I am trying to count the nuclei (DAPI stained) in 12 images using CellProfiler 3.1.8. The images have slightly different dimensions and illumination artefacts. The images also have stripes/banding which messes with the object detection (see screenshot).
I have removed most of the illumination artefacts (see screenshot), but haven’t had much luck with the bottom stripy half of the image.
How can I clean up this image and count the nuclei? I’ve experimented with EnhanceOrSuppressFeatures and TopHatTransform (which seems to find the stripes), but haven’t had any luck so far and am mostly stumbling around in the dark. Any ideas or suggestions?
I’ve attached a cropped region of the image (since the original tif is ~50 MB)dapi_cropped.tif (8.1 MB)