seung-lab repositories

crackle

Public

3D dense segmentation compression codec based on crack codes.

compression compression-algorithm crack-code

C++

•

BSD 3-Clause "New" or "Revised" License

•1•15•11•1•Updated

Apr 25, 2026

ng-extend

Public

Vue

•8•5•3•27•Updated

Apr 25, 2026

connected-components-3d

Public

Connected components on discrete and continuous multilabel 3D & 2D images. Handles 26, 18, and 6 connected variants; periodic boundaries (4, 8, & 6)

python algorithm cpp

python algorithm cpp numpy cython image-processing neighborhood decision-tree 3d 2d

C++

•

GNU Lesser General Public License v3.0

•48•450•15•4•Updated

Apr 24, 2026

tile-transcoder

Public

Transfer and convert the file format of image tiles.

Python

•

BSD 3-Clause "New" or "Revised" License

•1•3•0•0•Updated

Apr 24, 2026

cloud-volume

Public

Read and write Neuroglancer datasets programmatically.

python cloud big-data

python cloud big-data serverless numpy matrix s3 gcs mesh tensor

Python

•

BSD 3-Clause "New" or "Revised" License

•53•171•84•6•Updated

Apr 24, 2026

igneous

Public

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

visualization python docker

visualization python docker kubernetes cloud python3 meshing connectomics ccl multi-resolution

Python

•

GNU General Public License v3.0

•24•67•28•3•Updated

Apr 24, 2026

zmesh

Public

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

python meshing marching-cubes-algorithm

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

C++

•

GNU General Public License v3.0

•9•72•2•1•Updated

Apr 24, 2026

neuroglancer

Public

WebGL-based viewer for volumetric data

TypeScript

•

Apache License 2.0

•360•25•91•39•Updated

Apr 24, 2026

abiss

Public

Affinity based image segmentation system

C++

•

GNU General Public License v3.0

•4•6•0•2•Updated

Apr 24, 2026

KVDbClient

Public

generic key-value database client

Python

•

MIT License

•0•0•0•0•Updated

Apr 23, 2026

microviewer

Public

Multiplatform 3D numpy image browser based viewer with voxel painting.

3d-reconstruction biomedical-image-processing voxel-painting

JavaScript

•

GNU Lesser General Public License v2.1

•1•16•5•0•Updated

Apr 21, 2026

seuron

Public

SEUnglab neuRON pipeline

Python

•

MIT License

•7•7•1•2•Updated

Apr 20, 2026

fastmorph

Public

Multilabel and Grey 3D morphological image processing functions. Dilate, Erode, Opening, Closing, Hole Filling.

image-processing closing grayscale

image-processing closing grayscale erosion dilation 3d multi-label opening morphological-operators morphological-image-processing

C++

•

GNU Lesser General Public License v3.0

•3•19•2•0•Updated

Apr 18, 2026

fill_voids

Public

Fill holes in binary 2D & 3D images fast.

python cpp numpy

python cpp numpy morphology image-processing binary-image fill-gaps fill-holes fill-voids

C++

•

GNU Lesser General Public License v3.0

•5•29•2•1•Updated

Apr 18, 2026

vqsort

Public

Sort arrays with SIMD vqsort in Python

Python

•

BSD 3-Clause "New" or "Revised" License

•0•1•0•0•Updated

Apr 15, 2026

fastremap

Public

Remap, mask, renumber, unique, and in-place transposition of 3D labeled images. Point cloud too.

python numpy cython

python numpy cython looping point-cloud python3 remap biomedical-image-processing array-manipulations unique

C++

•

GNU Lesser General Public License v3.0

•9•65•4•1•Updated

Apr 15, 2026

ngl_bench

Public

Manipulating neuroglancer and unraveling connectomes is an agentic problem.

Python

•1•0•0•0•Updated

Mar 23, 2026

cloud-files

Public

Threaded Python and CLI client library for AWS S3, Google Cloud Storage (GCS), in-memory, and the local filesystem.

cli client key-value

cli client key-value s3 concurrency parallel google-cloud-storage bucket threading concurrent

Python

•

BSD 3-Clause "New" or "Revised" License

•9•44•15•0•Updated

Mar 20, 2026

messaging-client

Public

Python

•

GNU General Public License v3.0

•1•0•0•0•Updated

Mar 19, 2026

euclidean-distance-transform-3d

Public

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

python algorithm cpp

python algorithm cpp numpy parallel neuroscience signed-distance-field connectomics signed-distance-functions distance-transform

C++

•

GNU Lesser General Public License v3.0

•42•264•7•1•Updated

Mar 18, 2026

pyspng-seunglab

Public

pyspng fork with updated install, compression, and CLI.

python png png-decoder

python png png-decoder png-encoder

Python

•

Other

•0•4•1•0•Updated

Mar 17, 2026

osteoid

Public

Skeleton object used for representing neurons, adjacent cells, and organelles.

skeleton graph neuron

skeleton graph neuron medial-axis

C++

•

BSD 3-Clause "New" or "Revised" License

•2•3•2•1•Updated

Mar 13, 2026

compressedseg

Public

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

compression segmentation connectomics

compression segmentation connectomics compression-library neuroglancer

C++

•

Apache License 2.0

•3•4•2•0•Updated

Mar 12, 2026

DracoPy

Public

Python wrapper for Google's Draco mesh compression library.

python compression mesh

python compression mesh draco

C++

•

Apache License 2.0

•31•119•10•2•Updated

Mar 12, 2026

shard-computer

Public

Perform accelerated shard hash computation on numpy arrays.

C++

•

GNU Lesser General Public License v2.1

•0•4•0•0•Updated

Mar 12, 2026

pyfqmr-Fast-Quadric-Mesh-Reduction

Public

Mesh triangle reduction using quadrics

Python

•

MIT License

•15•0•0•0•Updated

Mar 7, 2026

mapbuffer

Public

Serialize dict of integers to bytes and read with near zero parsing. Specialization for int to int.

python map serialization

python map serialization dictionary binary-search associative-map associative-array eytzinger-binary-search

Python

•

BSD 3-Clause "New" or "Revised" License

•0•10•3•0•Updated

Mar 6, 2026

tem2ng

Public

Convert raw TEM microscope images into a neuroglancer volume.

Python

•

BSD 3-Clause "New" or "Revised" License

•1•1•3•0•Updated

Feb 19, 2026

corgie

Public

Command line tool for registration of very large 3D volumes.

Python

•

Apache License 2.0

•3•16•29•5•Updated

Jan 28, 2026

ostd

Public

Ostd Skeleton format based on Linked Paths

C++

•

BSD 3-Clause "New" or "Revised" License

•0•1•0•0•Updated

Jan 23, 2026

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seung-lab

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187 repositories

crackle

ng-extend

connected-components-3d

tile-transcoder

cloud-volume

igneous

zmesh

neuroglancer

abiss

KVDbClient

microviewer

seuron

fastmorph

fill_voids

vqsort

fastremap

ngl_bench

cloud-files

messaging-client

euclidean-distance-transform-3d

pyspng-seunglab

osteoid

compressedseg

DracoPy

shard-computer

pyfqmr-Fast-Quadric-Mesh-Reduction

mapbuffer

tem2ng

corgie

ostd

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Repositories list

187 repositories