region_grower.atlas_helper

An atlas helper to lookup the depths and orientations from an atlas.

This helper allows simple lookups without having to reason in term of [PH][1-6] and [PH]y.

Classes

AtlasHelper(atlas, region_structure_path)

Atlas helper for region grower.
class region_grower.atlas_helper.AtlasHelper(atlas: Atlas, region_structure_path: str)

Bases: object

Atlas helper for region grower.

compute_region_depth(region: str) → VoxelData

Compute the depth in all voxels of a given region.

Parameters:

region – the name of the region

get_layer_boundary_depths(position: List[float] | array, thicknesses: Atlas | None) → array

Return layer depths at the given position.

Parameters:

  • position – the position of a neuron in the atlas

  • thicknesses – the thicknesses in the layers

layer_thickness(layer: int | str) → Atlas

Returns an atlas of the layer thickness.

pia_coord(region) → Atlas

Returns an atlas of the pia coordinate along the principal axis.