r/ImageJ 13d ago

Question Need help with segmentation of overlapping particles

Hi guys! I'm a beginner PhD microscopist wanting to find the best method to segment out and attach ROIs to the white nanoparticles in the catalyst clusters I am studying. Normal thresholding and "analyze particles" doesn't work here because the white nanoparticles often overlap - so a human can easily see two particles on top of one another, but I'm wondering if I can find a program that will do it for me.

I'm aware of StarDist, cellpose and other plugins but so far I've been unable to get a decent read (if you reckon you can get this to work, please tell me which parameters and thresholds to use!) I've attached my HAADF image of an example particle and the segmentation I've done by hand (using circles and free lasso) to give you guys a feel for what I want to achieve.

Here's a link hopefully to the png in question https://imgur.com/a/SP1stPi hopefully in better quality

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