pyXenium.io.export_xenium_to_slide_zarr#

export_xenium_to_slide_zarr(base_path, *, output_path=None, overwrite=False, n_jobs=1, cells_boundaries=True, nucleus_boundaries=True, cells_as_circles=None, cells_labels=True, nucleus_labels=True, transcripts=True, morphology_mip=True, morphology_focus=True, aligned_images=True, cells_table=True)#

Export wrapper that writes pyXenium’s own XeniumSlide Zarr schema.

This surface intentionally keeps slide export independent from external slide-ecosystem runtime packages while preserving the optional XeniumSlide.to_spatialdata() bridge for users who separately install it.

Parameters:

  • base_path (str | Path)

  • output_path (str | Path | None)

  • overwrite (bool)

  • n_jobs (int)

  • cells_boundaries (bool)

  • nucleus_boundaries (bool)

  • cells_as_circles (bool | None)

  • cells_labels (bool)

  • nucleus_labels (bool)

  • transcripts (bool)

  • morphology_mip (bool)

  • morphology_focus (bool)

  • aligned_images (bool)

  • cells_table (bool)

Return type:

dict[str, Any]