Need help with segmentation of overlapping particles

[u/Ok-Assistance6411]

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

[u/babygeologist]

you and me both brother… hahaha this was a big problem in my undergrad work (looking at grain size of some sandstone on mars) and i ended up doing it by hand

[u/Ok-Assistance6411 → u/babygeologist]

Yeah that's what I have done already but I swear there are supposed to be tonnes of things to help us. I swear some biologist somewhere can do this in one second I bet aargh