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?


1 Like

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


I am having this exact same problem. Not sure how to correct this.

Hi, the thing that solved it for me was to uninstall and than reinstall the newest Java JDK and completely uninstall the cellprofiler (not just throwing it into the trash but removing all files from all folders) then after reinstalling the cellprofiler anything worked for me.


Thank you. I gave that a try, but unfortunately it didn’t help.

Maybe try on another computer and see if you get the same issue?

1 Like

Thanks for the suggestion. Just gave that a try, but it also failed.

Here’s the MASK file for my post on 4-30-19

MASK.tif (2.5 MB)

Ah, that’s too bad. Could you post the pipeline and an example image set?

1 Like

Thanks for your help. Here’s the pipelineRNAscope_Analysis43019.cpproj (962.6 KB)

Here’s an example image. I will have to upload the associated “MASK” file to my post from 4 days ago, because new users can only upload a single file with each post.

Adult3_2B_S7_PVDAPI_MAXcolorCROP.tif (5.0 MB)

Hi! Have you had any luck solving this issue? I have been running into the same problem recently, and cannot seem to figure it out…
Many thanks!

1 Like