I noticed that you guys use distance_transform_edt from scipy. Does this apply to 3D structures? Also, what does min_distance represent?
I’m asking because I’m interested in counting the number of nuclei after segmentation. My nuclei are slightly irregularly shaped and most of them look elliptical. I decided to go with the Nucleophosmin segmentation notebook. However, after segmentation, I’m interested in counting the number of nuclei present. I was hoping to do this using a distance transform followed by a counting of the maximum. However, this is not working for me. Do you have any suggestions?