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The Top 23 Connectomics Open Source Projects

Open source projects categorized as Connectomics
Categories > Connectomics
Ffn ⭐ 289
Flood-Filling Networks for instance segmentation in 3d volumes.
most recent commit 4 months ago
Euclidean Distance Transform 3d ⭐ 201
Euclidean distance & signed distance transform for multi-label 3D anisotropic images using marching parabolas.
dependent packages 18total releases 35most recent commit 5 months agopypi edt} Downloads
Dvid ⭐ 196
Distributed, Versioned, Image-oriented Dataservice
total releases 51most recent commit 5 months ago
Catmaid ⭐ 167
Collaborative Annotation Toolkit for Massive Amounts of Image Data
most recent commit a year ago
Pytorch_connectomics ⭐ 151
PyTorch Connectomics: segmentation toolbox for EM connectomics
most recent commit 6 months ago
Cloud Volume ⭐ 120
Read and write Neuroglancer datasets programmatically.
dependent packages 23total releases 319most recent commit 6 months agopypi cloud-volume} Downloads
Qsiprep ⭐ 120
Preprocessing and reconstruction of diffusion MRI
total releases 50most recent commit 4 months ago
Webknossos ⭐ 116
Visualize, share and annotate your large 3D images online
most recent commit 4 months ago
Kimimaro ⭐ 113
Skeletonize densely labeled 3D image segmentations with TEASAR. (Medial Axis Transform)
dependent packages 3total releases 48most recent commit 5 months agopypi kimimaro} Downloads
Skeletor ⭐ 109
3D skeleton extraction from meshes.
dependent packages 2total releases 7most recent commit 2 years agopypi skeletor} Downloads
Enigma ⭐ 101
The ENIGMA Toolbox is an open-source repository for accessing 100+ ENIGMA statistical maps, visualizing cortical and subcortical surface data, and relating neuroimaging findings to micro- and macroscale brain organization. 🤠
most recent commit 6 months ago
Braingraph ⭐ 94
Graph theory analysis of brain MRI data
dependent packages 2total releases 11most recent commit 3 years ago
Knossos ⭐ 71
KNOSSOS is a software tool for the visualization and annotation of 3D image data and was developed for the rapid reconstruction of neural morphology and connectivity.
most recent commit 5 months ago
Dotmotif ⭐ 65
A performant, powerful query framework to search for network motifs
total releases 12most recent commit 8 months ago
Micaopen ⭐ 58
Open Scripts and pipelines from the Multimodal Imaging and Connectome Analysis Lab at the Montreal Neurological Institute
most recent commit 4 months ago
Zmesh ⭐ 51
Marching Cubes & Mesh Simplification on multi-label 3D images.
dependent packages 3total releases 20most recent commit 7 months agopypi zmesh} Downloads
Sofima ⭐ 40
Scalable Optical Flow-based Image Montaging and Alignment
total releases 1most recent commit 5 months ago
Grandiso Networkx ⭐ 39
Performant, pure-Python subgraph isomorphism and monomorphism search (aka "motif search")
total releases 8most recent commit 7 months ago
Igneous ⭐ 37
Scalable Neuroglancer compatible Downsampling, Meshing, Skeletonizing, Contrast Normalization, Transfers and more.
dependent packages 1total releases 56most recent commit 4 months agopypi igneous-pipeline} Downloads
Syconn ⭐ 36
Toolkit for the generation and analysis of volume eletron microscopy based synaptic connectomes of brain tissue.
most recent commit a year ago
Uni Em ⭐ 35
A unified environment for DNN-based automated segmentation of neuronal EM images
most recent commit 9 months ago
Fpzip ⭐ 30
Cython bindings for fpzip, a floating point image compression algorithm.
dependent packages 1total releases 14most recent commit 5 months agopypi fpzip} Downloads
Cluster_tools ⭐ 30
Distributed segmentation for bio-image-analysis
dependent packages 1total releases 9most recent commit 10 months ago
The 9 Most Depended On Connectomics Open Source Projects
Cloud Volume ⭐ 120
Read and write Neuroglancer datasets programmatically.
dependent packages 23total releases 319latest release October 19, 2023most recent commit 6 months agopypi cloud-volume} Downloads
Euclidean Distance Transform 3d ⭐ 201
Euclidean distance & signed distance transform for multi-label 3D anisotropic images using marching parabolas.
dependent packages 18total releases 35latest release December 19, 2023most recent commit 5 months agopypi edt} Downloads
Kimimaro ⭐ 113
Skeletonize densely labeled 3D image segmentations with TEASAR. (Medial Axis Transform)
dependent packages 3total releases 48latest release March 24, 2022most recent commit 5 months agopypi kimimaro} Downloads
Zmesh ⭐ 51
Marching Cubes & Mesh Simplification on multi-label 3D images.
dependent packages 3total releases 20latest release November 02, 2023most recent commit 7 months agopypi zmesh} Downloads
Braingraph ⭐ 94
Graph theory analysis of brain MRI data
dependent packages 2total releases 11latest release September 29, 2020most recent commit 3 years ago
Skeletor ⭐ 109
3D skeleton extraction from meshes.
dependent packages 2total releases 7latest release November 09, 2022most recent commit 2 years agopypi skeletor} Downloads
Cluster_tools ⭐ 30
Distributed segmentation for bio-image-analysis
dependent packages 1total releases 9latest release October 07, 2022most recent commit 10 months ago
Fpzip ⭐ 30
Cython bindings for fpzip, a floating point image compression algorithm.
dependent packages 1total releases 14latest release July 31, 2023most recent commit 5 months agopypi fpzip} Downloads
Igneous ⭐ 37
Scalable Neuroglancer compatible Downsampling, Meshing, Skeletonizing, Contrast Normalization, Transfers and more.
dependent packages 1total releases 56latest release November 21, 2023most recent commit 4 months agopypi igneous-pipeline} Downloads
The 10 Latest Releases In Connectomics Open Source Projects
Euclidean Distance Transform 3d ⭐ 201
Euclidean distance & signed distance transform for multi-label 3D anisotropic images using marching parabolas.
dependent packages 18total releases 35latest release December 19, 2023most recent commit 5 months agopypi edt} Downloads
Igneous ⭐ 37
Scalable Neuroglancer compatible Downsampling, Meshing, Skeletonizing, Contrast Normalization, Transfers and more.
dependent packages 1total releases 56latest release November 21, 2023most recent commit 4 months agopypi igneous-pipeline} Downloads
Zmesh ⭐ 51
Marching Cubes & Mesh Simplification on multi-label 3D images.
dependent packages 3total releases 20latest release November 02, 2023most recent commit 7 months agopypi zmesh} Downloads
Cloud Volume ⭐ 120
Read and write Neuroglancer datasets programmatically.
dependent packages 23total releases 319latest release October 19, 2023most recent commit 6 months agopypi cloud-volume} Downloads
Qsiprep ⭐ 120
Preprocessing and reconstruction of diffusion MRI
total releases 50latest release October 05, 2023most recent commit 4 months ago
Dvid ⭐ 196
Distributed, Versioned, Image-oriented Dataservice
total releases 51latest release August 18, 2023most recent commit 5 months ago
Fpzip ⭐ 30
Cython bindings for fpzip, a floating point image compression algorithm.
dependent packages 1total releases 14latest release July 31, 2023most recent commit 5 months agopypi fpzip} Downloads
Dotmotif ⭐ 65
A performant, powerful query framework to search for network motifs
total releases 12latest release May 16, 2023most recent commit 8 months ago
Skeletor ⭐ 109
3D skeleton extraction from meshes.
dependent packages 2total releases 7latest release November 09, 2022most recent commit 2 years agopypi skeletor} Downloads
Cluster_tools ⭐ 30
Distributed segmentation for bio-image-analysis
dependent packages 1total releases 9latest release October 07, 2022most recent commit 10 months ago
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