How do analysis parameters work, when to use them?
Analysis parameters tell the software how to count the raw image of cells. You can adjust these to gate out cells based on their morphological characteristics such as size, roundness, etc. You can also adjust the parameters to selectively count cells based on their fluorescent intensities. Perhaps you only want to count the cells that are between 10-20 microns and have a bright GFP signal. In a way, analysis parameters allow you to inform the software based on the biological properties of your sample.