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BrainGlobe

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  • About
  • Tutorials
  • Documentation
  • Community
  • Blog
  • Projects
  • GitHub
  • Twitter
  • Mastodon
  • Bluesky
  • Zulip (Developer chat)
  • image.sc (Help forum)

Section Navigation

  • Setting up
    • Using conda
    • Setting up your GPU
    • Image space definition
  • BrainGlobe Atlas API (brainglobe-atlasapi)
    • Atlas details
    • Python API
    • Command line interface
    • Using the files directly
    • Adding a new atlas
  • brainglobe-space
  • brainglobe-utils
    • brainmapper cell transformation widget
    • Image IO submodule
    • Generating Citations for BrainGlobe tools
  • brainreg
    • Requirements
    • Napari plugin
    • Command line tool
    • Registration parameters
    • Checking orientation
    • Output files
    • Visualising brainreg output
    • Troubleshooting
  • brainglobe-segmentation
    • Prerequisites
    • Analysing segmentation from other napari plugins
  • brainglobe-workflows
    • brainmapper command line tool
      • Data requirements
      • Command line interface
        • Cell candidate detection
        • Cell candidate classification
        • Registration parameters
      • Visualisation
      • Output files
      • Debugging common error messages
      • Retraining the pre-trained network
        • Using supplied training data
      • Whole brain cell detection and registration with the brainmapper command line tool
        • Setting up
        • Running brainmapper
        • Visualising the results
        • Exploring the numerical results
        • Visualising your data in brainrender
  • brainrender
    • Installing brainrender
    • Usage
      • Scene
      • Actors
      • Using your own data in brainrender
        • Registering data
      • Using Notebooks
      • Videos, animations and exporting to html
  • brainglobe-heatmap
  • cellfinder
    • Installation
    • cellfinder napari plugin
      • Cell detection
      • Retraining the network for new data
      • Generating data to retrain the cellfinder classification network
      • All cell detection parameters
    • cellfinder.core API
    • Retraining the pre-trained network
      • Using supplied training data
    • Downloading the pre-trained model in advance
    • Troubleshooting
      • Speeding up cellfinder
      • Debugging common error messages
  • morphapi
    • Downloading data
    • Rendering data
  • Documentation
  • Setting up

Setting up#

  • Using conda
    • Introduction
    • Installation
    • Setup your conda environment
    • Further details
  • Setting up your GPU
    • Introduction
    • Installation
  • Image space definition
    • Orientation
    • Voxel sizes

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Using conda

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