spateo.io.seqscope
==================

.. py:module:: spateo.io.seqscope

.. autoapi-nested-parse::

   IO functions for SeqScope technology.



Functions
---------

.. autoapisummary::

   spateo.io.seqscope.read_seqscope_as_anndata
   spateo.io.seqscope.read_seqscope_positions_as_dataframe
   spateo.io.seqscope.read_seqscope


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

.. py:function:: read_seqscope_as_anndata(matrix_dir: str) -> anndata.AnnData

   Read SeqScope matrix directory as AnnData.

   :param matrix_dir: Path to directory containing matrix files.

   :returns: AnnData of barcode x genes.


.. py:function:: read_seqscope_positions_as_dataframe(path: str) -> pandas.DataFrame

   Read SeqScope barcode positions CSV as dataframe.

   :param path: Path to file

   :returns: DataFrame containing barcode positions.


.. py:function:: read_seqscope(matrix_dir: str, positions_path: str, binsize: Optional[int] = 1, add_props: bool = True, version: Literal['seqscope'] = 'seqscope') -> anndata.AnnData

   Read SeqScope data as AnnData.

   :param matrix_dir: Directory containing matrix files
                      (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)
   :param positions_path: Path to CSV containing spatial coordinates
   :param binsize: Size of pixel bins
   :param add_props: Whether or not to compute label properties, such as area,
                     bounding box, centroid, etc.
   :param version: SeqScope technology version. Currently only used to set the scale and
                   scale units of each unit coordinate. This may change in the future.