neuroanatomy

There are 1 repository under neuroanatomy topic.

• dipy / dipy

  DIPY is the paragon 3D/4D+ imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.

  diffusion-mridtitractographytractometryregistrationdenoisingspherical-harmonicsdkitrackingcontextual-enhancementneuroanatomyneuroimagingmedical-imagingmicrostructuremachine-learningpythonbundlessegmentationpatch2selfself-supervised-learning
  Language:Python 669
• cellfinder

  brainglobe / cellfinder

  Automated 3D cell detection in very large images

  microscopycell-detectiondeep-learningimage-analysisneurosciencepythonneuroanatomyimaging
  Language:Python 170

• brainglobe / brainreg

  Automated 3D brain registration with support for multiple species and atlases.

  registrationatlasesbrainneurosciencemicroscopyneuroanatomy
  Language:Python 111

• ai-med / quickNAT_pytorch

  PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty

  deep-learningbrain-imagingmri-imagessegmentationbiomarkersmachine-learningconvolutional-neural-networkscomputer-visionmedical-imagingaineuroanatomypytorchquality-controlbayesianuncertainty
  Language:Python 99

• navis-org / navis

  Python library for analysis of neuroanatomical data.

  neuronsswcanatomyvisualizationneurosciencepython3dneuprintskeletonssegmentationmeshesvolumesblenderhemibrainnblasttransformconnectomeneuroanatomymorphometricflywire
  Language:Python 80

• natverse / nat

  NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

  rneuroanatomy-toolboxcranneuronneuroscience3dvisualisationimage-analysisneuroanatomyneuron-morphology
  Language:R 60

• volBrain / AssemblyNet

  AssemblyNet: 3D Whole Brain MRI segmentation pipeline

  neuroscienceneuroimagingbrain-imagingmedical-imagingdeep-learningneuroanatomybrain-segmentationmrimri-segmentationniftineurodegenerative-diseasesdementiaalzheimerparkinsonschizophreniaautismdocker
  43

• francopestilli / life

  Please use the new version of LiFE: www.github.com/brain-life/encode

  neuroimagingbrainneurosciencediffusion-mridiffusion-networkmriconnectomestatisticsneuroanatomy
  Language:MATLAB 35

• brainglobe / brainglobe-segmentation

  Segmentation of anatomical structures in a common coordinate space

  segmentationnaparibrainregcellfinderneuroscienceneuroanatomy
  Language:Python 28
• brainglobe-heatmap

  brainglobe / brainglobe-heatmap

  Rendering anatomical heatmaps with brainrender and matplotlib

  atlasbrainglobeneuroanatomyvisualization
  Language:Python 27

• natverse / nat.nblast

  R package implementing the NBLAST neuron search algorithm, as an add-on for the NeuroAnatomy Toolbox (nat) R package.

  nblastneuroanatomy-toolboxneuronsneuroanatomymorphological-analysis
  Language:R 16

• YasPHP / BrainAR

  A neuroanatomy-based augmented reality experience powered by OpenCV. Features 3D visuals of the Atlas Brain Map slices with real-time ArUco marker detection.

  aruco-markerscomputer-visionbrain-atlasneuroanatomyaugmented-realityopencv
  Language:Python 12

• SainsburyWellcomeCentre / neuro

  Visualisation and analysis of brain imaging data

  pythonneuroscienceneuroanatomyimage-analysismicroscopyregistrationvisualisationcell-detection
  Language:Python 10

• natverse / mouselightr

  Bridge HHMI Janelia MouseLight Database and nat R Package

  rneuroanatomyneuroanatomy-toolboxneuroscience
  Language:R 9

• natverse / rcatmaid

  R package providing API access to the CATMAID web image annotation tool

  rcatmaidneuroanatomyneuroanatomy-toolbox
  Language:R 9

• obophenotype / brain_data_standards_ontologies

  A repository for co-ordinating work on ontologies for the Brain Data Standards Project

  ontologyneuronbrainobofoundrycell-typesmetadataneuroanatomyanatomy-ontologybrain-data
  Language:Python 9

• SWC-Advanced-Microscopy / BakingTray

  Serial-section automated anatomy extension for ScanImage

  microscopyimagingtomography2-photonserial-sectionmatlabscanimageanatomyneuroanatomyneuroscience
  Language:MATLAB 9

• natverse / elmr

  Support for working with light and electron microscopy fly brain data

  rneuroanatomy-toolboxneuroanatomy
  Language:R 7

• afids / afids-macaca

  anatomical fiducials protocol adapted for macaques

  brainwebafidsneuroanatomynhp3d-slicer
  Language:Jupyter Notebook 6

• volBrain / DeeplesionBrain

  medical-imagingneuroscienceneuroimagingneuroanatomybrain-imagingdeep-learningmrimri-segmentationmultiple-sclerosismri-brainnifti
  6

• yzx9 / swcgeom

  Neuron geometry library for swc format.

  neuron-morphologyneuroanatomyneurosciencepythonneuron
  Language:Python 6

• dicemt / DTI-NODDI

  :brain: DTI-NODDI: Create NODDI maps from DTI (either "FA and MD" or "L1, L2, and L3")

  diffusion-mridtinoddimrineuroimagingneurosciencebrain-imagingneuroanatomypython
  Language:Python 5

• HealthX-Lab / SONIA

  Customizable system for displaying and inspecting brain structures, connections, and subsystems in VR

  medical-imagingunityunity3duxvrbrain-connectivityeducationhuman-computer-interactionneuroanatomyvirtual-reality
  Language:C# 5

• scil-vital / tractolearn

  Tractography learning

  autoencoderbundlingdeep-learningdiffusion-mridmrifilteringgenerative-modelrepresentation-learningstreamlinetrackingtractographywhite-matterneuroanatomyneuroimaging
  Language:Python 5

• natverse / flycircuit

  R package flycircuit

  rneuroanatomy-toolboxneuroanatomydrosophilanatverse
  Language:R 4

• natverse / nat.templatebrains

  Support for 3D template brains used as targets for image registration

  rimage-registrationneuroanatomy-toolboxneuroanatomybridging-registrationsnatverse
  Language:R 3

• tferr / ASA

  Legacy project, now part of https://github.com/morphonets/SNT. Bitmap morphometry of neuronal arbors through Sholl

  javaimagejneuroanatomysholl-analysisfiji-pluginopen-sourceneuronal-arborsbitmap-imageslegacy
  Language:Java 3

• YasPHP / BrainEncyclopedia

  A discord bot that acts as an encyclopedia about brain anatomy. Provides brain region lookup, image search, crowd science neuro research, and retrieves neuroscience libraries.

  neuroscienceneuroanatomybrainatlasencyclopediapsychologybrain-regionsdiscord-bot
  Language:JavaScript 3

• afids / afids-protocol-old

  3dslicerafidsneuroanatomy
  Language:CSS 2

• afids / afids-validator

  Validator for the anatomical fiducial placement protocol

  neuroanatomybrainweb
  Language:Python 2

• BonsaiNet / Staining-methods-and-morphologies

  Staining Methods Bias Neuron Morphology

  morphologystainingdendriteneuroanatomyrodentimmunstaining
  Language:Jupyter Notebook 2

• jefferislab / LHlibrary

  A R Shiny app for sharing and viewing lateral horn data

  neuroanatomyneuroanatomy-toolboxrshiny
  Language:R 2

• natverse / nat.flybrains

  Support for Drosophila bridging/mirroring registrations in R

  rtemplate-brainsneuroanatomy-toolboxneuroanatomydrosophilabridging-registrationsnatverse
  Language:Haxe 2

• sergioluengosanchez / EMS_clustering

  A directional-linear finite mixture model for clustering

  clusteringdirectional-statisticsneuroanatomybayesian-network
  Language:R 2

• tferr / hIPNAT

  :microscope::deciduous_tree::computer: hIPNAT: Image Processing for NeuroAnatomy and Tree-like structures (Archived)

  imagejneuroanatomy
  Language:Java 2

• flyconnectome / fancr

  Support Acccess to the Female Adult Nerve Cord (FANC) Dataset

  rnatverseneuroanatomydrosophiladrosophila-brainsneuroscience
  Language:R 1