seung-lab

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185 repositories

cloud-volume
Public
Read and write Neuroglancer datasets programmatically.
python cloud big-data serverless numpy matrix s3 gcs mesh tensor
Python
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BSD 3-Clause "New" or "Revised" License
•52•169•84•7•Updated Jan 1, 2026Jan 1, 2026
seuron
Public
SEUnglab neuRON pipeline
Python
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MIT License
•7•7•1•0•Updated Dec 29, 2025Dec 29, 2025
neuroglancer
Public
WebGL-based viewer for volumetric data
TypeScript
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Apache License 2.0
•340•24•91•37•Updated Dec 22, 2025Dec 22, 2025
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 s3 concurrency parallel google-cloud-storage bucket threading concurrent
Python
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BSD 3-Clause "New" or "Revised" License
•9•44•16•0•Updated Dec 15, 2025Dec 15, 2025
crackle
Public
3D dense segmentation compression codec based on crack codes.
compression compression-algorithm crack-code
C++
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BSD 3-Clause "New" or "Revised" License
•1•14•11•1•Updated Dec 12, 2025Dec 12, 2025
fastremap
Public
Remap, mask, renumber, unique, and in-place transposition of 3D labeled images. Point cloud too.
python numpy cython looping point-cloud python3 remap biomedical-image-processing array-manipulations unique
C++
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GNU Lesser General Public License v3.0
•8•63•3•0•Updated Dec 10, 2025Dec 10, 2025
osteoid
Public
Skeleton object used for representing neurons, adjacent cells, and organelles.
skeleton graph neuron medial-axis
C++
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BSD 3-Clause "New" or "Revised" License
•2•3•2•1•Updated Dec 6, 2025Dec 6, 2025
DracoPy
Public
Python wrapper for Google's Draco mesh compression library.
python compression mesh draco
C++
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Apache License 2.0
•31•112•10•2•Updated Dec 5, 2025Dec 5, 2025
zmesh
Public
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
C++
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GNU General Public License v3.0
•9•70•2•1•Updated Dec 5, 2025Dec 5, 2025
mapbuffer
Public
Serialize dict of integers to bytes and read with near zero parsing. Specialization for int to int.
python map serialization dictionary binary-search associative-map associative-array eytzinger-binary-search
Python
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BSD 3-Clause "New" or "Revised" License
•0•10•3•0•Updated Dec 4, 2025Dec 4, 2025
igneous
Public
Scalable Neuroglancer compatible Downsampling, Meshing, Skeletonizing, Contrast Normalization, Transfers and more.
visualization python docker kubernetes cloud python3 meshing connectomics ccl multi-resolution
Python
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GNU General Public License v3.0
•23•63•28•3•Updated Dec 3, 2025Dec 3, 2025
euclidean-distance-transform-3d
Public
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
C++
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GNU Lesser General Public License v3.0
•39•260•7•0•Updated Nov 27, 2025Nov 27, 2025
microviewer
Public
Multiplatform 3D numpy image browser based viewer with voxel painting.
3d-reconstruction biomedical-image-processing voxel-painting
JavaScript
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GNU Lesser General Public License v2.1
•1•16•5•0•Updated Nov 19, 2025Nov 19, 2025
kimimaro
Public
Skeletonize densely labeled 3D image segmentations with TEASAR. (Medial Axis Transform)
python voxel image-segmentation centerline connectomics skeletons biomedical-image-processing skeletonization volumetric-data computer-vision-algorithms
C++
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GNU General Public License v3.0
•30•182•16•0•Updated Nov 13, 2025Nov 13, 2025
abiss
Public
Affinity based image segmentation system
C++
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GNU General Public License v3.0
•3•5•0•1•Updated Nov 11, 2025Nov 11, 2025
dijkstra3d
Public
Dijkstra's Shortest Path for 6, 18, and 26-Connected 3D (Volumetric) Image Volumes
python cpp pathfinding path-planning a-star dijkstra 3d 2d dijkstra-algorithm biomedical-image-processing
C++
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GNU General Public License v3.0
•14•83•7•1•Updated Nov 5, 2025Nov 5, 2025
CAVEpipelines
Public
Instructions for creating chunkedgraph, initial meshing, l2cache etc
HCL
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Mozilla Public License 2.0
•5•5•0•3•Updated Nov 5, 2025Nov 5, 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)
python algorithm cpp numpy cython image-processing neighborhood decision-tree 3d 2d
C++
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GNU Lesser General Public License v3.0
•47•439•14•4•Updated Nov 2, 2025Nov 2, 2025
ng-extend
Public
Vue
•8•5•3•27•Updated Oct 30, 2025Oct 30, 2025
pytorch-emvision
Public
PyTorch models.
Python
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MIT License
•4•0•0•0•Updated Oct 28, 2025Oct 28, 2025
fastmorph
Public
Multilabel and Grey 3D morphological image processing functions. Dilate, Erode, Opening, Closing, Hole Filling.
image-processing closing grayscale erosion dilation 3d multi-label opening morphological-operators morphological-image-processing
C++
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GNU Lesser General Public License v3.0
•3•19•2•0•Updated Oct 22, 2025Oct 22, 2025
cross-section
Public
Tools for computing properties of cross sections of 3D voxelized images.
python cpp numpy cross-section volumetric-images area-estimation
C++
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GNU Lesser General Public License v3.0
•2•6•2•3•Updated Oct 17, 2025Oct 17, 2025
shard-computer
Public
Perform accelerated shard hash computation on numpy arrays.
C++
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GNU Lesser General Public License v2.1
•0•4•0•0•Updated Oct 8, 2025Oct 8, 2025
tem2ng
Public
Convert raw TEM microscope images into a neuroglancer volume.
Python
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BSD 3-Clause "New" or "Revised" License
•1•1•3•0•Updated Sep 18, 2025Sep 18, 2025
fill_voids
Public
Fill holes in binary 2D & 3D images fast.
python cpp numpy morphology image-processing binary-image fill-gaps fill-holes fill-voids
C++
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GNU Lesser General Public License v3.0
•4•28•2•0•Updated Sep 10, 2025Sep 10, 2025
tile-transcoder
Public
Transfer and convert the file format of image tiles.
Python
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BSD 3-Clause "New" or "Revised" License
•1•2•0•0•Updated Aug 15, 2025Aug 15, 2025
ca3_paper
Public
Jupyter Notebook
•0•1•0•0•Updated Jul 21, 2025Jul 21, 2025
tinybrain
Public
Image pyramid generation for grayscale and segmentation image resize.
python resize cython image-processing image-segmentation resize-images biomedical-image-processing volumetric-data downsample image-pyramid
Python
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GNU General Public License v3.0
•0•11•5•0•Updated Jul 14, 2025Jul 14, 2025
python-task-queue
Public
Asynchronous serverless task queue with timed leasing of tasks. Threaded implementations for SQS and local filesystem.
python filesystem sqs asynchronous-tasks sqs-queue task-scheduler task-queue cloud-queues
Python
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BSD 3-Clause "New" or "Revised" License
•9•39•6•1•Updated Jul 2, 2025Jul 2, 2025
ngl_bench
Public
Manipulating neuroglancer and unraveling connectomes is an agentic problem.
Python
•0•0•0•0•Updated Jun 24, 2025Jun 24, 2025