seung-lab

All

185 repositories

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
•28•172•16•0•Updated Oct 8, 2025Oct 8, 2025
neuroglancer
Public
WebGL-based viewer for volumetric data
TypeScript
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Apache License 2.0
•329•24•91•37•Updated Oct 7, 2025Oct 7, 2025
igneous
Public
Scalable Neuroglancer compatible Downsampling, Meshing, Skeletonizing, Contrast Normalization, Transfers and more.
visualization docker kubernetes cloud python3 meshing connectomics ccl multi-resolution skeletonization
Python
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GNU General Public License v3.0
•23•54•26•3•Updated Oct 7, 2025Oct 7, 2025
zmesh
Public
Marching Cubes & Mesh Simplification on multi-label 3D images.
python meshing marching-cubes-algorithm mesh-generation connectomics biomedical-image-processing mesh-processing volumetric-data mesh-simplification marching-cubes
C++
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GNU General Public License v3.0
•8•66•2•1•Updated Oct 7, 2025Oct 7, 2025
cloud-volume
Public
Read and write Neuroglancer datasets programmatically.
big-data serverless matrix s3 gcs mesh tensor electron-microscopy connectomics microscopy
Python
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BSD 3-Clause "New" or "Revised" License
•50•159•84•5•Updated Oct 7, 2025Oct 7, 2025
crackle
Public
3D dense segmentation compression codec based on crack codes.
compression-algorithm crack-code compression
C++
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BSD 3-Clause "New" or "Revised" License
•1•11•10•1•Updated Oct 6, 2025Oct 6, 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
•46•425•14•5•Updated Oct 3, 2025Oct 3, 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•2•1•0•Updated Oct 3, 2025Oct 3, 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•2•0•Updated Sep 29, 2025Sep 29, 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
•8•43•15•1•Updated Sep 26, 2025Sep 26, 2025
seuron
Public
SEUnglab neuRON pipeline
Python
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MIT License
•6•7•1•0•Updated Sep 25, 2025Sep 25, 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•2•0•Updated Sep 18, 2025Sep 18, 2025
abiss
Public
Affinity based image segmentation system
C++
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GNU General Public License v3.0
•2•4•0•1•Updated Sep 12, 2025Sep 12, 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•26•2•0•Updated Sep 10, 2025Sep 10, 2025
DracoPy
Public
Python wrapper for Google's Draco mesh compression library.
compression mesh draco python
C++
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Apache License 2.0
•30•108•11•3•Updated Sep 8, 2025Sep 8, 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•3•0•Updated Sep 3, 2025Sep 3, 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•5•2•3•Updated Sep 1, 2025Sep 1, 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•15•5•0•Updated Aug 22, 2025Aug 22, 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
ca3_paper
Public
Jupyter Notebook
•0•0•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 image-pyramid image-hierarchy
Python
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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
pytorch-emvision
Public
PyTorch models.
Python
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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.
python asynchronous-tasks task-scheduler task-queue cloud-queues filesystem sqs sqs-queue
Python
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BSD 3-Clause "New" or "Revised" License
•9•37•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
chunkflow
Public
Compose chunk operators to create a pipeline for local or distributed petabyte-scale computation
chunk connectome volumetric-data 3d-images convnet-inference composable-operators image-processing image-segmentation
Python
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Apache License 2.0
•8•55•14•1•Updated Jun 20, 2025Jun 20, 2025
messaging-client
Public
Python
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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
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Other
•492•0•0•0•Updated Apr 20, 2025Apr 20, 2025
network-speed
Public
Application for testing network speed in a variety of configurations.
Python
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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
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MIT License
•1•3•1•0•Updated Mar 19, 2025Mar 19, 2025