seung-lab

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179 repositories

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•59•2•2•Updated Nov 7, 2024Nov 7, 2024
neuroglancer
Public
WebGL-based viewer for volumetric data
TypeScript
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Apache License 2.0
•295•22•91•35•Updated Nov 5, 2024Nov 5, 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
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
•17•44•19•4•Updated Nov 4, 2024Nov 4, 2024
cloud-volume
Public
Read and write Neuroglancer datasets programmatically.
big-data serverless matrix s3 gcs mesh tensor electron-microscopy connectomics microscopy
Python
•
BSD 3-Clause "New" or "Revised" License
•47•133•77•5•Updated Oct 30, 2024Oct 30, 2024
ng-extend
Public
TypeScript
•7•4•3•26•Updated Oct 25, 2024Oct 25, 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
•
Apache License 2.0
•8•50•14•1•Updated Oct 25, 2024Oct 25, 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•87•10•2•Updated Oct 22, 2024Oct 22, 2024
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++
•
GNU Lesser General Public License v3.0
•43•367•10•4•Updated Oct 9, 2024Oct 9, 2024
seuron
Public
SEUnglab neuRON pipeline
Python
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MIT License
•6•6•1•0•Updated Sep 30, 2024Sep 30, 2024
abiss
Public
Affinity based image segmentation system
C++
•
GNU General Public License v3.0
•1•4•0•1•Updated Sep 30, 2024Sep 30, 2024
tile-transcoder
Public
Transfer and convert the file format of image tiles.
Python
•
BSD 3-Clause "New" or "Revised" License
•0•2•0•0•Updated Sep 27, 2024Sep 27, 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
•
BSD 3-Clause "New" or "Revised" License
•8•38•14•0•Updated Sep 10, 2024Sep 10, 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•39•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
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 Aug 11, 2024Aug 11, 2024
zebrafish
Public template
Zebrafish Hindbrain Connectome
connectomics connectome electron-microscopy-datasets
Liquid
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MIT License
•902•1•0•0•Updated Aug 10, 2024Aug 10, 2024
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
•0•6•6•0•Updated Aug 6, 2024Aug 6, 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
•23•136•13•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
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•48•0•0•Updated Jul 18, 2024Jul 18, 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
•37•239•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
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•71•7•1•Updated Jul 6, 2024Jul 6, 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
zfp
Public
Compressed numerical arrays that support high-speed random access
C++
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BSD 3-Clause "New" or "Revised" License
•158•0•0•0•Updated Jul 4, 2024Jul 4, 2024
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•9•4•0•Updated Jun 28, 2024Jun 28, 2024
stitching
Public
Stitching Experiments with Sofima and AlignTK
Python
•3•0•0•0•Updated Jun 27, 2024Jun 27, 2024
em-fault-detection
Public
Detecting issues via online image analysis during high throughput electron microscopy.
Python
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BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Jun 25, 2024Jun 25, 2024
shard-computer
Public
Perform accelerated shard hash computation on numpy arrays.
C++
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GNU Lesser General Public License v2.1
•0•3•0•0•Updated Jun 24, 2024Jun 24, 2024