I am having a problem where the IdentifySecondary module finds a cell near the edge of an image but propagates a long straight area that isn’t part of the cell. This may be a problem with the image (though I doubt it), but my main problem is that MeasureObjectAreaShape module throws an out of memory error when trying to measure the secondary regions. If it didn’t error out I could filter the object out though I suspect it would be better if the propagation method didn’t behave like this.
It would be easiest if I could send the image and the pipeline, but I find that they are too big to attach. I will try to email a zip to someone after I post this. One image is a few nuclei stained with dapi and the other is the actin for those cells. Running the pipeline provided gives a cell outline that stretches along the bottom of the image as an extension of one of the objects.
Where would be the best place to catch this problem?
Thanks for taking a look at this! -John