seung-lab

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180 repositories

neuroglancer
Public
WebGL-based viewer for volumetric data
TypeScript
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Apache License 2.0
•300•23•91•36•Updated Jan 11, 2025Jan 11, 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
•18•45•22•4•Updated Jan 11, 2025Jan 11, 2025
seuron
Public
SEUnglab neuRON pipeline
Python
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MIT License
•6•6•1•0•Updated Jan 11, 2025Jan 11, 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•6•9•0•Updated Jan 11, 2025Jan 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 3d 2d dijkstra-algorithm biomedical-image-processing skeletonization
C++
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GNU General Public License v3.0
•13•77•7•1•Updated Jan 10, 2025Jan 10, 2025
CAVEpipelines
Public
Instructions for creating chunkedgraph, initial meshing, l2cache etc
HCL
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Mozilla Public License 2.0
•4•3•0•3•Updated Jan 10, 2025Jan 10, 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
•48•137•77•5•Updated Jan 10, 2025Jan 10, 2025
compresso
Public
Compresso: Efficient Compression of Segmentation Data For Connectomics
compression segmentation connectomics
C++
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Other
•4•4•3•0•Updated Jan 9, 2025Jan 9, 2025
ng-extend
Public
TypeScript
•7•4•3•26•Updated Jan 8, 2025Jan 8, 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•12•5•0•Updated Jan 3, 2025Jan 3, 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
•43•389•10•4•Updated Dec 20, 2024Dec 20, 2024
fastremap
Public
Remap, mask, renumber, unique, and in-place transposition of 3D labeled images. Point cloud too.
python cython looping point-cloud python3 biomedical-image-processing array-manipulations unique transpose masking
C++
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GNU Lesser General Public License v3.0
•6•49•0•0•Updated Dec 9, 2024Dec 9, 2024
DracoPy
Public
Python wrapper for Google's Draco mesh compression library.
compression mesh draco python
C++
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Apache License 2.0
•26•88•11•2•Updated Dec 5, 2024Dec 5, 2024
zebrafish
Public template
Zebrafish Hindbrain Connectome
connectomics connectome electron-microscopy-datasets
Liquid
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MIT License
•912•1•0•1•Updated Dec 5, 2024Dec 5, 2024
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•40•14•0•Updated Dec 4, 2024Dec 4, 2024
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•51•14•2•Updated Nov 27, 2024Nov 27, 2024
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•61•2•2•Updated Nov 26, 2024Nov 26, 2024
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 Nov 23, 2024Nov 23, 2024
fastmorph
Public
Multilabel and Grey 3D morphological image processing functions. Dilate, Erode, Opening, Closing.
image-processing closing grayscale erosion dilation 3d multi-label opening morphological-operators morphological-image-processing
C++
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GNU General Public License v3.0
•3•13•3•0•Updated Nov 21, 2024Nov 21, 2024
tem2ng
Public
Convert raw TEM microscope images into a neuroglancer volume.
Python
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BSD 3-Clause "New" or "Revised" License
•0•1•2•0•Updated Nov 19, 2024Nov 19, 2024
tile-transcoder
Public
Transfer and convert the file format of image tiles.
Python
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BSD 3-Clause "New" or "Revised" License
•0•2•0•0•Updated Nov 7, 2024Nov 7, 2024
pyfqmr-Fast-Quadric-Mesh-Reduction
Public
Mesh triangle reduction using quadrics
Python
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MIT License
•13•0•0•0•Updated Nov 5, 2024Nov 5, 2024
abiss
Public
Affinity based image segmentation system
C++
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GNU General Public License v3.0
•2•4•0•1•Updated Sep 30, 2024Sep 30, 2024
RealNeuralNetworks.jl
Public
A unified framework for skeletonization, morphological analysis, and connectivity analysis.
connectome neuron-morphology julia neurons skeletonization nblast
Julia
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Apache License 2.0
•2•40•17•4•Updated Aug 23, 2024Aug 23, 2024
fpzip
Public
Cython bindings for fpzip, a floating point image compression algorithm.
image-analysis floating-point connectomics python compression numpy
C++
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BSD 3-Clause "New" or "Revised" License
•5•34•2•1•Updated Aug 16, 2024Aug 16, 2024
kimimaro
Public
Skeletonize densely labeled 3D image segmentations with TEASAR. (Medial Axis Transform)
python voxel python3 image-segmentation python2 centerline connectomics skeletons biomedical-image-processing skeletonization
C++
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GNU General Public License v3.0
•25•141•16•0•Updated Aug 2, 2024Aug 2, 2024
cloud-volume-objects
Public
Meshes, Skeletons, VolumeCutout, and Annotation class definitions used by CloudVolume.
BSD 3-Clause "New" or "Revised" License
•0•1•0•0•Updated Jul 30, 2024Jul 30, 2024
euclidean-distance-transform-3d
Public
Euclidean distance & signed distance transform for multi-label 3D anisotropic images using marching parabolas.
algorithm cpp parallel neuroscience signed-distance-field connectomics signed-distance-functions distance-transform 3d 2d
C++
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GNU General Public License v3.0
•36•245•8•0•Updated Jul 17, 2024Jul 17, 2024
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•3•2•3•Updated Jul 10, 2024Jul 10, 2024
zfpc
Public
Exerimental container format for zfp encoded vector fields. zfpc = zfp container
Python
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GNU Lesser General Public License v2.1
•0•1•0•0•Updated Jul 5, 2024Jul 5, 2024