CellProfiler 3.1.9 - MeasureObjectSize/Shape in 3-D error?

Dear Cell Profiler team,

I hope this email finds you well. I wondered if I could ask for your help with something?

I have a CellProfiler3 pipeline that tries to measure object intensities and object size/shape features in 3-D. The intensity measurements run just fine, but whenever I try to measure size and shape, the pipeline hangs.

A copy of my files and pipeline can be found here:

At the current time, the pipeline is loading objects from ‘outside’ via ConvertImageToObjects. However, the problem still occurs if the segmentation is carried out internally as part of the pipeline(?)

Thanks for all you do + for the help,



The short answer is, you have a LOT of objects! While most of the object measurements run pretty fast, even with thousands of objects, one in particular for 3D (Surface Area) is pretty slow, about 3 seconds per object; your example image had 12K objects, which at 3 seconds per object, equals 36K seconds, or about 10 hours. I’m guessing if you let it run that long, it will finish, though obviously that’s longer than you probably wish it would take!

For our 4.0 release (which should be in ~the next month), we’ll make sure to do at least one of the two of a) switching to a faster algorithm if possible (there are some obvious things to try here) or b) making surface area calculation optional. You could do one or both yourself if you’re running from source in the meantime.

Thanks for letting us know this!

Hi Beth

Thanks so much for clearing this up for me - that’s really helpful. It would be brilliant if CellProfiler4 could include a faster algorithm and/or have the option to make the surface area calculation optional! This would bring 3-D blockwise processing of large image volumes in reach of CP’s user friendly environment - which would be great from our perspective : )

Many thanks, John