Identify objects manually problem?


I keep having the same issue when I attempt to use the manual drawing function to identify objects in Cell Profiler. When I attempt to load the image, the entire image is dark and I an unable to see my cells. Most of the time, the image is completely black but sometimes I can see a faint image. Any idea what I am doing wrong or what is causing this? I have tried this with and without adding the Illumination correction module. Thanks in advance to any response!


This is due to an oversight in the code in which the display image is not normalized according to the image bit depth. For example, if you have a 12-bit image which is stored in a 16-bit format (not unusual for automated microscopes), the image will appear dark if not scaled correctly. We have noted this as a bug, and it should be corrected for the next release.

To get around this, try using the RescaleIntensity module to rescale your input image and then use the result as input into IdentifyObjectsManually.


This fixed the problem- thank you!

Another note about this bug:

It seems that after rescaling the image and then running identify objects manually, the image that appears on the manual identification screen is flipped from top to bottom. I tried using the flip module to flip the original image, and then flip once more, but this will also disorient the objects once they have been identified manually. This bug occurs every time I try to run these modules.

Thanks for pointing this out. This has also been noted on the bug entry for this item.

This issue has been resolved in CellProfiler 2.1 and later, new releases of which can now be downloaded from