metaspace_converter.to_spatialdata module

metaspace_converter.to_spatialdata.get_ion_image_to_physical_transformation(dataset)[source]

Get the transformation from the ion image (pixels) to the world coordinate system (micrometers).

Parameters:

dataset (SMDataset) – A METASPACE dataset

Return type:

Scale

Returns:

A scale SpatialData transformation

metaspace_converter.to_spatialdata.metaspace_to_spatialdata(dataset=None, dataset_id=None, database=None, fdr=0.1, use_tic=False, metadata_as_obs=False, add_optical_image=True, optical_name_added='optical_image', add_points=True, points_name_added='maldi_points', sm=None, **annotation_filter)[source]

Download a METASPACE dataset as a SpatialData object.

See: https://metaspace2020.eu/about

Parameters:

  • dataset (Optional[SMDataset]) – A METASPACE dataset instance. If not provided, the dataset_id must be given.

  • dataset_id (Optional[str]) – The unique ID of a dataset on METASPACE, e.g. “2021-09-03_11h43m13s”

  • database (Optional[tuple[str, str]]) – A single METASPACE database given as a tuple of name and version. Usually it is displayed on METASPACE as “HMDB – v4” which corresponds to ("HMDB", "v4").

  • fdr (float) – Returns only annotations for which the false discovery rate is less or equal to this limit.

  • use_tic (bool) – When True, the output values will be scaled by the total ion count per pixel and will be in 0.0 to 1.0 range.

  • metadata_as_obs (bool) – Whether to store metadata in the obs dataframe instead of uns. For a single METASPACE dataset, metadata is the same for all pixels, so it would be duplicated for all obs. When combining multiple datasets, it would be preserved in obs but not in uns.

  • add_optical_image (bool) – Whether to also add the optical image (if one exists) to SpatialData images. If none exists, it is not added, and no error raised.

  • optical_name_added (str) – Name of the element where to store the image in the SpatialData object

  • add_points (bool) – Whether to also add ion image pixel coordinates as SpatialData points. This allows to spatially visualize the ion image values. If False, only ion intensities are added to the table and coordinates are added to obs.

  • points_name_added (str) – Name of the element where to store the points in the SpatialData object

  • sm (Optional[SMInstance]) – Optionally a cached SMInstance

  • annotation_filter – Additional keyword arguments passed to the METASPACE API.

Return type:

SpatialData

Returns:

A SpatialData object with

  • ion intensities and metadata: .table

  • optical image: .images["optical_image"] (or optical_name_added)

  • sampling coordinates: .points["maldi_points"] (or points_name_added) in a coordinate system relative to the top-left image corner and physical scale (micrometers)

Raises:
metaspace_converter.to_spatialdata.optical_image_to_spatial_image(dataset)[source]

Download the optical image of a METASPACE dataset to a SpatialImage object.

This function requires that the dataset has an optical image. Otherwise, an error is raised.

Parameters:

dataset (SMDataset) – A METASPACE dataset

Return type:

Optional[SpatialImage]

Returns:

A SpatialImage object with the image’s transformation to world coordinates