abagen.io.read_ontology¶

abagen.io.read_ontology(fname, copy=False)[source]¶

Loads Ontology.csv file found at fname

Ontology files contain information on the anatomical delineations used by the Allen Institute when obtaining samples from donor brains, and are used in their online Brain Viewer to colorize regions. These files should be the same for every donors.

This information can be used to ensure that microarray samples are appropriately matched to anatomical regions.

Parameters:

fname (str) – Path to Ontology.csv file
copy (bool, optional) – Whether to return a copy if fname is a pre-loaded pandas.Dataframe. Default: False

Returns:

ontology – Dataframe containing ontology information for R anatomical regions used by the Allen Institute. Columns include: ‘id’, ‘acronym’, ‘name’, ‘parent_structure_id’, ‘hemisphere’, ‘graph_order’, ‘structure_id_path’, and ‘color_hex_triplet’.

Return type:

(R, 8) pandas.DataFrame