Hello,

I’m working with 2D brain slice images and would like to visualize specific cells within a 3D rat brain model using Brainrender. I have downloaded the .nii files of the WHS Rat Brain Atlas and was wondering if they can be used in BrainJ for cell analysis.

Alternatively, is there a recommended software workflow to register 2D brain slices to a 3D atlas, then analyze the cells with Ilastik, and finally render them in Brainrender?

My goal is to accurately map extracted cell coordinates from 2D slices onto the 3D rat brain model. Any guidance on the best approach or tools for this process would be greatly appreciated.

Thank you!

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