Projects in Awesome Lists tagged with connectomics

https://github.com/cwatson/braingraph

Graph theory analysis of brain MRI data

brain-connectivity brain-imaging complex-networks connectome connectomics fmri graph-theory mri network-analysis neuroimaging neuroscience r statistics tractography

Last synced: 18 Feb 2026

https://github.com/zudi-lin/pytorch_connectomics

PyTorch Connectomics: segmentation toolbox for EM connectomics

biomedical-image-processing computer-vision connectomics deep-learning microscopy neuroscience pytorch segmentation

Last synced: 01 May 2025

https://github.com/cwatson/brainGraph

Graph theory analysis of brain MRI data

brain-connectivity brain-imaging complex-networks connectome connectomics fmri graph-theory mri network-analysis neuroimaging neuroscience r statistics tractography

Last synced: 29 Mar 2025

https://github.com/seung-lab/kimimaro

Skeletonize densely labeled 3D image segmentations with TEASAR. (Medial Axis Transform)

biomedical-image-processing centerline centerline-extraction computer-vision-algorithms connectomics cross-section cross-section-area image-segmentation medial-axis-transform python skeletonization skeletons teasar volumetric-data voxel

Last synced: 15 May 2025

https://github.com/seung-lab/cloud-volume

Read and write Neuroglancer datasets programmatically.

big-data biomedical-image-processing chunked-image cloud connectomics electron-microscopy gcs large-image matrix mesh microscopy microscopy-images neuroglancer numpy python s3 serverless skeletons tensor volumetric-data

Last synced: 15 May 2025

https://github.com/mica-mni/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. 🤠

analysis awesome connectomics enigma life-changing-magic mri multiscale multisite neuroimaging open-source straight-fire visualization workflows

Last synced: 24 Jul 2025

https://github.com/aplbrain/dotmotif

A performant, powerful query framework to search for network motifs

aplbrain bossdb connectome connectomics dotmotif graph graph-database graph-matching motif-discovery motifs neo4j networkx python query-language subgraph-isomorphism vf2

Last synced: 17 Mar 2025

https://github.com/MICA-MNI/micaopen

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

connectomics gradients histology machine-learning multi-scale multimodal networks neuroimaging neuroscience

Last synced: 01 May 2025

https://github.com/mica-mni/micaopen

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

connectomics gradients histology machine-learning multi-scale multimodal networks neuroimaging neuroscience

Last synced: 05 Apr 2025

https://github.com/google-research/sofima

Scalable Optical Flow-based Image Montaging and Alignment

2d 3d 4d alignment-algorithm biomedical-image-processing connectomics electron-microscopy jax microscopy python3 stitching-algorithm

Last synced: 05 Apr 2025

https://github.com/natverse/nat

NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

3d connectomics cran image-analysis neuroanatomy neuroanatomy-toolbox neuron neuron-morphology neuroscience r visualisation

Last synced: 22 Oct 2025

https://github.com/aplbrain/grandiso-networkx

Performant, pure-Python subgraph isomorphism and monomorphism search (aka "motif search")

algorithm aplbrain bossdb connectomics dotmotif grand-graphs grand-iso graphs network network-analysis network-biology subgraph-isomorphism ullman vf2

Last synced: 31 Oct 2025

https://github.com/sidchop/brainconn

Brainconn - an R package for visualising brain connectivity data in 2D and interactive 3D

connectivity connectivity-matrix connectomics eeg meg mri networks neuroimaging

Last synced: 02 May 2025

https://github.com/structuralneurobiologylab/syconn

Toolkit for the generation and analysis of volume eletron microscopy based synaptic connectomes of brain tissue.

connectivity-matrix connectomics image-analysis image-processing morphology-analysis semantic-segmentation

Last synced: 17 Mar 2026

https://github.com/google-research/connectomics

connectomics

Last synced: 06 Apr 2025

https://github.com/constantinpape/cluster_tools

Distributed segmentation for bio-image-analysis

3d-segmentation bio-image-analysis cluster-computing connectomics lifted-multicut microscopy-images multicut mutex-watershed segmentation watershed

Last synced: 08 Sep 2025

https://github.com/CAVEconnectome/CAVEclient

This is the python client for accessing REST APIs within the Connectome Annotation Versioning Engine.

connectomics

Last synced: 22 Jan 2026

https://github.com/seung-lab/fpzip

Cython bindings for fpzip, a floating point image compression algorithm.

compression connectomics floating-point image-analysis numpy python

Last synced: 16 Aug 2025

https://github.com/braph-software/BRAPH-2

BRAPH 2.0 is a comprehensive software package for the analysis and visualization of brain connectivity data, offering flexible customization, rich visualization capabilities, and a platform for collaboration in neuroscience research.

biomedical-engineering brain-connectivity-analysis brain-research computational-neuroscience connectomics data-analysis data-science data-visualization deep-learning graph-theory machine-learning matlab network-analysis neuroimaging neuroscience open-source reproducible-research research-tools scientific-software toolbox

Last synced: 01 May 2025

https://github.com/aschampion/diluvian

Flood filling networks for segmenting electron microscopy of neural tissue

connectomics keras-neural-networks

Last synced: 31 Jan 2026

https://github.com/janeliascicomp/workstation

Janelia Workstation

confocal-microscopy connectomics janelia neuroimaging neuroscience scientific-computing volume-rendering

Last synced: 21 Aug 2025

https://github.com/JaneliaSciComp/workstation

Janelia Workstation

confocal-microscopy connectomics janelia neuroimaging neuroscience scientific-computing volume-rendering

Last synced: 16 Apr 2025

https://github.com/ilastik/nature_methods_multicut_pipeline

connectomics neuron-segmentation

Last synced: 14 Mar 2026

https://github.com/natverse/fafbseg

Support functions for analysis of Drosophila connectomes especially the FAFB-FlyWire whole brain

connectomics neuroanatomy-toolbox neuroscience r

Last synced: 17 Feb 2026

https://github.com/lodurality/35_methods_miccai_2017

Code for MICCAI 2017 paper

connectomics neuroimaging quality-metrics reproducible-research structural-connectomes

Last synced: 23 Apr 2025

https://github.com/flyconnectome/cocoa

Comparative Connectomics for Python

celltypes clustering connectomics neurobiology neurons

Last synced: 17 Jan 2026

https://github.com/jakobtroidl/neuronal-motifs

interactive search and analysis for neuronal motifs

connectomics graph-visualization visualization

Last synced: 09 Apr 2026

https://github.com/bids-apps/ndmg

BIDS app for NeuroData's MRI to Graphs pipeline

bids bidsapp connectomics diffusion-mri docker-container singularity-container

Last synced: 29 May 2026

https://github.com/neurodata/mcc

Reproducible code for "Multiscale Comparative Connectomics"

connectomics graph-statistics

Last synced: 25 Apr 2025

https://github.com/natverse/neuprintr

R client utilities for interacting with the neuPrint connectome analysis service

connectomics neuroanatomy-toolbox neuroscience r

Last synced: 20 Jan 2026

https://github.com/neurodata/bgm

Repository for the paper "Bisected graph matching improves automated pairing of bilaterally homologous neurons from connectomes" https://direct.mit.edu/netn/article/doi/10.1162/netn_a_00287/113527/Bisected-graph-matching-improves-automated-pairing

connectomics graph-algorithms graph-analysis network-analysis network-science neuroscience python