Dear CellProfiler team,
Firstly - thank you so much for your incredible work!
I wondered if I could get some help with two error messages I’m running into whilst trying to migrate my CP2 pipelines into CP3?
In essence, the pipeline loads some channels and then selects a proportion of bit depth in each channel to work with downstream using ‘RescaleIntensity’. These are then combined into multichannel composite image via ‘GrayToColour’. So far so good.
Nuclei and cells are then identified, prior to trying to display the cell outlines and cell object numbers (via OverlayOutlines and DisplayDataOnImage) on the output of the earlier GrayToColour module…
This results in two errors:
“Error while processing OverlayOutlines: images of type float must be between -1 and 1”
“Error while processing DisplayDataOnImage: operands could not be broadcast together with shapes (1029,) (1023,)”
Meanwhile, the approach works fine in my old CP2.2.0 pipeline - I’d just used the original ‘ApplyThresholds’ module to discard intensities below the lower threshold and, then specified the upper limit of pixels to mask using a ‘RescaleIntensity’ module.
My source images and CP3 pipeline are here (~50MB):
Thanks in advance,