3D image capabilities: coming soon to CellProfiler!



Split channels and the pipeline is here:

Ideally I’d like to do tracking but it seems that the tracking module is not yet adapted to deal with 3D. Anyway, just spitting out positions and intensities would be fine, and the tracking I’d do externally.


@maciekd CellProfiler has been modified significantly since the Mar 17 post that shared the 3D demo pipeline. For an up-to-date demo with a tutorial please use the resources found in the CellProfiler/tutorials repository. Thanks!


Hey @maciekd, thanks for sharing your data and pipeline.

We don’t have support for 4D or 5D data in CellProfiler. I recommend splitting images by channel and time point, so you can process your data as a series of individual 3D grayscale images. It’s important to note as well that TrackObjects does not yet support 3D objects.

I’d encourage you to file any 3D processing issues to https://github.com/CellProfiler/CellProfiler/issues.