spateo.io.nanostring
====================

.. py:module:: spateo.io.nanostring

.. autoapi-nested-parse::

   IO functions for NanoString CosMx technology.



Attributes
----------

.. autoapisummary::

   spateo.io.nanostring.VERSIONS
   spateo.io.nanostring.FOV_PARSER


Functions
---------

.. autoapisummary::

   spateo.io.nanostring.read_nanostring_as_dataframe
   spateo.io.nanostring.stitch_images
   spateo.io.nanostring.read_nanostring


Module Contents
---------------

.. py:data:: VERSIONS

.. py:data:: FOV_PARSER

.. py:function:: read_nanostring_as_dataframe(path: str, label_columns: Optional[List[str]] = None) -> pandas.DataFrame

   Read a NanoString CSV tx or metadata file as pandas DataFrame.

   :param path: Path to file.
   :param label_columns: Column names, the combination of which indicates unique cells.

   :returns:

             Pandas Dataframe with the following standardized column names.
                 * `gene`: Gene name/ID (whatever was used in the original file)
                 * `x`, `y`: X and Y coordinates


.. py:function:: stitch_images(stain_dir: str, positions_path: str, labels: bool = False) -> numpy.ndarray

   Stitch multiple FOVs into a single image using position information.

   :param stain_dir: Directory containing JPEG or TIFF files with filenames
                     ending in '_FXXX' where XXX indicates the FOV index.
   :param positions_path: Path to CSV file containing FOV positions.
   :param labels: Whether these are labels (and therefore should be made unique).

   :returns:

             A numpy array containing the stitched image. May contain multiple channels,
                 which is the last dimension of the array.


.. py:function:: read_nanostring(path: str, meta_path: Optional[str] = None, binsize: Optional[int] = None, label_columns: Optional[Union[str, List[str]]] = None, add_props: bool = True, version: typing_extensions.Literal[cosmx] = 'cosmx') -> anndata.AnnData

   Read NanoString CosMx data as AnnData.

   :param path: Path to transcript detection CSV file.
   :param meta_path: Path to cell metadata CSV file.
   :param scale: Physical length per coordinate. For visualization only.
   :param scale_unit: Scale unit.
   :param binsize: Size of pixel bins
   :param label_columns: Columns that contain already-segmented cell labels. Each
                         unique combination is considered a unique cell.
   :param add_props: Whether or not to compute label properties, such as area,
                     bounding box, centroid, etc.
   :param version: NanoString technology version. Currently only used to set the scale and
                   scale units of each unit coordinate. This may change in the future.

   :returns: Bins x genes or labels x genes AnnData.