Drag and drop your image (composite of 4 channels) and the macro 4ch-2D-quantification.ijm in Fiji-imagej. Then fill the macro in the macro interpreter by following instructions in green and press run.
After following macro instructions (pop-up windows), the final output will be:
Resulting files will be stored in the output path (output folder) that you introduced in the macro interpreter:
Use the "Parsing_Results.py" script by using a python interpreter to merge data from multiple csv files into a simple excel (.xlsx) file.
Use the "Custom_Projection.ijm" ImageJ macro to project Z-stacks prior 2D quantification. Chose the kind of projection you want to use for each channel.
Use the "Test_all_Auto-Threshold-Methods.ijm" to try all possible Autothreshold Methods of ImageJ (similar to try all command).