Repositories list

• kimimaro

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

  pythonvoxelimage-segmentation+ 12centerlineconnectomicsskeletonsbiomedical-image-processingskeletonizationvolumetric-datacomputer-vision-algorithms+ 5

  C++

  •

  GNU General Public License v3.0

  •28•164•17•0•Updated Aug 22, 2025Aug 22, 2025

• igneous

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

  visualizationdockerkubernetes+ 13cloudpython3meshingconnectomicscclmulti-resolutionskeletonization+ 6

  Python

  •

  GNU General Public License v3.0

  •23•52•26•3•Updated Aug 22, 2025Aug 22, 2025

• osteoid

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

  skeletongraphneuron+ 1medial-axis

  Python

  •

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

  •2•2•1•1•Updated Aug 22, 2025Aug 22, 2025

• neuroglancer

  Public
  WebGL-based viewer for volumetric data

  TypeScript

  •

  Apache License 2.0

  •326•24•91•37•Updated Aug 21, 2025Aug 21, 2025

• cloud-volume

  Public
  Read and write Neuroglancer datasets programmatically.

  big-dataserverlessmatrix+ 17s3gcsmeshtensorelectron-microscopyconnectomicsmicroscopy+ 10

  Python

  •

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

  •51•156•83•5•Updated Aug 20, 2025Aug 20, 2025

• DracoPy

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

  compressionmeshdraco+ 1python

  C++

  •

  Apache License 2.0

  •30•107•11•3•Updated Aug 16, 2025Aug 16, 2025

• tile-transcoder

  Public
  Transfer and convert the file format of image tiles.

  Python

  •

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

  •1•2•0•0•Updated Aug 15, 2025Aug 15, 2025

• cloud-files

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

  cliclientkey-value+ 11s3concurrencyparallelgoogle-cloud-storagebucketthreadingconcurrent+ 4

  Python

  •

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

  •8•43•15•0•Updated Aug 15, 2025Aug 15, 2025

• zmesh

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

  pythonmeshingmarching-cubes-algorithm+ 7mesh-generationconnectomicsbiomedical-image-processingmesh-processingvolumetric-datamesh-simplificationmarching-cubes

  C++

  •

  GNU General Public License v3.0

  •8•65•2•1•Updated Aug 14, 2025Aug 14, 2025

• seuron

  Public
  SEUnglab neuRON pipeline

  Python

  •

  MIT License

  •6•7•1•0•Updated Aug 11, 2025Aug 11, 2025

• cross-section

  Public
  Tools for computing properties of cross sections of 3D voxelized images.

  pythoncppnumpy+ 3cross-sectionvolumetric-imagesarea-estimation

  C++

  •

  GNU Lesser General Public License v3.0

  •2•5•2•3•Updated Jul 28, 2025Jul 28, 2025

• 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+ 17numpycythonimage-processingneighborhooddecision-tree3d2d+ 10

  C++

  •

  GNU Lesser General Public License v3.0

  •46•424•14•5•Updated Jul 26, 2025Jul 26, 2025

• fastremap

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

  pythonnumpycython+ 13loopingpoint-cloudpython3remapbiomedical-image-processingarray-manipulationsunique+ 6

  C++

  •

  GNU Lesser General Public License v3.0

  •8•61•1•0•Updated Jul 23, 2025Jul 23, 2025

• ca3_paper

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jul 21, 2025Jul 21, 2025

• microviewer

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

  3d-reconstructionbiomedical-image-processingvoxel-painting

  JavaScript

  •

  GNU Lesser General Public License v2.1

  •1•15•5•0•Updated Jul 16, 2025Jul 16, 2025

• tinybrain

  Public
  Image pyramid generation for grayscale and segmentation image resize.

  pythonresizecython+ 12image-processingimage-segmentationresize-imagesbiomedical-image-processingvolumetric-dataimage-pyramidimage-hierarchy+ 5

  Python

  •

  GNU General Public License v3.0

  •0•10•5•0•Updated Jul 14, 2025Jul 14, 2025

• ng-extend

  Public
  Vue

  •8•5•3•27•Updated Jul 14, 2025Jul 14, 2025

• tem2ng

  Public
  Convert raw TEM microscope images into a neuroglancer volume.

  Python

  •

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

  •1•1•2•1•Updated Jul 11, 2025Jul 11, 2025

• pytorch-emvision

  Public
  PyTorch models.

  Python

  •

  MIT License

  •3•0•0•0•Updated Jul 7, 2025Jul 7, 2025

• python-task-queue

  Public
  Asynchronous serverless task queue with timed leasing of tasks. Threaded implementations for SQS and local filesystem.

  pythonasynchronous-taskstask-scheduler+ 5task-queuecloud-queuesfilesystemsqssqs-queue

  Python

  •

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

  •9•37•6•1•Updated Jul 2, 2025Jul 2, 2025

• crackle

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

  compression-algorithmcrack-codecompression

  C++

  •

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

  •1•9•10•1•Updated Jun 25, 2025Jun 25, 2025

• ngl_bench

  Public
  Manipulating neuroglancer and unraveling connectomes is an agentic problem.

  Python

  •0•0•0•0•Updated Jun 24, 2025Jun 24, 2025

• chunkflow

  Public
  Compose chunk operators to create a pipeline for local or distributed petabyte-scale computation

  chunkconnectomevolumetric-data+ 53d-imagesconvnet-inferencecomposable-operatorsimage-processingimage-segmentation

  Python

  •

  Apache License 2.0

  •8•55•14•1•Updated Jun 20, 2025Jun 20, 2025

• fill_voids

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

  pythoncppnumpy+ 6morphologyimage-processingbinary-imagefill-gapsfill-holesfill-voids

  C++

  •

  GNU Lesser General Public License v3.0

  •4•26•2•0•Updated Jun 16, 2025Jun 16, 2025

• fastmorph

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

  image-processingclosinggrayscale+ 9erosiondilation3dmulti-labelopeningmorphological-operatorsmorphological-image-processing+ 2

  C++

  •

  GNU Lesser General Public License v3.0

  •3•18•3•0•Updated Jun 16, 2025Jun 16, 2025

• messaging-client

  Public
  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Apr 28, 2025Apr 28, 2025

• openjpeg

  Public
  Official repository of the OpenJPEG project

  C

  •

  Other

  •490•0•0•0•Updated Apr 20, 2025Apr 20, 2025

• network-speed

  Public
  Application for testing network speed in a variety of configurations.

  Python

  •

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

  •0•0•0•0•Updated Mar 26, 2025Mar 26, 2025

• NeuroBlender

  Public
  Tutorial and source code based on CloudVolume and MeshParty for easy retrieval of neuron meshes and EM data for Blender visualization.

  Jupyter Notebook

  •

  MIT License

  •1•3•1•0•Updated Mar 19, 2025Mar 19, 2025

• fpzip

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

  image-analysisfloating-pointconnectomics+ 3pythoncompressionnumpy

  C++

  •

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

  •5•34•2•0•Updated Mar 19, 2025Mar 19, 2025