You can record a macro on ImageJ and save it to automate the steps you need to go through, it is how I usually solve this kind of issue.

Here a some examples:

https://youtu.be/hWrtH_OxV2Q?si=gK652CHEsRZhPw_A

https://youtu.be/V2mO4MC0dho?si=N8_tWh_Dm1YtONdC

Can you post some sample images, and draw what you exactly want?

Lambert Zijp So I have something like this and I have to move drop to drop to calculate grey values manually. It would half my work if atleast the visible drops could be automates. So to automate something like a mask of these circles and then I can set the diameter of the ROI and it simply labels and measures the grey value of this ROIs. Eg Drop 1 has grey value xyz. and so on..

Finding a good threshold for all drops is difficult and you will need to know the variability of your images. Often Otsu's method is recommended, but my experience with Otsu is not so good. It would help if you can avoid the high intensity streaks in the lower half of the image.

In Octave (like MatLab) you can analyse the binary (thresholded) image with the functions bwconncomp and regionprops. They give you how big and circular the blobs in the image are. Also capable of returning the convex hull of blobs, which comes in handy because some of the drops contain many high intensity islands but those drops as a whole would be below the threshold.

I would be pleasantly surprised if ImageJ can do all that. Maybe Caroline Fernandes-Santos knows and can help you on your way.

Good luck!

Lambert Zijp Thank you! Looks like it not entirely an easy job. In case I manage to do something, I'll update here!

Thank you again!