Cell counting with cell clusters

Hi, Im having trouble quantifying the amount of RD cells on a membrane from a migration assay using transwells. When trying to quantify using an image with many cells, clusters get counted as one and I was wondering if there was a way around this. Also, when quantifying cells with very few cells stained with crystal violet, the background noise is counted as cells. If I could get help with these two issues I’d be very grateful!

Hello @MHD26
I would suggest you try to segment your images with the Trainable Weka Segmentation plugin in Fiji - http://imagej.net/Trainable_Weka_Segmentation. Here is also a Youtube video about how to use the plugin - https://www.youtube.com/watch?v=8yfBHiGufFE.
Alternatively, i would also try the Find Maxima tool in Fiji. :slight_smile:


Thanks, that’s helped with the background noise problem, but I’m still having issues with a cluster of cells being counted as one.