I am a new user of FIJI. I am trying to quantify the fluorescence intensity of a yfp tagged protein of interest at the two poles(or multiple foci within a single cell) of bacteria vs the diffused fluorescence intensity. I want to analyze >100 cells using multiple 16 bit grayscale images from different field of views. I tried using Thresholding and Analyze particles and extending it to other images using macro and Multiple Image Processor plugin but i end up mean and max intensity for each cell. Is it possible to analyse multiple cells from multiple images at the same time and get a final output in excel for graphical representation. What can be the best possible way to perform this analysis?
Thanks for your suggestion