Error: index out of bounds



I am using the module IdentifyObjectsManually in order to identify certain nuclei on my images. During the manual selection it appears “IndexError: index 1414 is out of bounds for axis 1 with size 479”. After this I can not continue my selection. How can I avoid this? Thanks.

Maria Henriques


Hi Maria,

What version of CellProfiler are you using? That seems similar to a bug that was fixed a few years ago, so I’m wondering if perhaps it’s an old version and simply upgrading would fix the issue.

Otherwise, please provide us your OS, what version of CellProfiler this is happening in, under what circumstances you’re getting this error (is it when you’re drawing? Trying to erase? etc) and a pipeline and sample images to help us troubleshoot the issue.



I am using Cell Profiler: Stable (2.2.0). There are a latest version? This happens when I am drawing, more specifically, when I finish to draw the nuclei and I release the mouse button. Actualy, now I am able to keep drawing if I use another way to draw my nuclei (for example using the editing command N, which creates a new object under the curser). However, once in a while the error keeps appearing.