I need to count the number of sand granules within the ROIs to accurately quantify ants’ behavioural response. I have been working in open-cv so far, but FIJI seems to be more tailored for this kind of analysis.
I have tried skeletonisation followed by waterhsed, with different rounds of erosion and dilation, but the stones that are more closely clustered (top tail of the stone cluster in the middle ROI in the image below) are still identified and counted as 1 item. What’s the most efficient method to obtain a separate count?
Anything that can be run within python and inbed in the rest of the analysis would be much appreciated.