Fluorescence Intensity at the pole of the bacteria vs diffused intensity

Dear All,

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


Dear @TanM07,

welcome the forum! :slight_smile:

If that is not what you want, I am not sure that I have understood what you are trying to do. Are you trying to get one mean intensity and one maximum intensity for several regions of interest from different images?


Hi @stelfrich ,

Thanks for your reply. Here are the few info i am interesting in getting from my images
i) How many cells have one, two or more than two foci within them?(without going through manual counting if possible)
ii) There are two or more than two foci within a single bacterium. I want to quantify what are the intensity for each of these foci compared to the diffused localization of the tagged protein within the cell.
iii) Is there any particular foci type (polar vs non polar localization) increasingly more common?
iv) I am also interested in how far the non polar foci from the cell poles.

Thanks again

Before proposing to reinvent the wheel, Iā€™d suggest to give MicrobeJ a try. Sounds like it could be useful for your kind of analyses.