How to crop sub-images from a larger one?

I'm trying to get the sub-images of segmented cells from the attached image that I'm working. The screenshots pictures are from my reference paper. I don't want to use fit bounding box. And I want to make large box for each cell. I attach the m-file that I've tried. I'm getting the wrong output. Please fix me the wrong parts.

The following pictures are from my reference paper

The following picture is the output. This is not what I want.