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Section Navigation
Setting up
Using conda
Setting up your GPU
Image space definition
BrainGlobe Atlas API (brainglobe-atlasapi)
Atlas details
Command line interface
Adding a new atlas
API reference
brainglobe_atlasapi.cli
brainglobe_atlasapi.utils
atlas_name_from_repr
atlas_repr_from_name
check_internet_connection
check_s3_status
conf_from_file
conf_from_url
get_download_size
get_latest_version
load_structures_from_csv
read_json
read_tiff
retrieve_over_http
brainglobe_atlasapi.structure_class
Structure
StructuresDict
brainglobe_atlasapi.structure_tree_util
child_ids
get_structures_tree
postorder_depth_first_search
preorder_breadth_first_search
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_name
brainglobe_atlasapi.list_atlases
add_atlas_to_row
folder_version_to_dotted
get_all_atlases_lastversions
get_atlases_lastversions
get_downloaded_atlases
get_local_atlas_version
show_atlases
brainglobe_atlasapi.core
AdditionalRefDict
Atlas
brainglobe_atlasapi.bg_atlas
BrainGlobeAtlas
brainglobe_atlasapi.descriptors
format_annotation_stub
format_component_stub
format_hemispheres_stub
format_meshes_stub
format_template_stub
format_terminology_stub
brainglobe_atlasapi.atlas_generation.atlas_packaging_data
AnnotationInfo
AtlasPackagingData
ComponentInfo
CoordinateSpaceInfo
TemplateInfo
TerminologyInfo
check_requested_component
brainglobe_atlasapi.atlas_generation.wrapup
wrapup_atlas_from_data
brainglobe_atlasapi.atlas_generation.stacks
save_annotation
save_annotation_masks
save_hemispheres
save_reference
save_template
write_multiscale_ome_zarr
write_stack
brainglobe_atlasapi.atlas_generation.annotation_utils
apply_modal_filter
modal_filter_ignore_zeros
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
report_validation_results
validate_additional_references
validate_annotation_symmetry
validate_atlas
validate_atlas_files
validate_atlas_name
validate_atlas_name_listed
validate_checksum
validate_image_dimensions
validate_mesh_matches_image_extents
validate_metadata
validate_template_image_pixels
validate_unique_acronyms
brainglobe_atlasapi.atlas_generation.structures
check_struct_consistency
filter_structures_not_present_in_annotation
get_structure_children
get_structure_terminal_nodes
brainglobe_atlasapi.atlas_generation.metadata_utils
create_metadata_files
create_readme
create_structures_csv
generate_metadata_dict
brainglobe_atlasapi.atlas_generation.volume_utils
create_masked_array
create_masked_array_numba
brainglobe_atlasapi.atlas_generation.mesh_utils
Region
construct_meshes_from_annotation
create_region_mesh
extract_mesh_from_mask
write_mesh
write_mesh_info
brainglobe_atlasapi.atlas_generation.structure_json_to_csv
convert_structure_json_to_csv
get_parent_id
structure_id_path_to_string
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
API reference
brainrender.render
Render
brainrender.actor
Actor
make_actor_label
brainrender.camera
check_camera_param
get_camera
get_camera_params
set_camera
set_camera_params
brainrender.video
Animation
FrameGenerator
KeyframeCallback
VideoMaker
sigma
brainrender.atlas
Atlas
brainrender.cameras
brainrender.settings
brainrender.scene
Scene
brainrender.actors.volume
Volume
ruler
brainrender.actors.streamlines
Streamlines
make_streamlines
brainrender.actors.neurons
Neuron
make_neurons
brainrender.actors.line
Line
brainrender.actors.points
Point
Points
PointsBase
PointsDensity
brainrender.actors.cylinder
Cylinder
brainrender.atlas_specific.allen_brain_atlas.streamlines
experiments_source_search
get_streamlines_data
get_streamlines_for_region
brainrender.atlas_specific.allen_brain_atlas.gene_expression.ge_utils
check_gene_cached
download_and_cache
load_cached_gene
brainrender.atlas_specific.allen_brain_atlas.gene_expression.api
GeneExpressionAPI
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
brainrender
API reference
brainrender.settings
brainrender.settings
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Description
