omicverse.space.map_spatial_auto¶

omicverse.space.map_spatial_auto(adata_rotated, method='phase')[source]¶

Automatically map and align spatial transcriptomics data.

This function performs automatic alignment of spatial transcriptomics data with the corresponding tissue image using various alignment methods.

Parameters:

adata_rotated – AnnData Annotated data matrix containing spatial data to be aligned.
method (default: 'phase') – str, optional (default=’phase’) Alignment method to use: - ‘phase’: Phase correlation-based alignment - ‘feature’: Feature-based alignment - ‘hybrid’: Combination of phase and feature methods

Returns:

AnnData: Aligned AnnData object with updated spatial coordinates.

Notes

The function automatically selects the best alignment
Results can be verified using spatial plotting functions
Different methods may work better for different data types

Examples

>>> import scanpy as sc
>>> import omicverse as ov
>>> # Load and preprocess data
>>> adata = sc.read_visium(...)
>>> # Perform automatic alignment
>>> adata_aligned = ov.space.map_spatial_auto(
...     adata,
...     method='phase'
... )