Can QuPath handle 3D images?

Hi! Someone asked me if QuPath can handle 3D images and I wasn’t able to find the answer here explicitly (other than “no” in 2016)… is this still the case? Thanks!

Depends what ‘handle’ means… if you give it a z-stack or time series that it can recognize (with the help of Bio-Formats or ImageJ), then sliders will appear in the top left of the viewer to let you navigate through the different planes or timepoints. Although that was also the case in 2016…

But the analysis is pretty 2D-focused. There are no 3D ROIs to be found, but the 2D ones should at least appear on the correct plane (that might not always have been the case in 2016…).

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CellKai was working on 3D segmentation back in September 2018 in Gitter, but I don’t know what ended up becoming of it.