Fiji - The morphology plugins