Value error with data type


I’m trying to segment nuclei in images of an organoid. I’ve simplified one of your example pipelines to do this, but I’m getting the following error when I try to run the pipeline. Is there some sort of transformation/conversion I should apply to the images to make them readable? 45 PM

I’ve attached the pipeline and some example images. (8.0 MB)


Hi, @Lauren_Beck!

CellProfiler expects three-dimensional data to be stored as a multi-page TIFF. Either you can combine your slices into one TIFF or you can process the image in two-dimensions (e.g. disabling the Process as volume setting in the NamesAndTypes module fixes your problem).


Hmm, I’m actually getting the same error when I run the pipeline on a z-stack TIFF.


@Lauren_Beck Unfortunately, IdentifyPrimaryObjects only works for two-dimensional images. You would need to use the Watershed module from the Advanced category to segment your z-stack.


It might make sense for you to start with the 3D example pipeline (is it on the examples page, I imagine?)


Yes, the 3D example pipeline and details are explained here: