I’m having a problem with fragmentation of cells. I tried changing median filter radius and sigma, but I cannot fix fragmentation without loosing many cells. There are only a few big cells like this. Is it possible to manually fix these cells?
Large, poorly stained nuclei are a general problem. You might want to look at some of the options in this recent topic.
You can create manual annotations and turn them into detection objects through scripting, though it is not exactly straightforward. Editing “Detection” objects is not possible through the GUI.