I’ve been experiment with cell profiler for a while trying to get a good pipeline assembled for identifying bacterial cells.
I’ve tried a large number of permutations of algorithms and parameters for IdentifyPrimaryObjects (and greatly appreciate the exhaustive documentation), but I seem to be unable to avoid the problem of large clusters of cells being treated as a single cell.
I’ve added as an attachment a sample image file, a sample output file, and an image of the pipeline I’m using.
Any help would be greatly appreciated! Thanks!