Dear Ayman Khalifa

Could you please describe the problem in more details. Also an example image is always useful.

The workflow usually consists of defining regions of interest within your image, and then quantifying the number of counts within those pixels.

The intensities you want to measure are for what? for example, comparing levels of expression?

I also highly recommend that you reach out the image analysis community via the forum: https://forum.image.sc/

Best regards,

here as in this image for example,

Id like to measure the intensity of green color

So first, I used (image, color, channel tools) to discared the blue Dapi color of the nuclei

then in set of measurements I choose (area , integrated intensity and mean gray value).

I encircle each cell as possible then analyze then measure.

in addition I set up the length scale in image j using the scale bar of the image.

is that way correct?