ovrlpy.io.read_CosMx

ovrlpy.io.read_CosMx(filepath, scale={'xy': 0.12028, 'z': 0.8}, *, remove_targets=COSMX_CTRLS, additional_columns=[], n_threads=None)

Read a Nanostring CosMx transcripts file.

Parameters:

  • filepath (PathLike or str) – Path to the CosMx transcripts file.

  • scale (Mapping[str, float]) – The factors for scaling the coordinates from pixel space to um.

  • remove_targets (Collection[str], optional) – List of regex patterns to filter the ‘target’ column, ovrlpy.io.COSMX_CTRLS by default.

  • additional_columns (Collection[str], optional) – Additional columns to load from the transcripts file.

  • n_threads (int | None, optional) – Number of threads used for parsing the input file. If None, will default to number of available CPUs.

Return type:

polars.DataFrame