seung-lab

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181 repositories

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
•19•47•23•5•Updated Mar 2, 2025Mar 2, 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
•28•89•11•2•Updated Feb 28, 2025Feb 28, 2025
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++
•
GNU Lesser General Public License v3.0
•3•13•3•0•Updated Feb 28, 2025Feb 28, 2025
neuroglancer
Public
WebGL-based viewer for volumetric data
TypeScript
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Apache License 2.0
•311•23•91•37•Updated Feb 27, 2025Feb 27, 2025
pyspng-seunglab
Public
pyspng fork with updated install, compression, and CLI.
png png-decoder png-encoder python
Python
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Other
•0•4•1•0•Updated Feb 27, 2025Feb 27, 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 Feb 27, 2025Feb 27, 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•144•82•5•Updated Feb 27, 2025Feb 27, 2025
osteoid
Public
Skeleton object used for representing neurons, adjacent cells, and organelles.
skeleton graph neuron medial-axis
Python
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BSD 3-Clause "New" or "Revised" License
•0•1•0•0•Updated Feb 26, 2025Feb 26, 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
•25•144•13•0•Updated Feb 26, 2025Feb 26, 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•3•2•3•Updated Feb 22, 2025Feb 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
•8•40•14•0•Updated Feb 22, 2025Feb 22, 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•8•10•0•Updated Feb 22, 2025Feb 22, 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•13•5•0•Updated Feb 21, 2025Feb 21, 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•17•1•0•Updated Feb 21, 2025Feb 21, 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
•45•403•11•4•Updated Feb 20, 2025Feb 20, 2025
ng-extend
Public
TypeScript
•7•5•3•26•Updated Feb 19, 2025Feb 19, 2025
draco
Public
Draco is a library for compressing and decompressing 3D geometric meshes and point clouds. It is intended to improve the storage and transmission of 3D graphics.
C++
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Apache License 2.0
•984•0•0•0•Updated Feb 18, 2025Feb 18, 2025
messaging-client
Public
Python
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GNU General Public License v3.0
•1•0•0•0•Updated Feb 12, 2025Feb 12, 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
•
GNU General Public License v3.0
•0•9•5•0•Updated Feb 7, 2025Feb 7, 2025
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 Jan 29, 2025Jan 29, 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 Jan 27, 2025Jan 27, 2025
seuron
Public
SEUnglab neuRON pipeline
Python
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MIT License
•6•7•1•1•Updated Jan 26, 2025Jan 26, 2025
mapbuffer
Public
Serialize dict of integers to bytes and read with near zero parsing. Specialization for int to int.
map serialization dictionary binary-search associative-map associative-array eytzinger-binary-search python
Python
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BSD 3-Clause "New" or "Revised" License
•0•8•2•0•Updated Jan 25, 2025Jan 25, 2025
compressedseg
Public
compressed_segmentation for Neuroglancer volumes. This is the PyPI package fork.
compression segmentation connectomics compression-library neuroglancer
C++
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Apache License 2.0
•3•4•2•0•Updated Jan 23, 2025Jan 23, 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•79•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
•5•4•0•3•Updated Jan 10, 2025Jan 10, 2025
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•53•0•0•Updated Dec 9, 2024Dec 9, 2024
zebrafish
Public template
Zebrafish Hindbrain Connectome
connectomics connectome electron-microscopy-datasets
Liquid
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MIT License
•916•1•0•1•Updated Dec 5, 2024Dec 5, 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•62•2•2•Updated Nov 26, 2024Nov 26, 2024