RNAScope Analaysis - Single Cell Heatmaps Fiji Macro

This macro is designed to work with 4 channel confocal images where channel 1 is a nuclear stain and the other three channels are RNAscope puncta stains. The macro extracts the nuclei and classifies cells as positive or negative for each RNAscope marker based on a user defined cuttoff. Individual cells are also processed to count the raw number of RNAscope spots for each channel.



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