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.