I am very happy to announce that our software engineers are working hard to add true 3D capabilities to CellProfiler!
As you may know, you can currently load a 3D image file into CellProfiler and analyze it slice by slice. You can thus make maximum projections (and then analyze the 2D resulting images in a separate pipeline) or treat the 3D stack as a time lapse movie to “track” objects from one slice to the next. These strategies solve a surprising number of 3D image analysis problems, but of course sometimes you genuinely need to identify objects in true 3D and make volumetric measurements.
After this work is complete, you will be able to load 3D images and process them as a volume, including identifying objects in 3D, making 3D measurements and transformations of the image.
This work is made possible primarily through a collaboration with the Allen Institute for Cell Science, who is pushing the envelope on gathering gorgeous high-throughput 3D image stacks in their ongoing work.
Bookmark this post if you’d like updates on our 3D progress, especially if you’d like to test the beta version when it’s available. You can see what is going on with the code at GIthub: https://github.com/CellProfiler/CellProfiler/projects/1