wrapup_atlas_from_data#

brainglobe_atlasapi.atlas_generation.wrapup.wrapup_atlas_from_data(atlas_name, atlas_minor_version, citation, atlas_link, species, resolution, orientation, root_id, reference_stack, annotation_stack, structures_list, meshes_dict, working_dir, atlas_packager=None, hemispheres_stack=None, cleanup_files=False, compress=True, scale_meshes=False, resolution_mapping=None, additional_references={}, additional_metadata={})[source]#

Finalise an atlas with truly consistent format from all the data.

Parameters:

  • atlas_name (str) – Atlas name in the form author_species.

  • atlas_minor_version (int or str) – Minor version number for this particular atlas.

  • citation (str) – Citation for the atlas, if unpublished specify “unpublished”.

  • atlas_link (str) – Valid URL for the atlas.

  • species (str) – Species name formatted as “CommonName (Genus species)”.

  • resolution (tuple) – Three elements tuple, resolution on three axes

  • orientation – Orientation of the original atlas (tuple describing origin for BGSpace).

  • root_id – Id of the root element of the atlas.

  • reference_stack (str or Path or numpy array) – Reference stack for the atlas. If str or Path, will be read with tifffile.

  • annotation_stack (str or Path or numpy array) – Annotation stack for the atlas. If str or Path, will be read with tifffile.

  • structures_list (list of dict) – List of valid dictionary for structures.

  • meshes_dict (dict) – dict of meshio-compatible mesh file paths in the form {sruct_id: meshpath}

  • working_dir (str or Path obj) – Path where the atlas folder and compressed file will be generated.

  • atlas_packager (str or None) – Credit for those responsible for converting the atlas into the BrainGlobe format.

  • hemispheres_stack (str or Path or numpy array, optional) – Hemisphere stack for the atlas. If str or Path, will be read with tifffile. If none is provided, atlas is assumed to be symmetric.

  • cleanup_files (bool, optional) – (Default value = False)

  • compress (bool, optional) – (Default value = True)

  • scale_meshes (bool, optional) – (Default values = False). If True the meshes points are scaled by the resolution to ensure that they are specified in microns, regardless of the atlas resolution.

  • resolution_mapping (list, optional) – a list of three mapping the target space axes to the source axes only needed for mesh scaling of anisotropic atlases

  • additional_references (dict, optional) – (Default value = empty dict). Dictionary with secondary reference stacks.

  • additional_metadata (dict, optional) – (Default value = empty dict). Additional metadata to write to metadata.json