flyconnectome/cocoa

Comparative Connectomics for Python

Language: Python - Size: 1.88 MB - Last synced: about 6 hours ago - Pushed: about 11 hours ago - Stars: 1 - Forks: 0

zudi-lin/pytorch_connectomics

PyTorch Connectomics: segmentation toolbox for EM connectomics

Language: Python - Size: 92.1 MB - Last synced: about 14 hours ago - Pushed: 1 day ago - Stars: 163 - Forks: 74

seung-lab/igneous

Scalable Neuroglancer compatible Downsampling, Meshing, Skeletonizing, Contrast Normalization, Transfers and more.

Language: Python - Size: 5.48 MB - Last synced: about 6 hours ago - Pushed: 1 day ago - Stars: 40 - Forks: 15

bdpedigo/skedits

Examining the effect of proofreading on inferences in connectomics

Language: Python - Size: 572 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 0 - Forks: 0

natverse/fafbseg

Support functions for analysis of FAFB EM segmentation

Language: R - Size: 64.2 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 6 - Forks: 4

seung-lab/kimimaro

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

Language: Python - Size: 11.1 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 124 - Forks: 21

seung-lab/cloud-volume

Read and write Neuroglancer datasets programmatically.

Language: Python - Size: 65.7 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 125 - Forks: 42

janelia-flyem/dvid

Distributed, Versioned, Image-oriented Dataservice

Language: Go - Size: 16.2 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 195 - Forks: 33

CAVEconnectome/CAVEclient

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

Language: Python - Size: 11.9 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 19 - Forks: 12

JaneliaSciComp/workstation

Janelia Workstation

Language: Java - Size: 98 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 20 - Forks: 11

seung-lab/zmesh

Marching Cubes & Mesh Simplification on multi-label 3D images.

Language: C++ - Size: 621 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 55 - Forks: 8

bids-apps/ndmg

BIDS app for NeuroData's MRI to Graphs pipeline

Language: Dockerfile - Size: 70.3 KB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 5 - Forks: 8

catmaid/CATMAID

Collaborative Annotation Toolkit for Massive Amounts of Image Data

Language: JavaScript - Size: 76.3 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 181 - Forks: 56

PennLINC/qsiprep

Preprocessing and reconstruction of diffusion MRI

Language: HTML - Size: 178 MB - Last synced: 22 days ago - Pushed: 22 days ago - Stars: 129 - Forks: 52

google-research/connectomics

Language: Python - Size: 266 KB - Last synced: 6 days ago - Pushed: about 1 month ago - Stars: 22 - Forks: 8

google-research/sofima

Scalable Optical Flow-based Image Montaging and Alignment

Language: Jupyter Notebook - Size: 727 KB - Last synced: 6 days ago - Pushed: 2 months ago - Stars: 48 - Forks: 12

navis-org/skeletor

Extraction of 3D skeletons from meshes.

Language: Python - Size: 2.06 MB - Last synced: 28 days ago - Pushed: about 1 month ago - Stars: 175 - Forks: 24

aschampion/diluvian

Flood filling networks for segmenting electron microscopy of neural tissue

Language: Python - Size: 431 KB - Last synced: 14 days ago - Pushed: over 1 year ago - Stars: 23 - Forks: 13

scalableminds/webknossos

Visualize, share and annotate your large 3D images online

Language: TypeScript - Size: 667 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 118 - Forks: 16

google/ffn

Flood-Filling Networks for instance segmentation in 3d volumes.

Language: Python - Size: 3.43 MB - Last synced: 7 days ago - Pushed: 3 months ago - Stars: 292 - Forks: 97

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: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

seung-lab/euclidean-distance-transform-3d

Euclidean distance & signed distance transform for multi-label 3D anisotropic images using marching parabolas.

Language: C++ - Size: 6.51 MB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 217 - Forks: 36

ruizengalways/FOD-Net

FOD-Net: A Deep Learning Method for Fiber Orientation Distribution Angular Super Resolution

Language: Python - Size: 7.18 MB - Last synced: 9 days ago - Pushed: about 2 years ago - Stars: 17 - Forks: 5

aplbrain/grandiso-networkx

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

Language: Python - Size: 175 KB - Last synced: 25 days ago - Pushed: about 2 months ago - Stars: 49 - Forks: 10

cajal/microns-ta3 Fork of dimitri-yatsenko/microns-ta3

MICrONS TA3 connectivity database

Language: Jupyter Notebook - Size: 222 KB - Last synced: about 2 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 2

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. 🤠

Language: Python - Size: 132 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 113 - Forks: 26

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: 1.08 GB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 26 - Forks: 11

VCG/compresso

Compresso: Efficient Compression of Segmentation Data For Connectomics

Language: C++ - Size: 9.98 MB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 11 - Forks: 4

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: 2 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 1

seung-lab/fpzip

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

Language: C++ - Size: 975 KB - Last synced: 16 days ago - Pushed: 5 months ago - Stars: 32 - Forks: 4

sidchop/brainconn

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

Language: R - Size: 95.7 MB - Last synced: about 1 month ago - Pushed: 4 months ago - Stars: 33 - Forks: 5

constantinpape/cluster_tools

Distributed segmentation for bio-image-analysis

Language: Python - Size: 1.67 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 33 - Forks: 13

MICA-MNI/micaopen

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

Language: MATLAB - Size: 1.68 GB - Last synced: 2 months ago - Pushed: 4 months ago - Stars: 63 - Forks: 37

YuelongWu/feabas

Finite-Element Assisted Brain Assembly System for stitching & alignment of connectomics data

Language: Python - Size: 550 KB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 9 - Forks: 3

aplbrain/dotmotif

A performant, powerful query framework to search for network motifs

Language: Python - Size: 838 KB - Last synced: 13 days ago - Pushed: 8 months ago - Stars: 80 - Forks: 9

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: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

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: 45.1 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 72 - Forks: 18

biswasr/cits

Python package for CITS algorithm: Causal inference from time series data

Language: Python - Size: 4.74 MB - Last synced: 29 days ago - Pushed: 5 months ago - Stars: 2 - Forks: 0

natverse/neuprintr

R client utilities for interacting with the neuPrint connectome analysis service

Language: R - Size: 19.5 MB - Last synced: about 2 months ago - Pushed: 8 months ago - Stars: 3 - Forks: 3

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: 4 months ago - Pushed: 6 months ago - Stars: 39 - Forks: 8

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: 3 days ago - Pushed: 6 months ago - Stars: 2 - Forks: 0

schlegelp/clio-py Fork of janelia-flyem/clio-py

Python client for clio-store

Language: Python - Size: 39.1 KB - Last synced: 28 days ago - Pushed: 4 months ago - Stars: 0 - Forks: 1

ilastik/nature_methods_multicut_pipeline

Language: Python - Size: 3.46 MB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 18 - Forks: 2

seung-lab/zebrafish Fork of sylhare/Type-on-Strap

Zebrafish Hindbrain Connectome

Language: Liquid - Size: 117 MB - Last synced: about 1 month ago - Pushed: 5 months ago - Stars: 1 - Forks: 2

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: 4 months ago - Pushed: 8 months ago - Stars: 1 - Forks: 0

jakobtroidl/neuronal-motifs

interactive search and analysis for neuronal motifs

Language: JavaScript - Size: 2.04 GB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 4 - Forks: 0

cwatson/brainGraph

Graph theory analysis of brain MRI data

Language: R - Size: 5.65 MB - Last synced: 4 months ago - Pushed: about 3 years ago - Stars: 159 - Forks: 46

abejeyapratap/fly-connectome

Graph Theoretical Network Analysis on the Drosophila Hemibrain Connectome provided by Google Research

Language: HTML - Size: 43.3 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 2 - Forks: 0

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: 6 months ago - Pushed: 6 months ago - Stars: 4 - Forks: 1

wilson-lab/nat-tech

co-visualise confocal images of fly brains and connectome reconstructions in FIJI

Language: ImageJ Macro - Size: 112 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

flyconnectome/tracerutils

R tools for EM tracers

Language: R - Size: 225 KB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 0 - Forks: 1

urakubo/UNI-EM

A unified environment for DNN-based automated segmentation of neuronal EM images

Language: Python - Size: 166 MB - Last synced: 7 months ago - Pushed: 9 months ago - Stars: 36 - Forks: 12

sarastokes/SBFSEM-tools

Matlab toolbox for connectomics analysis and rendering

Language: MATLAB - Size: 45 MB - Last synced: 7 months ago - Pushed: 10 months ago - Stars: 4 - Forks: 7

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: 7 months ago - Pushed: over 5 years ago - Stars: 9 - Forks: 1

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: 7 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

constantinpape/skeletor

Tools and wrappers for skeletonization.

Language: Python - Size: 35.2 KB - Last synced: 8 months ago - Pushed: almost 5 years ago - Stars: 2 - Forks: 0

mackelab/sbi-for-connectomics

Research code and results for the paper "Simulation-based inference for computational connectomics" (Boelts et al. 2023, @janfb)

Language: Jupyter Notebook - Size: 8.94 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 1 - Forks: 2

lodurality/35_methods_MICCAI_2017

Code for MICCAI 2017 paper

Language: Python - Size: 192 MB - Last synced: 10 months ago - Pushed: over 6 years ago - Stars: 9 - 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: 10 months ago - Pushed: almost 3 years ago - Stars: 4 - Forks: 3

seung-lab/compressedseg Fork of janelia-flyem/compressedseg

compressed_segmentation for Neuroglancer volumes. This is the PyPI package fork.

Language: C++ - Size: 532 KB - Last synced: about 1 month ago - Pushed: about 2 months ago - Stars: 4 - Forks: 1

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: about 1 year ago - Pushed: about 1 year ago - Stars: 2 - Forks: 1

JackieZhai/awesome-vem-datasets

Open source volume electron microscopy (vEM) datasets for connectomics.

Size: 59.8 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 8 - Forks: 3

neurodata/connectomic-heritability

Language: Python - Size: 95.9 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

jabae/Cnapse

Automated synapse detection in C. elegans EM images.

Language: Jupyter Notebook - Size: 11.3 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 2 - Forks: 1

neurodata/MCC

Reproducible code for "Multiscale Comparative Connectomics"

Language: Jupyter Notebook - Size: 28.9 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 4 - Forks: 1

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: about 1 month ago - Pushed: over 5 years ago - Stars: 9 - Forks: 1

basiralab/MultigraphGNet

Predicting multigraph brain population from a single graph

Language: Python - Size: 2.39 MB - Last synced: about 1 year ago - Pushed: over 1 year 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: about 1 year ago - Pushed: almost 2 years ago - Stars: 5 - Forks: 2

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: about 1 year ago - Pushed: almost 3 years ago - Stars: 2 - Forks: 0

geekswaroop/cremi_alignment

Reverse script for CREMI Benchmark

Language: Python - Size: 2.72 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 1

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: about 1 year ago - Pushed: almost 5 years ago - Stars: 4 - Forks: 0

jesusdaniel/graphclass

Language: R - Size: 260 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 3 - Forks: 4

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: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 1

seung-lab/compresso Fork of VCG/compresso

Compresso: Efficient Compression of Segmentation Data For Connectomics

Language: C++ - Size: 37.4 MB - Last synced: 9 days ago - Pushed: 2 months ago - Stars: 4 - 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: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

brainhack-ch/conn-viz

OG 2019 - Project 09: Visualizing brain connectomics using D3.js

Language: JavaScript - Size: 25.3 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 6 - Forks: 1

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: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 2

catmaid/catpy

Python client for the CATMAID API

Language: Python - Size: 204 KB - Last synced: 4 days ago - Pushed: over 1 year ago - Stars: 4 - Forks: 2

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: about 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

natverse/drvid

Access to DVID API

Language: R - Size: 97.7 KB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 2

VirtualFlyBrain/VirtualFlyBrain.github.io

Virtual Fly Brain blog and documentation site

Language: JavaScript - Size: 65.3 MB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

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: about 1 year ago - Pushed: almost 4 years ago - Stars: 1 - Forks: 0

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: about 1 year ago - Pushed: about 5 years ago - Stars: 0 - Forks: 1

mental689/connectomics

Semantic segmentation architectures for connectomics.

Language: Python - Size: 245 MB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 1 - Forks: 0

RussTorres/catmaid_tools Fork of htem/catmaid_tools

Tools for accessing data from a catmaid server

Language: Python - Size: 1.07 MB - Last synced: about 1 year ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0