Sample image and/or code
Phase/DIC images of cells
I used ilastik to generate probability maps which I am now trying to segment those probability outputs using CellProfiler. I want to perform a cell count, then measure the size of cells. From there, I want to compare the proportion of small rounded cells vs proportion of larger flattened cells (which I think the ClassifyObjects module is best for, haven’t gotten there yet!)
After testing my pipeline in Test mode, everything seemed to be working fine. However when I click ‘Analyze Images’ I get the following error message (screenshot attached):
Error while processing (remote worker):
(Worker) FileNotFoundError: [Errno 2] No such file or directory: 'g\my drive\1 results\cellprofiler\Cpmeasurementsvwxvzmb.hdf5
Do you want to stop processing?
I tried to set the temp folder to a location I was sure I had admin access (taking advice form this thread) to no avail. I also tried relaunching the program, no change.
If I click “Continue processing” on the error message, the progress bar doesn’t move and time just keeps increasing.
Any help hugely appreciated, TIA!!