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Learn more about BrainGlobe at the Neuroinformatics Unit Open Software Summer School in London, August 2026!

BrainGlobe

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  • About
  • Tutorials
  • Documentation
  • Community
  • Blog
  • Projects
  • Contact
  • GitHub
  • 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
    • Command line interface
    • Using the files directly
    • Adding a new atlas
    • API reference
      • brainglobe_atlasapi.structure_class
        • Structure
        • StructuresDict
      • brainglobe_atlasapi.utils
        • atlas_name_from_repr
        • atlas_repr_from_name
        • check_gin_status
        • check_internet_connection
        • conf_from_file
        • conf_from_url
        • get_download_size
        • read_json
        • read_tiff
        • retrieve_over_http
      • brainglobe_atlasapi.descriptors
      • brainglobe_atlasapi.cli
      • brainglobe_atlasapi.bg_atlas
        • BrainGlobeAtlas
      • brainglobe_atlasapi.list_atlases
        • add_atlas_to_row
        • get_all_atlases_lastversions
        • get_atlases_lastversions
        • get_downloaded_atlases
        • get_local_atlas_version
        • show_atlases
      • brainglobe_atlasapi.core
        • AdditionalRefDict
        • Atlas
      • brainglobe_atlasapi.structure_tree_util
        • child_ids
        • get_structures_tree
        • preorder_depth_first_search
      • brainglobe_atlasapi.config
        • cli_modify_config
        • get_brainglobe_dir
        • read_config
        • write_config_value
        • write_default_config
      • brainglobe_atlasapi.update_atlases
        • install_atlas
        • update_atlas
      • brainglobe_atlasapi.atlas_generation.annotation_utils
        • read_itk_labels
        • split_label_text
        • write_itk_labels
      • brainglobe_atlasapi.atlas_generation.validate_atlases
        • catch_missing_mesh_files
        • catch_missing_structures
        • get_all_validation_functions
        • open_for_visual_check
        • validate_additional_references
        • validate_annotation_symmetry
        • validate_atlas
        • validate_atlas_files
        • validate_atlas_name
        • validate_checksum
        • validate_image_dimensions
        • validate_mesh_matches_image_extents
        • validate_metadata
        • validate_reference_image_pixels
        • validate_unique_acronyms
      • brainglobe_atlasapi.atlas_generation.wrapup
        • filter_structures_not_present_in_annotation
        • wrapup_atlas_from_data
      • brainglobe_atlasapi.atlas_generation.mesh_utils
        • Region
        • construct_meshes_from_annotation
        • create_region_mesh
        • extract_mesh_from_mask
      • brainglobe_atlasapi.atlas_generation.stacks
        • save_annotation
        • save_hemispheres
        • save_reference
        • save_secondary_reference
        • write_stack
      • brainglobe_atlasapi.atlas_generation.structure_json_to_csv
        • convert_structure_json_to_csv
        • get_parent_id
        • structure_id_path_to_string
      • brainglobe_atlasapi.atlas_generation.volume_utils
        • create_masked_array
      • brainglobe_atlasapi.atlas_generation.metadata_utils
        • create_metadata_files
        • create_readme
        • create_structures_csv
        • generate_metadata_dict
      • brainglobe_atlasapi.atlas_generation.structures
        • check_struct_consistency
        • get_structure_children
        • get_structure_terminal_nodes
  • 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
    • Axes
    • Dimensions in image stacks
    • napari
    • Orientation
    • Voxel sizes
    • Napari 3D Orientation for brainrender
    • Handedness

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Using conda

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