Save all marked objects (nuclei) in a FISH image as separate file



Dear all,

Many thanks for providing such a great tool for free!

In accordance with a previously asked question in 2012 #1498 (Cropping Object into Separate Image Files?) I would like to know whether it is now possible to crop each identified object from an original input image and save all sub-images as individual image files.

My goal is to mark all nuclei in a FISH image and then export each nuclei as separate file. The saving needs to be done in one step.

Thanks for your answer



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:

  1. 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.

  2. 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.

  3. 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:

  4. Use a module “Crop”, where your original image will be cropped by the binary position-masks

  5. 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.


Dear Minh,

many thanks for your answer! I will try your approach and let you know how it works.



I agree with everything @Minh said but this:

If you have a lot of original images, you may have to look for solutions outside CellProfiler.

You can definitely do this relatively easily for lots of images in CellProfiler!


Hi, I’m interested in that problem too, how can I do that for a lot of images?



this worked for me:



(Quoting myself from another post)

In CP, you can first run a pipeline that takes all your hundreds of images and makes masks for each with SaveCroppedObjects (we strongly suggest saving each image’s masks into a folder with that image’s name, which you can do using the “DefaultOutputFolder-Subfolder” save option), then run a second pipeline to apply the masks to your images (and optionally crop them down). It can be done though, and we do it in the lab.