Hi, we call our variant the "QUINT" workflow, https://quint-workflow.readthedocs.io/en...

At a minimal level it consists of the 2D->3D registration (QuickNII/DeepSlice), cell analysis (Ilastik), and then combining the two (Nutil). This results in 3D point clouds, so coordinate listings. We have a viewer for it of course, but it can be used anywhere else - the format is JSON, so it's text.

We offer this workflow as part of EBRAINS ( https://www.ebrains.eu/tools/quint-workf... ), and provide user support for it too ( https://www.ebrains.eu/contact ).

I hope this helps, best regards,

Gergely