omicverse.space.rotate_space_visium

omicverse.space.rotate_space_visium(adata, angle, center=None, spatial_key='spatial', res='hires', library_id=None, interpolation_order=1)[source]

Rotate Visium spatial data image and coordinates by a specified angle.

This function performs rotation of both the tissue image and spot coordinates while maintaining proper alignment and scaling.

Parameters:

  • adata – AnnData Annotated data matrix containing Visium spatial data.

  • angle – float Rotation angle in degrees (positive for counterclockwise).

  • center (default: None) – tuple, optional (default=None) (x, y) coordinates of rotation center. If None, uses center of spatial coordinates.

  • spatial_key (default: 'spatial') – str, optional (default=’spatial’) Key in adata.obsm containing spatial coordinates.

  • res (default: 'hires') – str, optional (default=’hires’) Image resolution to use (‘hires’ or ‘lowres’).

  • library_id (default: None) – str Library ID for the spatial data in adata.uns[‘spatial’].

  • interpolation_order (default: 1) – int, optional (default=1) Order of interpolation for image rotation: 0: nearest neighbor, 1: bilinear, 3: cubic spline.

Returns:

AnnData

Rotated AnnData object with transformed coordinates and image.

Notes

  • The function preserves the original coordinate system scaling

  • Both image and spot coordinates are rotated around the same center

  • The rotation is performed counterclockwise for positive angles

  • Image interpolation can be adjusted for quality vs speed tradeoff

Examples

>>> import scanpy as sc
>>> import omicverse as ov
>>> # Load Visium data
>>> adata = sc.read_visium(...)
>>> # Rotate 45 degrees counterclockwise
>>> adata_rotated = ov.space.rotate_space_visium(
...     adata,
...     angle=45,
...     library_id='V1_Human_Brain'
... )