Neuroanatomy Python Packages

dipy

DIPY is the paragon 3D/4D+ medical imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.

cellfinder

Automated 3D cell detection in very large images

brainreg

Automated 3D brain registration with support for multiple species and atlases.

navis

Python library for analysis of neuroanatomical data.

swcgeom

Neuron geometry library for swc format.

brainreg-segment

Manual segmentation of 3D brain structures in a common anatomical space

brainglobe-segmentation

Segmentation of anatomical structures in a common coordinate space

brainglobe-heatmap

Rendering anatomical heatmaps with brainrender and matplotlib

quicknat-pytorch

QuickNAT, Brain segmentation.

neuro-scan

LLM Neuroanatomy Explorer — map what each transformer layer does