Repositories list

• messaging-client

  Public

  seung-lab/messaging-client’s past year of commit activity
  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Mar 19, 2026Mar 19, 2026

• cloud-files

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

  cliclientkey-value+ 11

  cliclientkey-values3concurrencyparallelgoogle-cloud-storagebucketthreadingconcurrent+ 4

  Python

  •

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

  •10•44•15•0•Updated Mar 19, 2026Mar 19, 2026

• ng-extend

  Public
  Vue

  •8•5•3•27•Updated Mar 19, 2026Mar 19, 2026

• zmesh

  Public

  seung-lab/zmesh’s past year of commit activity
  Marching Cubes & Mesh Simplification on multi-label 3D images.

  pythonmeshingmarching-cubes-algorithm+ 7

  pythonmeshingmarching-cubes-algorithmmesh-generationmarching-cubesconnectomicsbiomedical-image-processingmesh-processingvolumetric-datamesh-simplification

  C++

  •

  GNU General Public License v3.0

  •9•72•2•1•Updated Mar 18, 2026Mar 18, 2026

• euclidean-distance-transform-3d

  Public

  seung-lab/euclidean-distance-transform-3d’s past year of commit activity
  Euclidean distance & signed distance transform for multi-label 3D anisotropic images using marching parabolas.

  pythonalgorithmcpp+ 16

  pythonalgorithmcppnumpyparallelneurosciencesigned-distance-fieldconnectomicssigned-distance-functionsdistance-transform+ 9

  C++

  •

  GNU Lesser General Public License v3.0

  •41•262•7•1•Updated Mar 18, 2026Mar 18, 2026

• igneous

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

  visualizationpythondocker+ 13

  visualizationpythondockerkubernetescloudpython3meshingconnectomicscclmulti-resolution+ 6

  Python

  •

  GNU General Public License v3.0

  •23•66•27•3•Updated Mar 17, 2026Mar 17, 2026

• pyspng-seunglab

  Public
  pyspng fork with updated install, compression, and CLI.

  pythonpngpng-decoder+ 1

  pythonpngpng-decoderpng-encoder

  Python

  •

  Other

  •0•4•1•0•Updated Mar 17, 2026Mar 17, 2026

• cloud-volume

  Public
  Read and write Neuroglancer datasets programmatically.

  pythoncloudbig-data+ 17

  pythoncloudbig-dataserverlessnumpymatrixs3gcsmeshtensor+ 10

  Python

  •

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

  •54•170•84•7•Updated Mar 17, 2026Mar 17, 2026

• fastremap

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

  pythonnumpycython+ 13

  pythonnumpycythonloopingpoint-cloudpython3remapbiomedical-image-processingarray-manipulationsunique+ 6

  C++

  •

  GNU Lesser General Public License v3.0

  •8•63•4•0•Updated Mar 17, 2026Mar 17, 2026

• neuroglancer

  Public
  WebGL-based viewer for volumetric data

  TypeScript

  •

  Apache License 2.0

  •351•24•91•37•Updated Mar 16, 2026Mar 16, 2026

• abiss

  Public
  Affinity based image segmentation system

  C++

  •

  GNU General Public License v3.0

  •4•6•0•2•Updated Mar 15, 2026Mar 15, 2026

• osteoid

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

  skeletongraphneuron+ 1

  skeletongraphneuronmedial-axis

  C++

  •

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

  •2•3•2•1•Updated Mar 13, 2026Mar 13, 2026

• KVDbClient

  Public
  generic key-value database client

  Python

  •

  MIT License

  •0•0•0•0•Updated Mar 13, 2026Mar 13, 2026

• compressedseg

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

  compressionsegmentationconnectomics+ 2

  compressionsegmentationconnectomicscompression-libraryneuroglancer

  C++

  •

  Apache License 2.0

  •3•4•2•0•Updated Mar 12, 2026Mar 12, 2026

• DracoPy

  Public
  Python wrapper for Google's Draco mesh compression library.

  pythoncompressionmesh+ 1

  pythoncompressionmeshdraco

  C++

  •

  Apache License 2.0

  •31•117•10•2•Updated Mar 12, 2026Mar 12, 2026

• crackle

  Public
  3D dense segmentation compression codec based on crack codes.

  compressioncompression-algorithmcrack-code

  compressioncompression-algorithmcrack-code

  C++

  •

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

  •1•15•11•1•Updated Mar 12, 2026Mar 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, 2026Mar 12, 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 Mar 9, 2026Mar 9, 2026

• pyfqmr-Fast-Quadric-Mesh-Reduction

  Public
  Mesh triangle reduction using quadrics

  Python

  •

  MIT License

  •15•0•0•0•Updated Mar 7, 2026Mar 7, 2026

• mapbuffer

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

  pythonmapserialization+ 5

  pythonmapserializationdictionarybinary-searchassociative-mapassociative-arrayeytzinger-binary-search

  Python

  •

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

  •0•10•3•0•Updated Mar 6, 2026Mar 6, 2026

• seuron

  Public
  SEUnglab neuRON pipeline

  Python

  •

  MIT License

  •7•7•1•2•Updated Mar 3, 2026Mar 3, 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, 2026Feb 19, 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)

  pythonalgorithmcpp+ 17

  pythonalgorithmcppnumpycythonimage-processingneighborhooddecision-tree3d2d+ 10

  C++

  •

  GNU Lesser General Public License v3.0

  •48•450•15•4•Updated Feb 5, 2026Feb 5, 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, 2026Jan 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, 2026Jan 23, 2026

• kimimaro

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

  pythonvoxelimage-segmentation+ 12

  pythonvoxelimage-segmentationcenterlineconnectomicsskeletonsbiomedical-image-processingskeletonizationvolumetric-datacomputer-vision-algorithms+ 5

  C++

  •

  GNU General Public License v3.0

  •30•195•16•0•Updated Jan 15, 2026Jan 15, 2026

• microviewer

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

  3d-reconstructionbiomedical-image-processingvoxel-painting

  3d-reconstructionbiomedical-image-processingvoxel-painting

  JavaScript

  •

  GNU Lesser General Public License v2.1

  •1•16•5•0•Updated Nov 19, 2025Nov 19, 2025

• dijkstra3d

  Public
  Dijkstra's Shortest Path for 6, 18, and 26-Connected 3D (Volumetric) Image Volumes

  pythoncpppathfinding+ 16

  pythoncpppathfindingpath-planninga-stardijkstra3d2ddijkstra-algorithmbiomedical-image-processing+ 9

  C++

  •

  GNU General Public License v3.0

  •14•84•7•1•Updated Nov 5, 2025Nov 5, 2025

• CAVEpipelines

  Public
  Instructions for creating chunkedgraph, initial meshing, l2cache etc

  HCL

  •

  Mozilla Public License 2.0

  •6•5•0•4•Updated Nov 5, 2025Nov 5, 2025

• pytorch-emvision

  Public
  PyTorch models.

  Python

  •

  MIT License

  •4•0•0•0•Updated Oct 28, 2025Oct 28, 2025