connectomics

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

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

janelia-flyem/dvid

Distributed, Versioned, Image-oriented Dataservice

navis-org/skeletor

Extraction of 3D skeletons from meshes.

catmaid/CATMAID

Collaborative Annotation Toolkit for Massive Amounts of Image Data

cwatson/brainGraph

Graph theory analysis of brain MRI data

zudi-lin/pytorch_connectomics

PyTorch Connectomics: segmentation toolbox for EM connectomics

PennLINC/qsiprep

Preprocessing and reconstruction of diffusion MRI

seung-lab/cloud-volume

Read and write Neuroglancer datasets programmatically.

seung-lab/kimimaro

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

scalableminds/webknossos

Visualize, share and annotate your large 3D images online

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. 🤠

aplbrain/dotmotif

A performant, powerful query framework to search for network motifs

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.

MICA-MNI/micaopen

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

seung-lab/zmesh

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

aplbrain/grandiso-networkx

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

google-research/sofima

Scalable Optical Flow-based Image Montaging and Alignment

seung-lab/igneous

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

StructuralNeurobiologyLab/SyConn

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

sidchop/brainconn

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

urakubo/UNI-EM

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

constantinpape/cluster_tools

Distributed segmentation for bio-image-analysis

seung-lab/fpzip

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

google-research/connectomics

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.

aschampion/diluvian

Flood filling networks for segmenting electron microscopy of neural tissue

JaneliaSciComp/workstation

Janelia Workstation

CAVEconnectome/CAVEclient

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

ilastik/nature_methods_multicut_pipeline

ruizengalways/FOD-Net

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

VCG/compresso

Compresso: Efficient Compression of Segmentation Data For Connectomics

pykao/BraTS2018-survival-prediction

We provide a method to extract the tractographic features from structural MR images for patients with brain tumor

YuelongWu/feabas

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

JackieZhai/awesome-vem-datasets

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

lodurality/35_methods_MICCAI_2017

Code for MICCAI 2017 paper