I am trying to run the MeasurePopulationContext plugin on CellProfiler to calculate local cell density but keep getting the following error:
“ValueError: NumPy Boolean array indexing assignment cannot assign 61 input values to the 32 output values where the mask is true”
The log reports an issue with line 154 of the plugin:
ii[ii>half_shape] =shape -ii
So far, I have identified my nuclei as objects (there are 61 in my ROI). I tried increasing/decreasing the search radius and/or object diameter, but it doesn’t help.
Any ideas what the problem might be? Thanks!