Simulate the C. Elegans worm brain in your browser and interact with the worm as it moves around

Graph theory analysis of brain MRI data

micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below

A dynamic connectome mapping module in python.

Python library for analysis of neuroanatomical data.

STAGIN: Spatio-Temporal Attention Graph Isomorphism Network

A performant, powerful query framework to search for network motifs

Connectome Mapper 3 is a BIDS App that implements full anatomical, diffusion, resting/state functional MRI, and recently EEG processing pipelines, from raw T1 / DWI / BOLD , and preprocessed EEG data to multi-resolution brain parcellation with corresponding connection matrices.

Compose chunk operators to create a pipeline for local or distributed petabyte-scale computation

A unified framework for skeletonization, morphological analysis, and connectivity analysis.

Please use the new version of LiFE: www.github.com/brain-life/encode

A prediction-based extension of network-based statistics.

A Hugo theme with backlinks for online communities

Tools to work with the FlyWire connectome. Fully interoperable with navis.

A multipurpose matlab-based MEG/EEG overlay & network plotter

Fast and memory efficient approach for connectome-wide association studies in R and C++. Uses custom implementation of multivariate distance matrix regression to associate brain and behavior.

An Explainable Geometric-Weighted Graph Attention Network (xGW-GAT) for Identifying Functional Networks Associated with Gait Impairment

GNN with summarization/grouping layer for speed and interpretability

Code for implementing the Aggregation-Network diffusion model (AND), as described in the paper: "Combined Model of Aggregation And Network Diffusion Recapitulates Alzheimer’s Regional Tau-PET " by Ashish Raj*, Veronica Tora, Xiao Gao, Hanna Cho, Jae Yong Choi, Young Hoon Ryu, Chul Hyoung Lyoo, Bruno Franchi. *Department of Radiology and Biomedical Imaging, University of California at San Francisco

Pipelines and tools for MRI analysis

Supplemental source code for Nern et al. 2025: "Connectome-driven neural inventory of a complete visual system" (https://doi.org/10.1038/s41586-025-08746-0). The Cell type explorer repository is at https://github.com/reiserlab/male-drosophila-visual-system-connectome

Weakly Object Localization on brain dMRI using CAM

ABMT (Adversarial Brain Multiplex Translator) for brain graph translation using geometric generative adversarial network (gGAN).

Spectral graph model base code and examples

Meta-learning using graph neural networks for brain connectivity regression.

A paper investigating bilateral symmetry of connectome networks.

Code base for our paper "Connectivity-Inspired Network for Context-Aware Recognition" (ECCV 2024, Human-inspired Computer Vision workshop)

Methods for estimating time-varying functional connectivity (TVFC)

EM segmentation of mitochondria from SNEMI3D data

Fast and easy visualization of fMRI data quality using carpet plots.