I wish to input instance segmentation masks into CellProfiler (4.0.7) to measure and export some features. I’m using the “select image type as objects” option in the NamesAndTypes module to obtain the objects from the masks. In the exported measurements using ExportToSpreadsheet, I figured that the ObjectNumber field corresponds to the increasing order of pixel values in the input mask.
For one particular mask in my dataset, there are 2 objects with NaN features at the end in the exported csv. The mask image contains 136 objects with pixel labels 1, 2, …, 138 (except 98 and 108). It seems cellprofiler created 2 “empty” objects in their place. Moreover, the Location_Center_X and Location_Center_Y features for ObjectNumber corresponding to the missing pixel values (98 and 108) are NaN and the “empty” objects seem to have these values instead! I tried to recreate this issue with a dummy example (labels 1, 2, 3 and 5). However, I did not get any NaN object corresponding to the missing pixel label (4) in this case.
Is this a bug and/or is there an issue with my mask image that I am missing?
nuclei_features.zip (54.6 KB)