GitHub topics: connectome
navis-org/navis
Python library for analysis of neuroanatomical data.
Language: Python - Size: 295 MB - Last synced at: 5 days ago - Pushed at: about 1 month ago - Stars: 95 - Forks: 33
navis-org/fafbseg-py
Tools to work with the FlyWire connectome. Fully interoperable with navis.
Language: Python - Size: 97.1 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 13 - Forks: 5
IHB-IBR-department/TMFC_toolbox Fork of Masharipov/TMFC_toolbox
TMFC toolbox - a new SPM toolbox for whole-brain task-modulated functional connectivity (TMFC) analysis with user-friendly graphical interface.
Language: MATLAB - Size: 42.7 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 1 - Forks: 1
connectomicslab/connectomemapper3
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.
Language: HTML - Size: 354 MB - Last synced at: 2 days ago - Pushed at: 3 months ago - Stars: 73 - Forks: 29
reiserlab/male-drosophila-visual-system-connectome-code
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
Language: Python - Size: 58.9 MB - Last synced at: 12 days ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 2
Masharipov/TMFC_toolbox
TMFC toolbox - a new SPM toolbox for whole-brain task-modulated functional connectivity (TMFC) analysis with user-friendly graphical interface.
Language: MATLAB - Size: 42.6 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 2
MICA-MNI/micapipe
micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below
Language: Shell - Size: 356 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 97 - Forks: 34
BlueBrain/brain-indexer 📦
Create indexes of simple shapes and find all indexed elements that intersect with a query region.
Language: C++ - Size: 3.67 MB - Last synced at: 14 days ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 1
BlueBrain/appositionizer 📦
Detect physical locations for synapses
Language: C++ - Size: 2.29 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 2 - Forks: 2
heyseth/worm-sim
Simulate the C. Elegans worm brain in your browser and interact with the worm as it moves around.
Language: JavaScript - Size: 63.5 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 377 - Forks: 35
makism/dyconnmap
A dynamic connectome mapping module in python.
Language: Python - Size: 105 MB - Last synced at: 2 days ago - Pushed at: almost 2 years ago - Stars: 103 - Forks: 31
aplbrain/dotmotif
A performant, powerful query framework to search for network motifs
Language: Python - Size: 888 KB - Last synced at: 21 days ago - Pushed at: 8 months ago - Stars: 84 - Forks: 9
eminSerin/NBS-Predict
A prediction-based extension of network-based statistics.
Language: MATLAB - Size: 33 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 31 - Forks: 6
seung-lab/RealNeuralNetworks.jl
A unified framework for skeletonization, morphological analysis, and connectivity analysis.
Language: Julia - Size: 5.55 MB - Last synced at: 3 months ago - Pushed at: 8 months ago - Stars: 40 - Forks: 2
seung-lab/zebrafish Fork of sylhare/Type-on-Strap
Zebrafish Hindbrain Connectome
Language: Liquid - Size: 117 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 3
favour-nerrise/xGW-GAT
An Explainable Geometric-Weighted Graph Attention Network (xGW-GAT) for Identifying Functional Networks Associated with Gait Impairment
Language: Python - Size: 70.3 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 13 - Forks: 2
seung-lab/chunkflow
Compose chunk operators to create a pipeline for local or distributed petabyte-scale computation
Language: Python - Size: 9.7 MB - Last synced at: 2 days ago - Pushed at: 5 months ago - Stars: 51 - Forks: 8
kausalflow/connectome
A Hugo theme with backlinks for online communities
Language: CSS - Size: 28.1 MB - Last synced at: 5 months ago - Pushed at: over 1 year ago - Stars: 35 - Forks: 8
navis-org/fastcore
[WIP] Fast core functions for navis re-implemented in Cython.
Language: Jupyter Notebook - Size: 250 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 2
gianlucarloni/CoCoReco
Code base for our paper "Connectivity-Inspired Network for Context-Aware Recognition" (ECCV 2024, Human-inspired Computer Vision workshop)
Language: Python - Size: 979 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0
zaidanfaza/Math-Modelling-Neurodegenerative-Disease
Supporting Files of paper titled "Dynamic Simulation of Parkinson's Disease and ALS Propagation in the Brain: A Reaction-Diffusion on Brain Networks Approach"
Language: MATLAB - Size: 29.3 MB - Last synced at: 4 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 1
OnnoKampman/phd-thesis
LaTeX code for my PhD thesis.
Language: TeX - Size: 7.68 MB - Last synced at: 5 months ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 1
OnnoKampman/FCEst
Methods for estimating time-varying functional connectivity (TVFC)
Language: Python - Size: 111 KB - Last synced at: 5 months ago - Pushed at: 11 months ago - Stars: 5 - Forks: 1
fgaz/GoPiGo Fork of Connectome/GoPiGo
GoPiGo Connectome Code
Language: Python - Size: 345 KB - Last synced at: about 1 year ago - Pushed at: almost 9 years ago - Stars: 1 - Forks: 0
connectlab/tvfc-heritability_Jun
Custom MATLAB code for Jun et al. NeuroImage 2022; https://doi.org/10.1016/j.neuroimage.2022.119274
Language: MATLAB - Size: 473 KB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0
bdpedigo/neuropull
A (soon to be) lightweight Python package for accessing single-cell connectome networks with metadata.
Language: Python - Size: 1.67 MB - Last synced at: 2 days ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0
neurodata/bilateral-connectome
A paper investigating bilateral symmetry of connectome networks.
Language: Python - Size: 559 MB - Last synced at: 21 days ago - Pushed at: about 1 year ago - Stars: 6 - Forks: 3
zhiyunl/CAM-dMRI
Weakly Object Localization on brain dMRI using CAM
Language: Jupyter Notebook - Size: 283 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 7 - Forks: 0
clintg6/DSN
Python tool for spatially normalizing diffusion MRI data
Language: Python - Size: 10.7 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 3
cwatson/brainGraph
Graph theory analysis of brain MRI data
Language: R - Size: 5.65 MB - Last synced at: about 1 year ago - Pushed at: about 4 years ago - Stars: 159 - Forks: 46
alexandershaw4/SourceMesh
A multipurpose matlab-based MEG/EEG overlay & network plotter
Language: MATLAB - Size: 217 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 13 - Forks: 7
rcruces/MRI_analytic_tools
Pipelines and tools for MRI analysis
Language: HTML - Size: 2.97 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 9 - Forks: 8
mballarin97/DrosophilaNetwork
Analysis from the point of view of network science of the connectome of the drosophila
Language: Jupyter Notebook - Size: 6.68 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0
eminSerin/NBSPredict_SpringerNature
The repository for the chapter about NBS-Predict in “Methods for analyzing large neuroimaging datasets” by Springer Nature.
Language: Jupyter Notebook - Size: 440 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0
isabelannwingert/Conchshell
Connectome Quality Control Software Development in-line with DiCIPHR's DTI Processing pipeline
Language: Python - Size: 56.6 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0
Raj-Lab-UCSF/spectrome
Spectral graph model base code and examples
Language: Jupyter Notebook - Size: 212 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 5 - Forks: 5
Raj-Lab-UCSF/Aggregation-Network-Diffusion
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
Language: MATLAB - Size: 5.52 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 2
JRam02/conn_fingerprint_neurodev
Language: Jupyter Notebook - Size: 157 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1
sumiya-kuroda/EMsegmentation-mito
EM segmentation of mitochondria from SNEMI3D data
Language: Jupyter Notebook - Size: 96 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 2
egyptdj/stagin
STAGIN: Spatio-Temporal Attention Graph Isomorphism Network
Language: Python - Size: 1.21 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 55 - Forks: 13
francopestilli/life
Please use the new version of LiFE: www.github.com/brain-life/encode
Language: Matlab - Size: 5.42 MB - Last synced at: 8 months ago - Pushed at: over 7 years ago - Stars: 35 - Forks: 15
czarrar/connectir
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.
Language: R - Size: 3.8 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 15 - Forks: 9
jchrispang/evolution-brain-tuning
Code supporting 'Evolutionary shaping of human brain dynamics'
Language: MATLAB - Size: 151 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 1
pfdamasceno/cortography
Cartographical collection of cortical atlases (neuroscience)
Language: Jupyter Notebook - Size: 7.15 MB - Last synced at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 3 - Forks: 0
Mengbo-Li/brainClass
Code and example data for transcriptional-data-guided brain network classification
Language: R - Size: 76.1 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0
basiralab/Meta-RegGNN
Meta-learning using graph neural networks for brain connectivity regression.
Language: Python - Size: 18.2 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0
merqurio/connectome-ml 📦
An essay on comparing 2 ML applications on connectomes
Language: TeX - Size: 442 KB - Last synced at: 16 days ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 1
basiralab/ABMT
ABMT (Adversarial Brain Multiplex Translator) for brain graph translation using geometric generative adversarial network (gGAN).
Language: Python - Size: 17.7 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 6 - Forks: 2
PavanChaggar/ConnectomesOld.jl
A package for handling and plotting brain connectomes obtained thorugh tractography.
Language: Julia - Size: 518 MB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 1
GemsLab/GroupINN
GNN with summarization/grouping layer for speed and interpretability
Language: Python - Size: 359 KB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 13 - Forks: 4
sidchop/carpetplotR
Fast and easy visualization of fMRI data quality using carpet plots.
Language: R - Size: 14.5 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 6 - Forks: 2
morteza/kaggle-trends
Kaggle TReNDS Neuroimaging
Language: Python - Size: 996 KB - Last synced at: 2 months ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0
csinva/abide-multitask-learning
Multi-task learning of functional connectivity on the ABIDE dataset.
Language: Jupyter Notebook - Size: 24.3 MB - Last synced at: 22 days ago - Pushed at: over 7 years ago - Stars: 3 - Forks: 1
ivan-ea/celegans_connectome
Language: Python - Size: 141 KB - Last synced at: almost 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0
VirtualFlyBrain/VirtualFlyBrain.github.old Fork of barryclark/jekyll-now
Virtual Fly Brain is the only resource integrating Drosophila neurobiology images, data and knowledge all regions of the nervous system from larva to adult.
Language: SCSS - Size: 8.12 MB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0
neurodata/connectocross
Connectocross: statistical characterizations and comparisons of nanoscale connectomes across taxa (A paper in progress)
Language: Jupyter Notebook - Size: 134 MB - Last synced at: 5 days ago - Pushed at: almost 4 years ago - Stars: 3 - Forks: 3
AlxndrMlk/Functional_Connectivity_Measures
Python 3 implementations of various Functional Connectivity measures
Language: Jupyter Notebook - Size: 219 KB - Last synced at: about 2 years ago - Pushed at: about 7 years ago - Stars: 3 - Forks: 0
levchenkoegor/cni_challenge
Solution for CNI Machine Learning Challenge
Language: Python - Size: 45.1 MB - Last synced at: 5 months ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0
brain-modelling-group/geomsurr Fork of breakspear/geomsurr
Generate random surrogate weighted networks that preserve the effect of distance on the weights.
Language: MATLAB - Size: 2.93 KB - Last synced at: almost 2 years ago - Pushed at: over 8 years ago - Stars: 1 - Forks: 1
gmalik9/BabyConnectome
maintainance of the code for complex network analysis based modeling of Event Related Potential (ERP) electroencephalography (EEG) data from baby brain, can be applied to other data, including human brain.
Language: Python - Size: 24.4 KB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 4 - Forks: 2
brainlife/ui-fibernavigator
Docker container for FiberNavigator for Brainlife.io
Language: Shell - Size: 1.47 MB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0
OldBonhart/EDA-NLP-PubMed-and-bioRxiv
Rapid analysis of scientific papers from bioRxiv and PubMed
Language: Jupyter Notebook - Size: 324 MB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0
malceore/connectbot
Modified GoPiGo bot connectome source to work on my custom robot.
Language: Python - Size: 19.5 KB - Last synced at: about 2 years ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0
karanaggarwal1994/life-gpu-opt
LiFE-GPU-opt software is an optimized implementation of the compute-intensive matrix operations of the LiFE algorithm for GPUs.
Language: MATLAB - Size: 129 KB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0
mental689/connectomics
Semantic segmentation architectures for connectomics.
Language: Python - Size: 245 MB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 0
seung-lab/emirt
EM Image Reconstruction Tools using Python
Language: Python - Size: 255 KB - Last synced at: about 1 year ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0