All

189 repositories

dijkstra3d
Public
Dijkstra's Shortest Path for 6, 18, and 26-Connected 3D (Volumetric) Image Volumes
python cpp pathfinding
python cpp pathfinding path-planning a-star dijkstra 3d 2d dijkstra-algorithm biomedical-image-processing
C++
•
GNU General Public License v3.0
•14•88•7•1•Updated Aug 19, 2026Aug 19, 2026
gaara
Public
Skeleton thinning algorithm for large images using sand based attacks.
skeleton binary voxel
skeleton binary voxel multilabel thinning multivalued palagyi
C++
•
BSD 3-Clause "New" or "Revised" License
•0•1•0•0•Updated Aug 19, 2026Aug 19, 2026
neuroglancer
Public
WebGL-based viewer for volumetric data
TypeScript
•
Apache License 2.0
•378•25•91•41•Updated Aug 19, 2026Aug 19, 2026
ng-extend
Public
JavaScript
•8•5•3•27•Updated Aug 18, 2026Aug 18, 2026
messaging-client
Public
Python
•
GNU General Public License v3.0
•1•0•0•0•Updated Aug 17, 2026Aug 17, 2026
CAVEpipelines
Public
Instructions for creating chunkedgraph, initial meshing, l2cache etc
Python
•
Mozilla Public License 2.0
•6•6•0•4•Updated Aug 17, 2026Aug 17, 2026
cross-section
Public
Compute cross sectional area and 2D projections of 3D images.
python cpp numpy
python cpp numpy cross-section volumetric-images area-estimation
C++
•
GNU Lesser General Public License v3.0
•2•7•2•3•Updated Aug 17, 2026Aug 17, 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 Aug 16, 2026Aug 16, 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
•52•175•86•6•Updated Aug 13, 2026Aug 13, 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
•10•45•16•2•Updated Aug 12, 2026Aug 12, 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
•50•458•15•3•Updated Aug 6, 2026Aug 6, 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•74•3•1•Updated Aug 5, 2026Aug 5, 2026
crackle
Public
3D dense segmentation compression codec based on crack codes.
compression compression-algorithm crack-code
compression compression-algorithm crack-code
C++
•
BSD 3-Clause "New" or "Revised" License
•1•17•11•2•Updated Aug 1, 2026Aug 1, 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•70•28•3•Updated Aug 1, 2026Aug 1, 2026
tinybrain
Public
Image pyramid generation for grayscale and segmentation image resize.
python resize cython
python resize cython image-processing image-segmentation resize-images biomedical-image-processing volumetric-data downsample image-pyramid
Python
•
GNU General Public License v3.0
•0•12•5•0•Updated Jul 30, 2026Jul 30, 2026
seuron
Public
SEUnglab neuRON pipeline
Python
•
MIT License
•7•7•1•2•Updated Jul 29, 2026Jul 29, 2026
kimimaro
Public
Skeletonize densely labeled 3D image segmentations with TEASAR. (Medial Axis Transform)
python voxel image-segmentation
python voxel image-segmentation centerline connectomics skeletons biomedical-image-processing skeletonization volumetric-data computer-vision-algorithms
C++
•
GNU General Public License v3.0
•29•214•16•0•Updated Jul 24, 2026Jul 24, 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•267•7•1•Updated Jul 23, 2026Jul 23, 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•120•10•2•Updated Jul 20, 2026Jul 20, 2026
abiss
Public
Affinity based image segmentation system
C++
•
GNU General Public License v3.0
•4•6•0•2•Updated Jul 13, 2026Jul 13, 2026
KVDbClient
Public
generic key-value database client
Python
•
MIT License
•1•0•0•0•Updated Jun 29, 2026Jun 29, 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
•1•10•3•0•Updated Jun 26, 2026Jun 26, 2026
YACCLAB
Public
YACCLAB: Yet Another Connected Components Labeling Benchmark
C
•
BSD 3-Clause "New" or "Revised" License
•44•0•0•0•Updated Jun 22, 2026Jun 22, 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•3•0•Updated Jun 11, 2026Jun 11, 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
•1•3•3•1•Updated Jun 2, 2026Jun 2, 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 May 6, 2026May 6, 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•30•2•0•Updated Apr 29, 2026Apr 29, 2026
microviewer
Public
Multiplatform 3D numpy image browser based viewer with voxel painting.
3d-reconstruction biomedical-image-processing voxel-painting
3d-reconstruction biomedical-image-processing voxel-painting
JavaScript
•
GNU Lesser General Public License v2.1
•1•16•5•0•Updated Apr 21, 2026Apr 21, 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, 2026Apr 15, 2026
ngl_bench
Public
Manipulating neuroglancer and unraveling connectomes is an agentic problem.
Python
•1•0•0•0•Updated Mar 23, 2026Mar 23, 2026

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189 repositories

dijkstra3d

gaara

neuroglancer

ng-extend

messaging-client

CAVEpipelines

cross-section

fastmorph

cloud-volume

cloud-files

connected-components-3d

zmesh

crackle

igneous

tinybrain

seuron

kimimaro

euclidean-distance-transform-3d

DracoPy

abiss

KVDbClient

mapbuffer

YACCLAB

fastremap

osteoid

tile-transcoder

fill_voids

microviewer

vqsort

ngl_bench

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189 repositories