One of the most basic functions of Fiji is the automatic counting of objects based on their intensity. This can be stained cellular nuclei, nanoparticles, or other structures. The objects can either be bright with dark background (e.g., fluorescent structures) or dark with a bright background (e.g., nanoparticles on TEM images).
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More information can be found here: https://imagej.nih.gov/ij/docs/menus/process.html#find-maxima
