Analyze particles inside individual ROIs

Dear all,
I am trying to analyse the size and signal intensity of particles (dots) in the nucleus and cytoplasm of cells. Each image contains multiple cells, so I started to define ROIs identifying each cell and each nuclei. Then, I “thresholded” the image and proceeded to the Analyse Particle menu… I ended up generating hundreds of additional ROIs (for each dot in the entire image)… but I cannot identify the ones present in each cell/nucleus.
Is there a way to assign the analyse particle tool to a specific ROI?

I thank you in advance for your help,
All the best

Hello Ricardo,

I suggest you use the ROI manager to store the ROIs of each cell and each nuclei, and click on the specific one before calling the particle analyzer. That way you should get different set of results per ROI:


Just select the particular ROI’s in the ROI Manager and then only these will be measured.

Vice versa you an select a specific ROI in the image and it will be selected in the ROI Manager.

Hello iarganda and Bio7,

Thank you for your replies. It definitely works.


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