Others may have better ideas, here is my work-around:
If you are working with just a few original image, it’s relatively simple to do:
It’s best to do it in 2 separate pipelines. In the first pipeline: identify the objects-of-interest, in your case it’s the “nuclei” object.
Add module SaveCroppedObjects (category: “File Processing”). This will save the binary position-mask of each identified nucleus. i.e. you will have a full size image, completely black, but the location of nuclei are highlighted white, one at a time in each file.
Once you finished running this first pipeline, make another simple pipeline: load the original image as single image, and all the position-mask images with their metadata set accordingly:
Use a module “Crop”, where your original image will be cropped by the binary position-masks
Save the resulting cropped images into individual files
If you have a lot of original images, you may have to look for solutions outside CellProfiler.
Hope that helps.