I am new to CellProfiler, and am looking for advice to get a basic workflow going.
My goal is to quantify the number of pollen grains, and their size over a series of images.
My problem (I think) is that the IdentifyPrimaryObjects Module is not recognizing pollen grains, because they are being read more like rings than blobs, and often those rings are not 100% complete.
My images were captured with DIC microscopy which provides good edge contrast around each pollen grain, but poor contrast between the center of the grain and the background.
My pipeline, so far, is very simple: LoadImages > Apply Threshold > IdentifyPrimaryObjects.
I have attatched some screenshots, and the sample image I have been working with.
Any guidance greatly appreciated!
note: I had trouble uploading tifs to the forum, so converted to JPG and compressed, therefore the diameter in pixel units set in the IdentifyPrimaryObjects module may seem inaccurate but it was set according to the original tif image.