create_region_mesh

brainglobe_atlasapi.atlas_generation.mesh_utils.create_region_mesh(args)

Automate the creation of a region’s mesh. Given a volume of annotations and a structures tree, it takes the volume’s region corresponding to the region of interest and all of its children’s labels and creates a mesh. It takes a tuple of arguments to facilitate parallel processing with multiprocessing.pool.map.

Note, by default it avoids overwriting a structure’s mesh if the .obj file exists already.

Parameters:

• meshes_dir_path (pathlib Path object with folder where meshes are saved)

• tree (treelib.Tree with hierarchical structures information)

• node (tree's node corresponding to the region whose mesh is being created)

• labels (list of unique label annotations in annotated volume,)

• (list(np.unique(annotated_volume)))

• annotated_volume (3d numpy array path to a zarr store with annotations)

• ROOT_ID (int,)

• that) (id of root structure (mesh creation is a bit more refined for)