Brain Atlas¶

BrainGlobe-backed atlas integration. Downloads atlas data on first use and registers anatomical meshes into the lab coordinate frame. See the Brain Atlas user guide.

BG_Atlas ¶

BG_Atlas(
    atlas_name=None,
    region_names=None,
    *,
    whs_voxels=None,
    manual_fit=None,
    verbose=False,
)

Wrap a BrainGlobe atlas and align it to the eSDIva brain coordinate space.

Parameters:

Name	Type	Description	Default
`atlas_name`	`str`	BrainGlobe atlas name (e.g. `"whs_sd_rat"`). If None, a list of available atlases is printed. Default is None.	`None`
`region_names`	`str or list[str]`	Structure name(s) to load. Default is None (falls back to `"root"`).	`None`
`whs_voxels`	`dict`	Landmark voxel coordinates with keys `"origin"`, `"bregma"`, `"lambda"` (each a length-3 ndarray). Default is None.	`None`
`manual_fit`	`dict`	Manual alignment with keys `"origin"` (voxel, length-3 ndarray) and `"bregma_lambda_um"` (scalar distance in micrometres). Default is None.	`None`
`verbose`	`bool`	If True, print intermediate matrices during alignment. Default is False.	`False`

set_bgatlas ¶

set_bgatlas(
    atlas_name,
    region_names=None,
    *,
    whs_voxels=None,
    manual_fit=None,
    verbose=False,
)

Load a BrainGlobe atlas and update the instance attributes.

Parameters:

Name	Type	Description	Default
`atlas_name`	`str`	The name of the BrainGlobe atlas to load.	required
`region_names`	`str or list[str]`	Structure name(s) to retrieve. Default is None (falls back to `"root"`).	`None`
`whs_voxels`	`dict`	Landmark voxel coordinates with keys `"origin"`, `"bregma"`, `"lambda"`. Default is None.	`None`
`manual_fit`	`dict`	Manual alignment with keys `"origin"` and `"bregma_lambda_um"`. Default is None.	`None`
`verbose`	`bool`	If True, print intermediate matrices. Default is False.	`False`

get_pv_mesh_from_atlas ¶

get_pv_mesh_from_atlas(bg_atlas, region_names)

Load PyVista mesh(es) from a BrainGlobe atlas for the given structures.

Parameters:

Name	Type	Description	Default
`bg_atlas`	`BrainGlobeAtlas`	The BrainGlobe atlas object.	required
`region_names`	`str or list[str]`	The name(s) of the structure(s) to retrieve.	required

Returns:

Type	Description
`dict[str, PolyData]`	Mapping of region name to its PyVista mesh.

transform ¶

transform(T_matrix=None, pv_mesh=None, *, inplace=False)

Apply an affine transformation to the stored or supplied PyVista mesh.

Parameters:

Name	Type	Description	Default
`T_matrix`	`(4, 4) numpy.ndarray`	Homogeneous transformation matrix to apply. If None, no transformation is performed. Default is None.	`None`
`pv_mesh`	`dict[str, PolyData]`	Mesh(es) to transform. If None, the atlas mesh stored on the instance is used. Default is None.	`None`
`inplace`	`bool`	If True, mutate the instance's mesh in place and return None. If False, return a transformed copy. Default is False.	`False`

Returns:

Type	Description
`dict[str, PolyData] or None`	Transformed mesh(es), or None when `inplace=True`.

reset_mesh ¶

reset_mesh()

Reload the PyVista mesh from the atlas and re-apply the BPS transform.

Returns:

Type	Description
`dict[str, PolyData]`	The freshly loaded and transformed mesh(es).

summary ¶

summary()

Print a summary of the BG_Atlas object.

show_atlases ¶

show_atlases()

Show available BrainGlobe atlases.