I am receiving essentially the same error. I downloaded the current version of CP and am using a set of plates from Neil Carragher’s Molecular Cancer Research paper from the BBBC as a teaching case study.
The error message is: Error while processing MeasureObjectIntensity:
(Worker) IndexError: index 86 is out of bounds for axis 0 with size 86
I get the error about 30 times for 240 image sets. I can continue the run and it completes but when I open the data file, it appears that the pipeline can count the nuclei, but all area-shape measurements are NaN, but ironically, the intensity measurements are reported.