Negative row index found with IdentifyPrimaryObjects

Firstly, thanks for a magnificent piece of software! It has opened many doors in my research.

I generally quantify dots per nucleus using IdentifyPrimaryObjects. Sometimes an image which seems just like any other image in my set gives the error “negative row index found,” and the processing stops. The reason to this eludes me, as I can’t tell how the image is different from the others in the set.

Attached is the pipeline, a screen capture of the error message and the images I try to analyse.
Thank you for any advice!
error in CP.rar (9.09 MB)

The problem seems to have something to do with the number of quantified objects in the image. Because, when I increase the “Threshold correction factor” the problem doesn’t occur.

Thus, the problem is image dependent. If I remove the image from the analysis that gave the error, the pipeline can continue. Is there any solution other than increasing the threshold or removing the image?


This is a problem that was fixed in our code, but has not yet been released. If you like, you can download a developer build of CellProfiler which is available from here with the caveats mentioned. In particular, take note of the fact that pipelines made with the trunk build are not backwards compatible.


Thank you very much! It works perfectly!
This made my week.