squidpy.read.nanostring(path, *, counts_file, meta_file, fov_file=None)[source]

Read Nanostring formatted dataset.

In addition to reading the regular Nanostring output, it loads the metadata file, CellComposite and CellLabels directories containing the images and optionally the field of view file.

See also

  • path (Union[str, Path]) – Path to the root directory containing Nanostring files.

  • counts_file (str) – File containing the counts. Typically ends with _exprMat_file.csv.

  • meta_file (str) – File containing the spatial coordinates and additional cell-level metadata. Typically ends with _metadata_file.csv.

  • fov_file (Optional[str]) – File containing the coordinates of all the fields of view.

Return type



Annotated data object with the following keys:

  • anndata.AnnData.obsm ['spatial'] - local coordinates of the centers of cells.

  • anndata.AnnData.obsm ['spatial_fov'] - global coordinates of the centers of cells in the field of view.

  • anndata.AnnData.uns ['spatial']['{fov}']['images'] - hires and segmentation images.

  • anndata.AnnData.uns ['spatial']['{fov}']['metadata']]['{x,y}_global_px'] - coordinates of the field of view. Only present if fov_file != None.