Trying to analyze 3D volumes of cells in a monolayer. Following the cell profiler example pipeline. This works well on example data (obviously, but suggests my Cell Profiler 4 is setup correctly). When I bring in my own two channel (WGA stain and DAPI stained) TIF files, and try RescaleIntensity I get the following in the terminal viewer:
Failed to run module RescaleIntensity
Traceback (most recent call last):
File “cellprofiler\gui\pipelinecontroller.py”, line 3361, in do_step
File “cellprofiler\modules\rescaleintensity.py”, line 444, in display
File “cellprofiler\gui\utilities\figure.py”, line 90, in wrapper
File “cellprofiler\gui\figure_figure.py”, line 1685, in subplot_imshow
File “cellprofiler\gui\figure_figure.py”, line 1265, in get_imshow_menu
AttributeError: ‘NoneType’ object has no attribute ‘Check’
I also get an error pop up claiming
Error while processing RescaleIntensity:
‘NoneType’ object has no attribute ‘Check’.
Do you want to stop processing?
Images were acquired in Olympus Cell Sens V2.3; with a hammamatsu ORCA Flash 4. VSI files were converted to single channel TIF using BioFormats importer in ImageJ. All images are 2048x2048px. I tried downsizing to 50% and images still failed.
XY = 325nm, Z = 570nm from a 20x obj.
C0001 = WGA membrane stain, C0002 = DAPI
Has anyone ran into this problem before and if so how did you resolve it?
basic from scratch.cpproj (612.5 KB)
Images are large, here is a drive link https://drive.google.com/drive/folders/1VnB1KtouoHu2AQIRL5KEJHGzX2D_Qzng?usp=sharing