Hi Everyone,

I would like to generate a very simple ImageJ macro, which first measures the area in a user-selected region of interest (ROI) and then the fluorescence signal intensity within the same ROI that is adjusted by manual thresholding.

Attached is a PDF, which shows the steps in the macro, ROIs are indicated with yellow selection.

As the ROI selection and the thresholding needs to be done manually in every image by the user, I would need this macro to ask the user after an image is opened:

“Select your region of interest” (=> I guess this could even be skipped by starting the macro after the manual selection of the ROI.)

And then again the macro should stop to have the user set the threshold.

Any suggestions how can I incorporate these into such a macro?

Thanks very much for any suggestions,

Sinem