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connectomics

Here are 69 public repositories matching this topic...

google / ffn

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

segmentation connectomics instance-segmentation ffn flood-filling-networks

Updated May 10, 2021
Python

janelia-flyem / dvid

Distributed, Versioned, Image-oriented Dataservice

go big-data key-value neuroscience versioning image-storage connectomics http-service dataservice

Updated Sep 6, 2022
Go

catmaid / CATMAID

Collaborative Annotation Toolkit for Massive Amounts of Image Data

image-annotation neuroscience network-analysis connectomics

Updated Sep 9, 2022
JavaScript

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

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

python algorithm cpp numpy parallel neuroscience signed-distance-field connectomics signed-distance-functions distance-transform 3d 2d biomedical-image-processing 1d anisotropy euclidean-distance anisotropic euclidean-distance-transform marching-parabolas

Updated May 20, 2022
C++

cwatson / brainGraph

Graph theory analysis of brain MRI data

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

Updated Mar 26, 2021
R

zudi-lin / pytorch_connectomics

PyTorch Connectomics: segmentation toolbox for EM connectomics

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

Updated Sep 13, 2022
Python

navis-org / skeletor

3D skeleton extraction from meshes.

python skeleton mesh neurons volumes connectomics meshes 3d skeletonization teasar skeleton-extraction skeletonize

Updated Aug 2, 2022
Python

seung-lab / cloud-volume

Read and write Neuroglancer datasets programmatically.

Updated Sep 14, 2022
Python

kimimaro

seung-lab / kimimaro

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

python voxel python3 image-segmentation python2 centerline connectomics skeletons biomedical-image-processing skeletonization volumetric-data computer-vision-algorithms teasar medial-axis-transform centerline-extraction

Updated Mar 24, 2022
Python

PennLINC / qsiprep

Preprocessing and reconstruction of diffusion MRI

python pipelines connectomics diffusion-mri tractography

Updated Sep 13, 2022
HTML

webknossos

scalableminds / webknossos

A fully cloud- and browser-based 3D annotation tool for distributed large-scale data analysis in light- and electron-microscopy based Connectomics

neurobiology reconstruction connectomics em microscopy hacktoberfest microscopy-images

Updated Sep 13, 2022
TypeScript

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.

visualization windows macos linux image-annotation cross-platform desktop neuroscience connectomics

Updated Sep 14, 2022
C++

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. 🤠

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

Updated Aug 11, 2022
Python

MICA-MNI / micaopen

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

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

Updated Mar 11, 2022
MATLAB

seung-lab / zmesh

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

python meshing marching-cubes-algorithm mesh-generation marching-cubes connectomics biomedical-image-processing mesh-processing volumetric-data mesh-simplification

Updated Sep 1, 2022
C++

aplbrain / dotmotif

A performant, powerful query framework to search for network motifs

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

Updated Sep 13, 2022
Python

aplbrain / grandiso-networkx

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

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

Updated Dec 21, 2021
Python

urakubo / UNI-EM

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

segmentation connectomics micro-connectomics

Updated Sep 4, 2022
Python

SyConn

StructuralNeurobiologyLab / SyConn

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

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

Updated Sep 10, 2022
Python

seung-lab / igneous

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

visualization python docker kubernetes cloud python3 meshing connectomics ccl multi-resolution skeletonization volumetric-data downsample neuroglancer downsampling connected-components-labeling

Updated Aug 19, 2022
Python

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