Error when using Classify Objects in CP3


Hi there, I am analyzing 42 microscopic images per group. Each image is divided into 3 sub images representing 3 fluorescent channels.
I am using

First I identify nuclei and use these primary objects as region of interest for an intensity measurement in the other fluorescent channels.
Next I would like to classify the objects according to the intensity of the two fluorescent channels.
I chose “classify objects” with pair of measurements. There I chose my primary objects, category= intensity, measurement = mean intensity, image = fluorescence channel 2 / 3.
For both measurements I defined custom bins.

When I run the analysis, I am seeing the following error: “boolean index did not match indexed array along dimension 0; dimension is 671 but corresponding boolean dimension is 670”

I am using cell profiler 3.0.0 on macOS.





Can you share your pipeline and couple of images with me?



Hi Hamdah, thank you very much for your response. The issue vanished without any action from my site. I can not tell why, but I am not able to reproduce the problem anymore, so I will flag this issue as solved.

Best regards