Hi, I am using Cell profiler for my research work. On certain microscopic images of cells, the segmentation did not work well as the size of the cells are very random in the scene. I used another software to segment them. But in that case how can i use the segmented results to extract the features using Cellprofiler.


It depends on how they are saved.
*If they are binary masks (not so great), then you can use IdentifyPrimaryObjects to (re)segment the images with a Threshold Strategy = Binary Image.

  • If they are label matrices (better), then you can use NamesAndTypes to set “Assign a name” = Images Matching Rules, and then se the “Image type” = “Objects”.

Hope that helps,