metaspace_converter package

Submodules

Module contents

metaspace_converter.anndata_to_image_array(adata, layer=None)[source]

Extracts an array of ion images from an AnnData object (that has been generated through the metaspace_to_anndata function).

Parameters:

  • adata (AnnData) – An AnnData object.

  • layer (Optional[str]) – AnnData.layer that should be extracted to an image array. Default is None, which means that adata.X will be used.

Return type:

ndarray

Returns:

A three-dimensional Numpy array in the following shape

  • Dimension 0: Number of ion images in the order of adata.var_names

  • Dimension 1: Image height adata.uns["metaspace"]["image_size"]["y"]

  • Dimension 2: Image width adata.uns["metaspace"]["image_size"]["x"]

Raises:

ValueError – If the AnnData object has been modified. E.g. Pixel have been removed/added and the number of pixels and their coordinates do not match the original image dimensions.

metaspace_converter.metaspace_to_anndata(dataset=None, dataset_id=None, database=None, fdr=0.1, use_tic=False, metadata_as_obs=False, add_optical_image=False, sm=None, **annotation_filter)[source]

Downloads a METASPACE dataset to an AnnData 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 (Optional[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 embed the optical image for SquidPy

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

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

Return type:

AnnData

Returns:

An AnnData object with

  • ion intensities: .X

  • ion image pixel coordinates: .obs[["ion_image_pixel_x", "ion_image_pixel_y"]]

  • spatial coordinates: .obsm["spatial"]

  • ion properties: .var, for example “formula”, “adduct”, “mz”, “fdr”, “moleculeNames”, “moleculeIds”, “intensity”…

  • METASPACE metadata: .uns["metaspace"] if not metadata_as_obs

  • SquidPy metadata: .uns["spatial"] if add_optical_image

Raises:
metaspace_converter.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: