connectomics

There are 3 repositories under connectomics topic.

google / ffn
Flood-Filling Networks for instance segmentation in 3d volumes.
connectomics segmentation ffn flood-filling-networks instance-segmentation
Language:Python 297
seung-lab / euclidean-distance-transform-3d
Euclidean distance & signed distance transform for multi-label 3D anisotropic images using marching parabolas.
cpp python distance-transform euclidean-distance 3d 2d 1d connectomics neuroscience algorithm biomedical-image-processing numpy anisotropy anisotropic parallel euclidean-distance-transform marching-parabolas signed-distance-field signed-distance-functions
Language:C++ 219
janelia-flyem / dvid
Distributed, Versioned, Image-oriented Dataservice
go dataservice image-storage http-service connectomics big-data neuroscience key-value versioning
Language:Go 195
navis-org / skeletor
Extraction of 3D skeletons from meshes.
python skeletonization skeleton-extraction meshes 3d skeletonize mesh neurons volumes skeleton connectomics teasar
Language:Python 183
catmaid / CATMAID
Collaborative Annotation Toolkit for Massive Amounts of Image Data
connectomics neuroscience image-annotation network-analysis
Language:JavaScript 181
cwatson / brainGraph
Graph theory analysis of brain MRI data
graph-theory network-analysis neuroscience neuroimaging mri r statistics brain-connectivity connectome complex-networks brain-imaging connectomics tractography fmri
Language:R 163
zudi-lin / pytorch_connectomics
PyTorch Connectomics: segmentation toolbox for EM connectomics
computer-vision neuroscience connectomics pytorch segmentation biomedical-image-processing microscopy deep-learning
Language:Python 163
PennLINC / qsiprep
Preprocessing and reconstruction of diffusion MRI
python diffusion-mri tractography connectomics pipelines
Language:HTML 132
seung-lab / cloud-volume
Read and write Neuroglancer datasets programmatically.
neuroglancer volumetric-data python cloud numpy connectomics microscopy microscopy-images chunked-image biomedical-image-processing s3 gcs mesh skeletons serverless big-data electron-microscopy tensor matrix large-image
Language:Python 125
kimimaro
seung-lab / kimimaro
Skeletonize densely labeled 3D image segmentations with TEASAR. (Medial Axis Transform)
biomedical-image-processing teasar skeletonization connectomics python3 python2 python skeletons volumetric-data image-segmentation voxel centerline medial-axis-transform centerline-extraction computer-vision-algorithms cross-section cross-section-area
Language:Python 125
webknossos
scalableminds / webknossos
Visualize, share and annotate your large 3D images online
connectomics em reconstruction microscopy microscopy-images neurobiology hacktoberfest
Language:TypeScript 120
MICA-MNI / ENIGMA
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. 🤠
enigma mri neuroimaging open-source multisite awesome visualization multiscale analysis life-changing-magic connectomics workflows straight-fire
Language:Python 116
aplbrain / dotmotif
A performant, powerful query framework to search for network motifs
graph query-language motifs motif-discovery python connectomics connectome neo4j graph-database subgraph-isomorphism graph-matching networkx vf2 aplbrain bossdb dotmotif
Language:Python 80
knossos-project / knossos
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.
image-annotation visualization neuroscience connectomics desktop cross-platform windows linux macos
Language:C++ 72
MICA-MNI / micaopen
Open Scripts and pipelines from the Multimodal Imaging and Connectome Analysis Lab at the Montreal Neurological Institute
neuroimaging connectomics multimodal histology machine-learning multi-scale networks neuroscience gradients
Language:MATLAB 70
seung-lab / zmesh
Marching Cubes & Mesh Simplification on multi-label 3D images.
marching-cubes marching-cubes-algorithm connectomics biomedical-image-processing mesh-simplification volumetric-data meshing mesh-generation mesh-processing python
Language:C++ 55
aplbrain / grandiso-networkx
Performant, pure-Python subgraph isomorphism and monomorphism search (aka "motif search")
algorithm grand-graphs graphs network network-analysis network-biology connectomics bossdb aplbrain grand-iso dotmotif subgraph-isomorphism vf2 ullman
Language:Python 49
google-research / sofima
Scalable Optical Flow-based Image Montaging and Alignment
connectomics stitching-algorithm alignment-algorithm 2d 3d 4d biomedical-image-processing electron-microscopy microscopy jax python3
Language:Jupyter Notebook 49
seung-lab / igneous
Scalable Neuroglancer compatible Downsampling, Meshing, Skeletonizing, Contrast Normalization, Transfers and more.
neuroglancer python cloud kubernetes docker visualization python3 connectomics downsample meshing skeletonization downsampling volumetric-data multi-resolution ccl connected-components-labeling
Language:Python 40
SyConn
StructuralNeurobiologyLab / SyConn
Toolkit for the generation and analysis of volume eletron microscopy based synaptic connectomes of brain tissue.
connectomics morphology-analysis semantic-segmentation connectivity-matrix image-analysis image-processing
Language:Python 38
sidchop / brainconn
Brainconn - an R package for visualising brain connectivity data in 2D and interactive 3D
neuroimaging networks mri eeg meg connectivity connectivity-matrix connectomics
Language:R 36
urakubo / UNI-EM
A unified environment for DNN-based automated segmentation of neuronal EM images
micro-connectomics connectomics segmentation
Language:Python 35
constantinpape / cluster_tools
Distributed segmentation for bio-image-analysis
segmentation watershed connectomics bio-image-analysis multicut mutex-watershed lifted-multicut cluster-computing 3d-segmentation microscopy-images
Language:Python 33
seung-lab / fpzip
Cython bindings for fpzip, a floating point image compression algorithm.
numpy compression floating-point python connectomics image-analysis
Language:C++ 32
google-research / connectomics
connectomics
Language:Python 27
BRAPH-2
braph-software / BRAPH-2
BRAPH 2.0 is a comprehensive software package for the analysis and visualization of brain connectivity data, offering flexible customization, rich visualization capabilities, and a platform for collaboration in neuroscience research.
open-source computational-neuroscience data-science data-visualization machine-learning matlab neuroscience biomedical-engineering brain-connectivity-analysis brain-research connectomics data-analysis graph-theory network-analysis neuroimaging research-tools scientific-software deep-learning reproducible-research toolbox
Language:MATLAB 26
aschampion / diluvian
Flood filling networks for segmenting electron microscopy of neural tissue
connectomics keras-neural-networks
Language:Python 23
JaneliaSciComp / workstation
Janelia Workstation
confocal-microscopy connectomics janelia neuroimaging neuroscience scientific-computing volume-rendering
Language:Java 21
CAVEconnectome / CAVEclient
This is te python client for accessing REST APIs within the Connectome Annotation Versioning Engine.
connectomics
Language:Python 19
ilastik / nature_methods_multicut_pipeline
connectomics neuron-segmentation
Language:Python 18
ruizengalways / FOD-Net
FOD-Net: A Deep Learning Method for Fiber Orientation Distribution Angular Super Resolution
connectomics deep-learning diffusion-mri fod medical-imaging mrtrix3 tractography
Language:Python 17
VCG / compresso
Compresso: Efficient Compression of Segmentation Data For Connectomics
compression connectomics encoding segmantation mri bockwurst
Language:C++ 11
pykao / BraTS2018-survival-prediction
We provide a method to extract the tractographic features from structural MR images for patients with brain tumor
survival-prediction brats2018 tractography fiber-tracts overall-survival-prediction tractographic-feature machine-learning glioma connectomics
Language:Python 10
awesome-vem-datasets
JackieZhai / awesome-vem-datasets
Open source volume electron microscopy (vEM) datasets for connectomics.
awesome connectomics datasets neuroscience
9
lodurality / 35_methods_MICCAI_2017
Code for MICCAI 2017 paper
neuroimaging structural-connectomes reproducible-research connectomics quality-metrics
Language:Python 9
YuelongWu / feabas
Finite-Element Assisted Brain Assembly System for stitching & alignment of connectomics data
alignment connectomics finite-elements stitching python3 electron-microscopy
Language:Python 9