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Top 11 connectomics open source projects

Distributed segmentation for bio-image-analysis

✭ 26

python shell segmentation connectomics bio-image-analysis watershed cluster-computing multicut 3d-segmentation microscopy-images lifted-multicut mutex-watershed

Skeletonize densely labeled 3D image segmentations with TEASAR.

✭ 85

python cython C++Dockerfile shell voxel image-segmentation centerline connectomics skeletons biomedical-image-processing skeletonization volumetric-data computer-vision-algorithms teasar medial-axis-transform centerline-extraction

Marching Cubes & Mesh Simplification on multi-label 3D images.

✭ 37

C++python cython meshing marching-cubes-algorithm mesh-generation marching-cubes connectomics biomedical-image-processing mesh-processing volumetric-data mesh-simplification

Cython bindings for fpzip, a floating point image compression algorithm.

✭ 24

C++c CMake cython python Makefile Dockerfile compression numpy image-analysis floating-point connectomics

grandiso-networkx

Performant, pure-Python subgraph isomorphism and monomorphism search (aka "motif search")

✭ 30

python algorithm network graphs network-analysis connectomics ullman subgraph-isomorphism network-biology bossdb vf2 grand-graphs aplbrain grand-iso dotmotif

A unified environment for DNN-based automated segmentation of neuronal EM images

✭ 33

python javascript CSS HTML Jupyter Notebook segmentation connectomics micro-connectomics

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. 🤠

✭ 66

python matlab visualization open-source awesome multisite analysis mri enigma neuroimaging connectomics workflows multiscale straight-fire life-changing-magic

Graph theory analysis of brain MRI data

✭ 136

r statistics neuroscience mri graph-theory neuroimaging complex-networks fmri network-analysis connectomics brain-imaging connectome brain-connectivity tractography

Toolkit for the generation and analysis of volume eletron microscopy based synaptic connectomes of brain tissue.

✭ 31

python cython image-processing image-analysis connectomics semantic-segmentation connectivity-matrix morphology-analysis

3D skeleton extraction from meshes.

✭ 115

python Jupyter Notebook skeleton mesh neurons volumes connectomics meshes 3d skeletonization teasar skeleton-extraction skeletonize

Preprocessing and reconstruction of diffusion MRI

✭ 94

HTML python pipelines connectomics diffusion-mri tractography

1-11 of 11 connectomics projects