omicverse.space.map_spatial_auto

omicverse.space.map_spatial_auto#

omicverse.space.map_spatial_auto(adata_rotated, method='phase', library_id=None, library_key=None, res='hires')[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 - ‘torch’: Torch-accelerated phase correlation

  • library_id (default: None) – str or None Spatial library whose image should be aligned. Required when more than one library is present.

  • library_key (default: None) – str or None Observation column identifying library membership. Required for a multi-library AnnData.

  • res (default: 'hires') – str, default=’hires’ Image resolution used for registration.

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'
... )
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