After I updated to the latest version of CellProfiler (v9978) the IdentifyPrimaryObject module stopped working on my images. The exact same pipeline will identify 250-350 cells in my images with version 9977, but identifies zero cells with the latest version of CellProfiler. This was the case with multiple thresholding methods, including Robust Background Global, MoG Global, and MoG Adaptive. I noticed that if I cropped the image and only ran the pipeline on that small subset of the image, the cell segmentation was identical for both versions as I’d expect. This has been the case for all of the 200MB images that I’ve tried.