Topic: "connectomics"
google/ffn
Flood-Filling Networks for instance segmentation in 3d volumes.
Language: Python - Size: 3.49 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 325 - Forks: 99
seung-lab/euclidean-distance-transform-3d
Euclidean distance & signed distance transform for multi-label 3D anisotropic images using marching parabolas.
Language: C++ - Size: 6.54 MB - Last synced at: 7 days ago - Pushed at: 3 months ago - Stars: 249 - Forks: 36
navis-org/skeletor
Extraction of 3D skeletons from meshes.
Language: Python - Size: 2.41 MB - Last synced at: 20 days ago - Pushed at: 9 months ago - Stars: 227 - Forks: 27
janelia-flyem/dvid
Distributed, Versioned, Image-oriented Dataservice
Language: Go - Size: 15.6 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 200 - Forks: 33
catmaid/CATMAID
Collaborative Annotation Toolkit for Massive Amounts of Image Data
Language: JavaScript - Size: 78.8 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 189 - Forks: 57
zudi-lin/pytorch_connectomics
PyTorch Connectomics: segmentation toolbox for EM connectomics
Language: Python - Size: 91.1 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 182 - Forks: 78
cwatson/brainGraph
Graph theory analysis of brain MRI data
Language: R - Size: 5.65 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 159 - Forks: 46
seung-lab/cloud-volume
Read and write Neuroglancer datasets programmatically.
Language: Python - Size: 65.8 MB - Last synced at: 2 days ago - Pushed at: 4 days ago - Stars: 152 - Forks: 51
seung-lab/kimimaro
Skeletonize densely labeled 3D image segmentations with TEASAR. (Medial Axis Transform)
Language: C++ - Size: 13.1 MB - Last synced at: 9 days ago - Pushed at: 15 days ago - Stars: 151 - Forks: 27
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. ðŸ¤
Language: Python - Size: 132 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 145 - Forks: 35
scalableminds/webknossos
Visualize, share and annotate your large 3D images online
Language: TypeScript - Size: 758 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 142 - Forks: 27
aplbrain/dotmotif
A performant, powerful query framework to search for network motifs
Language: Python - Size: 888 KB - Last synced at: 26 days ago - Pushed at: 9 months ago - Stars: 85 - Forks: 10
MICA-MNI/micaopen
Open Scripts and pipelines from the Multimodal Imaging and Connectome Analysis Lab at the Montreal Neurological Institute
Language: Jupyter Notebook - Size: 1.7 GB - Last synced at: 6 days ago - Pushed at: 22 days ago - Stars: 77 - Forks: 42
knossos-project/knossos
KNOSSOS is a software tool for the visualization and annotation of 3D image data and was developed for the rapid reconstruction of neural morphology and connectivity.
Language: C++ - Size: 45.4 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 74 - Forks: 19
google-research/sofima
Scalable Optical Flow-based Image Montaging and Alignment
Language: Jupyter Notebook - Size: 4.73 MB - Last synced at: 6 days ago - Pushed at: 3 months ago - Stars: 73 - Forks: 16
natverse/nat
NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.
Language: R - Size: 61.1 MB - Last synced at: 25 days ago - Pushed at: 8 months ago - Stars: 68 - Forks: 28
seung-lab/zmesh
Marching Cubes & Mesh Simplification on multi-label 3D images.
Language: C++ - Size: 621 MB - Last synced at: 28 days ago - Pushed at: 3 months ago - Stars: 62 - Forks: 8
aplbrain/grandiso-networkx
Performant, pure-Python subgraph isomorphism and monomorphism search (aka "motif search")
Language: Python - Size: 175 KB - Last synced at: 23 days ago - Pushed at: 10 months ago - Stars: 62 - Forks: 10
sidchop/brainconn
Brainconn - an R package for visualising brain connectivity data in 2D and interactive 3D
Language: R - Size: 95.7 MB - Last synced at: 30 days ago - Pushed at: about 2 months ago - Stars: 53 - Forks: 7
seung-lab/igneous
Scalable Neuroglancer compatible Downsampling, Meshing, Skeletonizing, Contrast Normalization, Transfers and more.
Language: Python - Size: 5.48 MB - Last synced at: 3 days ago - Pushed at: 11 days ago - Stars: 49 - Forks: 22
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.
Language: MATLAB - Size: 1.12 GB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 47 - Forks: 13
google-research/connectomics
Language: Python - Size: 412 KB - Last synced at: 6 days ago - Pushed at: 9 days ago - Stars: 41 - Forks: 14
StructuralNeurobiologyLab/SyConn
Toolkit for the generation and analysis of volume eletron microscopy based synaptic connectomes of brain tissue.
Language: Python - Size: 156 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 39 - Forks: 8
constantinpape/cluster_tools
Distributed segmentation for bio-image-analysis
Language: Python - Size: 1.71 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 38 - Forks: 14
urakubo/UNI-EM
A unified environment for DNN-based automated segmentation of neuronal EM images
Language: Python - Size: 166 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 35 - Forks: 11
seung-lab/fpzip
Cython bindings for fpzip, a floating point image compression algorithm.
Language: C++ - Size: 982 KB - Last synced at: 4 days ago - Pushed at: 2 months ago - Stars: 34 - Forks: 5
CAVEconnectome/CAVEclient
This is the python client for accessing REST APIs within the Connectome Annotation Versioning Engine.
Language: Python - Size: 14.2 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 28 - Forks: 13
JaneliaSciComp/workstation
Janelia Workstation
Language: Java - Size: 97.8 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 23 - Forks: 12
aschampion/diluvian
Flood filling networks for segmenting electron microscopy of neural tissue
Language: Python - Size: 431 KB - Last synced at: 2 days ago - Pushed at: over 2 years ago - Stars: 23 - Forks: 13
ilastik/nature_methods_multicut_pipeline
Language: Python - Size: 3.46 MB - Last synced at: about 1 month ago - Pushed at: about 4 years ago - Stars: 20 - Forks: 2
ruizengalways/FOD-Net
FOD-Net: A Deep Learning Method for Fiber Orientation Distribution Angular Super Resolution
Language: Python - Size: 7.18 MB - Last synced at: 10 months ago - Pushed at: about 3 years ago - Stars: 17 - Forks: 5
YuelongWu/feabas
Finite-Element Assisted Brain Assembly System for stitching & alignment of connectomics data
Language: Python - Size: 936 KB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 16 - Forks: 5
JackieZhai/awesome-vem-datasets
Open source volume electron microscopy (vEM) datasets for connectomics.
Size: 63.9 MB - Last synced at: 4 days ago - Pushed at: 7 months ago - Stars: 13 - Forks: 3
VCG/compresso
Compresso: Efficient Compression of Segmentation Data For Connectomics
Language: C++ - Size: 9.98 MB - Last synced at: 8 days ago - Pushed at: over 3 years ago - Stars: 12 - Forks: 4
seung-lab/data-cube-x Fork of william-silversmith/data-cube-x
JS biomedical 3D image stack. Fast CPU rendering. Easy web app integration.
Language: JavaScript - Size: 16.1 MB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 9 - Forks: 1
pykao/BraTS2018-survival-prediction
We provide a method to extract the tractographic features from structural MR images for patients with brain tumor
Language: Python - Size: 67.4 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 9 - Forks: 1
lodurality/35_methods_MICCAI_2017
Code for MICCAI 2017 paper
Language: Python - Size: 192 MB - Last synced at: about 1 month ago - Pushed at: over 7 years ago - Stars: 9 - Forks: 3
natverse/fafbseg
Support functions for analysis of Drosophila connectomes especially the FAFB-FlyWire whole brain
Language: R - Size: 49 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 8 - Forks: 4
natverse/coconatfly
Comparative Connectomics of Public and In Progress Drosophila Datasets
Language: R - Size: 14.2 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 7 - Forks: 1
markschoene/MeLeCoLe
Metric learning and contrastive learning for neuron segmentation
Language: Python - Size: 32.2 KB - Last synced at: 12 months ago - Pushed at: over 2 years ago - Stars: 7 - Forks: 0
brainhack-ch/conn-viz
OG 2019 - Project 09: Visualizing brain connectomics using D3.js
Language: JavaScript - Size: 25.3 MB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 6 - Forks: 1
flyconnectome/cocoa
Comparative Connectomics for Python
Language: Python - Size: 2.04 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 5 - Forks: 2
jakobtroidl/neuronal-motifs
interactive search and analysis for neuronal motifs
Language: JavaScript - Size: 2.04 GB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 5 - Forks: 0
bids-apps/ndmg
BIDS app for NeuroData's MRI to Graphs pipeline
Language: Dockerfile - Size: 71.3 KB - Last synced at: about 1 month ago - Pushed at: 7 months ago - Stars: 5 - Forks: 8
sarastokes/SBFSEM-tools
Matlab toolbox for connectomics analysis and rendering
Language: MATLAB - Size: 44.9 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 5 - Forks: 7
basiralab/MultigraphGNet
Predicting multigraph brain population from a single graph
Language: Python - Size: 2.39 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 1
connectomics-vis-survey/connectomics-vis-survey.github.io
Resources for the EuroVis 2022 survey paper on Visualization and Analysis in High-Resolutiuon Connectomics
Language: JavaScript - Size: 193 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 5 - Forks: 2
neurodata/MCC
Reproducible code for "Multiscale Comparative Connectomics"
Language: Jupyter Notebook - Size: 28.9 MB - Last synced at: about 1 month ago - Pushed at: almost 3 years ago - Stars: 5 - Forks: 2
natverse/neuprintr
R client utilities for interacting with the neuPrint connectome analysis service
Language: R - Size: 19.6 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 4 - Forks: 3
seung-lab/compresso Fork of VCG/compresso
Compresso: Efficient Compression of Segmentation Data For Connectomics
Language: C++ - Size: 37.5 MB - Last synced at: 2 days ago - Pushed at: 3 months ago - Stars: 4 - Forks: 1
seung-lab/compressedseg Fork of janelia-flyem/compressedseg
compressed_segmentation for Neuroglancer volumes. This is the PyPI package fork.
Language: C++ - Size: 541 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 4 - Forks: 1
htem/raygun
An image enhancement and segmentation pipeline for generating connectomic reconstructions from X-ray holographic nanotomography, using CycleGANs, Local Shape Descriptors, and Mutex Watershed. Built with PyTorch, Daisy, and Gunpowder.
Language: Python - Size: 145 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1
catmaid/catpy
Python client for the CATMAID API
Language: Python - Size: 204 KB - Last synced at: 4 days ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 3
DynamicsAndNeuralSystems/humanStructureFunction
Analysis code for connecting time-series properties of BOLD dynamics to connectivity properties using human fMRI and DWI data from HCP
Language: MATLAB - Size: 370 KB - Last synced at: almost 2 years ago - Pushed at: almost 4 years ago - Stars: 4 - Forks: 3
Animadversio/FloodFillNetwork-Notes
Flood Fill Network for 3d Electron Microscopy volume neuron segmentation. Adapt from google FFN-master add notes and custom variation and parallelization (for windows and our retina & LGN data)
Language: Python - Size: 1.69 MB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 4 - Forks: 0
mackelab/sbi-for-connectomics
Research code and results for the paper "Simulation-based inference for computational connectomics" (Boelts et al. 2023 PLoS CB, @janfb)
Language: Jupyter Notebook - Size: 8.94 MB - Last synced at: 10 months ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 3
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
Language: Python - Size: 82 MB - Last synced at: about 2 months ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 2
jesusdaniel/graphclass
Language: R - Size: 260 MB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 3 - Forks: 4
biswasr/cits
Python package for CITS algorithm: Causal inference from time series data
Language: Python - Size: 4.74 MB - Last synced at: about 3 hours ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0
jabae/Cnapse
Automated synapse detection in C. elegans EM images.
Language: Jupyter Notebook - Size: 11.3 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 1
abejeyapratap/fly-connectome
Graph Theoretical Network Analysis on the Drosophila Hemibrain Connectome provided by Google Research
Language: HTML - Size: 43.3 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - 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
sgoldt/reconstructing_memories
Code for "Bayesian reconstruction of memories stored in neural networks from their connectivity" https://arxiv.org/abs/2105.07416
Language: Python - Size: 37.1 KB - Last synced at: about 1 year ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 1
constantinpape/skeletor
Tools and wrappers for skeletonization.
Language: Python - Size: 35.2 KB - Last synced at: about 2 months ago - Pushed at: almost 6 years ago - Stars: 2 - Forks: 0
wilson-lab/nat-tech
co-visualise confocal images of fly brains and connectome reconstructions in FIJI
Language: Jupyter Notebook - Size: 325 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0
seung-lab/zebrafish Fork of sylhare/Type-on-Strap
Zebrafish Hindbrain Connectome
Language: Liquid - Size: 117 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 3
giovannivolpe/BRAPH-2-Matlab-beta Fork of 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.
Language: MATLAB - Size: 933 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0
geekswaroop/cremi_alignment
Reverse script for CREMI Benchmark
Language: Python - Size: 2.72 MB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 1
geekswaroop/Awesome-Connectomics
A curated list of resources, papers and articles for 3D volumetric segmentation of connectomics in EM Images.
Size: 0 Bytes - Last synced at: about 2 years ago - Pushed at: almost 5 years ago - Stars: 1 - 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
pschuber/SyConn
Toolkit for the generation and analysis of volume eletron microscopy based synaptic connectomes of brain tissue.
Last synced at: 11 months ago - Stars: 1 - Forks: 1
schlegelp/clio-py Fork of janelia-flyem/clio-py
Python client for clio-store
Language: Python - Size: 54.7 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 1
JiangYi0311/Mito-SegEM
A mitochondrial analysis tool for the vEM dataset.
Language: Python - Size: 6.17 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0
bdpedigo/skedits
Examining the effect of proofreading on inferences in connectomics
Language: Python - Size: 1.35 GB - Last synced at: 3 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0
ShkalikovOleh/connectomics_segmentation
Semantic segmentation of the connectomics volume with limited amount of labeled data. It is my research project at TU Dresden.
Language: Python - Size: 8.07 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
neurodata/connectomic-heritability
Language: Python - Size: 95.9 MB - Last synced at: 3 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
LPNC-LANG/SENECA
Repo for the article on "Modeling the Neurocognitive Dynamics of Language across the Lifespan"
Language: R - Size: 6.74 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
FCP-INDI/app-C-PAC-brainlife.io
This is the official C-PAC (Configurable Pipeline for the Analysis of Connectomes) brainlife.io app. Currently this app runs either the default pipeline or one of our preconfigured pipelines.
Language: Shell - Size: 204 KB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 2
Ariel-Flint-Ashery/3D-Connectome-VDERM
Repository for code built during 3 month internship with Barabasi Lab (Oct 22 - Jan 23). In this project, we aim to build a diffusion-based method for density-equalizing the 3D connectome. Supervisors: Albert-Laszlo Barabasi & Csaba Both.
Language: Python - Size: 2.49 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
megancostello/3d-synapse-detection
Final Project for CSCI 3397 - Biomedical Image Analysis. Using Pytorch Connectomics and 3D UNet model to implement 3D segmentation for synapse detection, using semi-unsupervised learning
Language: Jupyter Notebook - Size: 6.91 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 1
dxlnr/EManalysis
This repository aims to make analysis on human brain tissue (EM data). This work is done within the chair of Lichtman Lab. at Harvard University.
Language: Jupyter Notebook - Size: 56.9 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 1
adrameshiu/c-elegans-wiring
Study the connectome structure in C. Elegans by finding paths between a set of neuron classes present.
Language: Python - Size: 2.58 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0
adrameshiu/NetViz
Visualize neural networks into a heirarchial graph using networkx. Weights and signs will be respected.
Language: Python - Size: 4.47 MB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0
VirtualFlyBrain/VirtualFlyBrain.github.io
Virtual Fly Brain blog and documentation site
Language: JavaScript - Size: 65.3 MB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0
natverse/drvid
Access to DVID API
Language: R - Size: 97.7 KB - Last synced at: about 1 year ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 2
flyconnectome/tracerutils
R tools for EM tracers
Language: R - Size: 225 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 1
sarastokes/RabbitGammaCell
Code and data used in Bordt et al (2019) Synaptic inputs and connectivity of a sparsely branched ganglion cell in rabbit retina
Language: MATLAB - Size: 943 KB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 1
cajal/microns-ta3 Fork of dimitri-yatsenko/microns-ta3
MICrONS TA3 connectivity database
Language: Jupyter Notebook - Size: 222 KB - Last synced at: about 1 year ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 2
RussTorres/catmaid_tools Fork of htem/catmaid_tools
Tools for accessing data from a catmaid server
Language: Python - Size: 1.07 MB - Last synced at: about 2 years ago - Pushed at: over 8 years ago - Stars: 0 - Forks: 0
