Hi Man Hei,

You could try using 3D Objects Counter, just make sure you first redirect your measurements. Go to Analyze>3D OC Options, select your parameter to calculate to be mean gray value and at the bottom of the window select the GFP channel to redirect to. Now if you apply 3D Objects Counter to the DAPI channel your measurements will be done on the GFP channel, but only within the DAPI positive compartment. You get your results nucleus-by-nucleus in a table. You can also call all of this from a macro.

Hope this helps!

Máté

Hi Man Hei Cheung ,

I haven't check Máté approach but it seemed to be a plugin based variation of the approach that I would suggest.

First you dublicate the DAPI Image, make a binary by thresholding (you may also use a watershed filter) than you go to analyze particles you can now analyze the nuclei in the binary image make sure that you have clicked "add to manager". Thereby, you are creating ROIs in the manager that you can apply now to the original DAPI and GFP image and measure the intensities matched.

Kind regards

Soenke

Máté and Sönke,

Thanks a lot for the suggestions! I have tried and seems it works well for me!