How to quantify puncta within ROIs in Fiji?

28 December 2020 1 2K Report

I need to figure out a workflow to measure puncta (only in ROIs) in a z-stack in Fiji. I can get the program to count the cells in each image, but I the program ignores the segmentation boundaries of the ROIs. I only need the cells within the ROIs, not the whole image. Does anyone know of a plugin or download that can help me with this?

Ijaz Durrani

Dr Loren: Measuring cell fluorescence using ImageJ

From the Analyze menu select “set measurements”. Make sure you have area integrated intensity and mean grey value selected (the rest can be ignored).

Now select “Measure” from the analyze menu. ...

Now go and select a region next to your cell that has no fluroence, this will be your background.

https://theolb.readthedocs.io/en/latest/imaging/measuring-cell-fluorescence-using-imagej.html

Regards-

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