I hope support and development for CP 2.x isn’t going to cease with the release of CP 3.0. Because I really miss some of the features: 1) Identifying Primary Objects per object (Otsu or Robust background). For example, this was really useful for identifying puncta in cells with different expression level after segmenting into cells; 2) Test mode slider; 3) Tophat in Morph, specifically repeated application of the filter; 4) Retaining outlines of the objects. Just a few of the modules I tested. I did not do a thorough side-by-side comparison of the version, but indeed I did see a speed improvement in CP 3.0 with some modules, but not all. I think I’ll keep using 2.2.0 for now. Thanks!
As far as our team is concerned, it’s my understanding 2.X will no longer be maintained or updated, though of course it’s possible others may have interest in working on this.
I do recommend checking out our two blog posts on switching between 2.X and 3; that should somewhat address your issues 2 and 4 (right now other than adding multiple EnhanceOrSuppressFeatures modules, there’s no workaround for 3).
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.
IdentifyPrimaryObjects Threshold per object