IdentifyPrimaryObjects Threshold per object



Could it be that the “per object” threshold option disappeared in CellProfiler3.0.0 ?


Being terribly tacky and quoting myself:

The removal of per-object was never meant to be permanent; the option was removed because we were not convinced the previous implementation actually worked properly so we wanted to write a new version. If you have a pipeline plus sample images for 2.2 that convincingly demonstrates otherwise, I’d be interested to see it- it means our previous implementation DID actually work and doesn’t need to be rebuilt, which will get it into 3.0 a whole lot faster.


oh, I see, I always used it and it appeared to work…I never really tested it mathematically.
I guess you just have to make sure that only pixels inside the cell objects are taken into account for the threshold algorithms. Couldn’t you simply see in the python code if that is the case?


If you have some example images and a pipeline that you think would be helpful, we’d be happy to take a look :slight_smile:


Just discovering exactly the same issue. I have a pipeline that uses this to identify objects within previously identified objects. I always thought “per object” worked much better than any other threshold strategy (at least that’s the only one for which I managed to get satisfactory identifications). When the background within each object is very variable, the global strategy obviously fails, and the adaptive fails also since objects with different background can be very close. In a way, wasn’t the “per object” strategy like an adaptive strategy, with the difference that the “adaptive window” of the “per object” strategy could be defined more specifically than just by a square of a given size? Please let me know how to share images and pipeline, I’d be very interested to keep this one (if that’s as useful as it seemed to be of course). Something like this:


Pull together the pipeline plus an image set then you can either

  • Zip the files and upload them here
  • Upload them to GoogleDrive/Dropbox etc and post a link here.

We’d really appreciate it!


Sure, see below the link. Let me know if you need anything else and when you finished the download so I can close that door.