ibllib.atlas.regions

Functions

regions_from_allen_csv

Reads csv file containing the ALlen Ontology and instantiates a BrainRegions object :return: BrainRegions object

Classes

`BrainRegions`	The Allen atlas ids are kept intact but lateralized as follows: labels are duplicated and ids multiplied by -1, with the understanding that left hemisphere regions have negative ids.
`FranklinPaxinosRegions`

class FranklinPaxinosRegions[source]

Bases: _BrainRegions

id: ndarray

name: object

acronym: object

rgb: uint8

level: ndarray

parent: ndarray

order: uint16

class BrainRegions(brainmap='Allen')[source]

Bases: _BrainRegions

The Allen atlas ids are kept intact but lateralized as follows: labels are duplicated and ids multiplied by -1, with the understanding that left hemisphere regions have negative ids.

compute_hierarchy()[source]: Creates a self.hierarchy attributes that is a n_levels by n_region array of indices. This is useful to perform fast vectorized computations of ancestors and descendants. :return:

remap(region_ids, source_map='Allen', target_map='Beryl')[source]

Remap atlas regions ids from source map to target map

Parameters

region_ids – atlas ids to map
source_map – map name which original region_ids are in
target_map – map name onto which to map

Returns

id: ndarray

name: object

acronym: object

rgb: uint8

level: ndarray

parent: ndarray

order: uint16

regions_from_allen_csv()[source]: Reads csv file containing the ALlen Ontology and instantiates a BrainRegions object :return: BrainRegions object