Error with IdentifyPrimaryObjects after updating to v9978

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.

Rachel

That’s certainly alarming! Could you upload your pipeline plus an image, one that gave you the different object counts between the two versions?
-Mark

Here’s one of the pipelines that produced different results in v9777 and v9778. I’m not able to upload the 200MB image to the forum because there’s a 10MB file limit. Is there somewhere else that I can upload that image for you?

Rachel
pipeline version check MoG.cp (3.79 KB)

One point of clarification: Is one image 200MB in size or do you have a collection of images totaling 200MB in size?
-Mark

Each image is 200MB in size. The image is a 7x7 montage of images from our microscope. We’re using it to track individual cell survival in each well of a 96-well plate over a week so can’t break up the images into smaller images and as effectively track the cells across time points.

Rachel

I’m actually sort of surprised that such a large image worked in either version :smile: . In any case, you can use YouSendIt to post large images; if you use it, just post the link here when done.

Regards,
-Mark