Object Cropping

We would like a way crop just an individual object, very similar to what CellProfiler Analyst does, and then proceed to save those individual images, that can also be related/referenced back to that specific object within the data table. Would we have to customize a module to being to do this?

Thank you,


Hi Heather,
I think you would have to write your own module. Part of the difficulty here would be how you would associate each object’s image on disk with its measurement in the object table. CellProfilerAnalyst uses the X and Y location stored in the object table to crop its images. We have a collaborator that uses an alternative strategy: they convert the objects to images using the ConvertObjectsToImage module. If you use the “uint16” option, each pixel of the resulting image will either have a value that corresponds to the object number of that pixel’s object in the object table or will have a zero value to indicate that it’s not in any image. After that, you can save the image as a 16-bit TIF.

Your data analysis application can load the 16-bit TIF images and use the numbers to crop other images to single objects and to associate values in the object table with these objects. Hopefully, this is adequate for your application; it might turn out to be a better strategy than managing separate files for each object.

Hope this helps.