I’ve attaching two of the problematic images and the pipeline. The images are fluorescent lectin-stained sheets of cells. The first is nearly confluent but with a couple of empty patches and the second is much more sparse (the third and fourth images are the corresponding nuclei). The problem seems to be setting a lower bound on the threshold that achieves a balance between producing secondary objects that are almost identical to the primary nuclei and segmenting the empty space in image 2 to be part of giant cells. In the case of the former image, I’ve not been able to find parameters that are able to exclude the empty space at the lower right… I’ve played around with the regularization factor and the lower bound on the threshold but haven’t changed the method to identify secondary objects or the thresholding method.
I’ve also attached the first half of the pipeline (through identifying secondary objects).
(I want the segmenting to be as precise as possible because I’m looking for bacteria in the cells and don’t want to get results that classify extracellular bacteria as intracellular.)
Thanks for your help!
LectinObjectsOnly.cp (9.63 KB)