I have many images from electron microscopy of round structures. I am looking for a way to measure the area of these in an automated way. Any suggestions would be very much appreciated.
The CellProfiler program from Broad Institute is useful and user-friendly.
Erik Martin I have been attempting this. However, I cannot figure a way to do it due to the different colour inside compared to out.
If you can just get the dark circles detected using 'identify primary objects' you can then tell it to fill in the space inside each object. And/or, you can use a mask on your image or a copy of the image as a different approach. If you search for a CellProfiler forum you can probably find a good pipeline or instructions how to make one. Good luck. -you could always 'identify primary objects manually' and draw circles around them all too, but that would obviously be much more involved.
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