In default IdentifyPrimaryObjects, there's certain level of smoothing. So the segmentation algorithm would see a nucleus in the non-deconvoluted images as a whole (a bit blurry) object. With the same algorithms, the grainy crystal-clear complex structure of a nucleus in deconvoluted images will result in over-segmentation.
You can try to do either:
- Use the original (non-deconvoluted) images to do segmentation, then overlay on deconvoluted images. OR
- Use the deconvoluted images, but uncheck "Automatically calculate size of smoothing filter" and "Automatically calculate minimum allowed distance between local maxima", and manually tune these parameters (recommend to increase) .
Hope that helps.