Analysing serial section data

Elastix-based registration

Registering images in MATLAB using Elastix

Repo

NiftyReg-based registration

Register brains using NiftyReg in Python

Repo

Automatic cell counting

Automatically count labelled cells with this cross-platform Python package

Repo

Related tools

• ClearMap - An Elastix/Python pipeline related to iDISCO
• SimpleElastix - A nice Elastix wrapper for multiple languages
• BIRDS (pre-print)
• Whole Brain Software
• MelastiX - Elastix wrapper for MATLAB.