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BrainGlobe

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Site Navigation

  • About
  • Tutorials
  • Documentation
  • More
  • GitHub
  • Twitter

Section Navigation

  • General BrainGlobe documentation
    • Using conda
    • Setting up your GPU
    • Image space definition
  • Developer’s guide
    • Tooling
    • Conventions
    • Testing
    • Publishing new releases
    • Code of conduct
    • cellfinder-core
      • Cell detection
    • cellfinder
  • BrainGlobe Atlas API (bg-atlasapi)
    • Atlas details
    • Python API
    • Command line interface
    • Using the files directly
    • Adding a new atlas
  • bg-space
  • brainreg
    • Requirements
    • Napari plugin
    • Command line tool
    • Registration parameters
    • Checking orientation
    • Output files
    • Visualising brainreg output
    • Troubleshooting
  • brainreg-segment
    • Prerequisites
    • Segmenting 1D tracks
    • Segmenting 2/3D structures
    • Analysing segmentation from other napari plugins
  • brainrender
    • Installing brainrender
    • Usage
      • Scene
      • Actors
      • Using your own data in brainrender
        • Registering data
      • Using Notebooks
      • Videos, animations and exporting to html
  • cellfinder
    • Requirements
    • cellfinder command line tool
      • Data requirements
      • Command line interface
        • Cell candidate detection
        • Cell candidate classification
        • Registration parameters
        • Using cellfinder at the SWC
      • Visualisation
      • Output files
      • Training the network
        • Using supplied training data
      • Use with docker
    • cellfinder napari plugin
      • Cell detection
      • Generating data to retrain the cellfinder classification network
      • Retraining the network for new data
      • All cell detection parameters
    • cellfinder-core API
    • Retraining the pre-trained network
    • Troubleshooting
      • Speeding up cellfinder
      • Debugging common error messages
    • Whole brain cell detection and registration with the cellfinder command line tool
      • Setting up
      • Running cellfinder
      • Visualising the results
      • Exploring the numerical results
      • Visualising your data in brainrender
  • morphapi
    • Downloading data
    • Rendering data
  • Documentation

Documentation#

General#

  • General BrainGlobe documentation
  • Developer’s guide

Individual tools#

  • BrainGlobe Atlas API (bg-atlasapi)
  • bg-space
  • brainreg
  • brainreg-segment
  • brainrender
  • cellfinder
  • morphapi

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