SUMMARY.md

Table of contents

• About
• Help forum
• Contributing
• Github organisation

bg-atlasapi

• BG-AtlasAPI
• Atlas details
• Usage
  • Command line interface
  • Using the files directly
• Adding a new atlas
• API documentation
  • bg_atlas
  • cli
  • list_atlases
  • config
  • core
  • structure_tree_util
  • structure_class
  • update_atlases
  • utils
• BrainGlobe's publications
• Work using BrainGlobe's tools
• GitHub repository

cellfinder

• Introduction
• Installation
  • System requirements
  • Cluster installation
    • Installation with SLURM
  • Downloading files
  • Setting up your GPU
  • Installation with docker
• User guide
  • Data requirements
  • Command line interface
    • Cell candidate detection
    • Cell candidate classification
    • Historical options
    • Output files
  • Training the network
    • Using supplied training data
  • Visualisation
• Tutorial
  • Setting up
  • Running cellfinder
  • Visualising the results
  • Exploring the numerical results
  • Visualising your data in brainrender
• Troubleshooting
  • Speeding up cellfinder
  • Error messages
• Using conda
• Image definition
• Getting in touch
• Release notes
• Citing cellfinder
• Misc
  • Cell detection manuscript
  • Data underlying the paper
  • Using cellfinder at the SWC
• GitHub repository

cellfinder-core

• Introduction
• GitHub repository

cellfinder-napari

• Introduction
• User guide
  • Cell detection
    • Parameters to set
  • Training data generation
  • Training the network
• GitHub repository

brainreg

• Introduction
• Installation
• User guide
  • Registration parameters
  • Output files
• Tutorial
• Visualisation
• GitHub repository

BRAINREG-NAPARI

• Introduction
• User guide
• Checking orientation
• Tutorial
• GitHub repository

brainreg-segment

• Introduction
• User guide
  • Segmenting 1D tracks
  • Segmenting 2/3D structures
• Applications
  • Silicon probe tracking
• GitHub repository

bg-space

• BG-Space
• Usage
• GitHub repository

morphapi

• Morphapi
• Usage
  • Downloading data
  • Rendering data
• GitHub repository

Brainrender

• Brainrender
• GitHub repository

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• Governance model