donghui1119

syncopy

Systems Neuroscience Computing in Python: user-friendly analysis of large-scale electrophysiology data

neurogym

A curated collection of neuroscience tasks with a common interface.

conn2res

A reservoir computing toolbox for neuroscientists

nighres

Processing tools for high-resolution neuroimaging

alignment_macaque-human

cross-species alignment (joint-embedding between human and macaque)

RheMAP

Non-linear warps between common rhesus macaque brain templates

PyReliMRI

Python-based Reliability in MRI: Calculating Group level and Individual Level Similarity between runs and sessions.

python-time-series-handbook

Material for the course "Time series analysis with Python"

ANTsPy

A fast medical imaging analysis library in Python with algorithms for registration, segmentation, and more.

RHOSTS

Code associated with the paper 'Higher-order structure of multivariate time series' (https://www.nature.com/articles/s41567-022-01852-0)

hypergraphx

HGX is a multi-purpose, open-source Python library for higher-order network analysis

GWAS

GWAS Summary Statistics for Brain Imaging Phenotypes

osl-dynamics

Methods for studying dynamic functional brain activity in neuroimaging data.

deepbet

Fast brain extraction using neural networks

torchreg

Lightweight image registration library using PyTorch

Imaging-transcriptomics

A package, and script, to perform imaging transcriptomics on a neuroimaging scan.

ENIGMA

The ENIGMA Toolbox is an open-source repository for accessing 100+ ENIGMA statistical maps, visualizing cortical and subcortical surface data, and relating neuroimaging findings to micro- and macroscale brain organization. 🤠

pypyls

A Python implementation of Partial Least Squares (PLS) decomposition

pyCirclize

Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

neuromaps

A toolbox for comparing brain maps

altair

Declarative statistical visualization library for Python

cerebellar_atlases

segment-anything

The repository provides code for running inference with the SegmentAnything Model (SAM), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.

CEBRA

Learnable latent embeddings for joint behavioral and neural analysis - Official implementation of CEBRA

PyNIDM

micaopen

Open Scripts and pipelines from the Multimodal Imaging and Connectome Analysis Lab at the Montreal Neurological Institute

gif_your_nifti

How to create fancy GIFs from an MRI brain image

scikit-image

Image processing in Python

BrainGB

Officially Accepted to IEEE Transactions on Medical Imaging (TMI, IF: 11.037) - Special Issue on Geometric Deep Learning in Medical Imaging.

load_confounds

Load fMRIprep confounds in python