ovrlpy.io.read_MERSCOPE

ovrlpy.io.read_MERSCOPE(filepath, z_scale=1.5, *, remove_genes=MERSCOPE_CTRLS, additional_columns=[], n_threads=None)

Read a Vizgen transcripts file.

Parameters:

  • filepath (PathLike or str) – Path to the Vizgen transcripts file. Both, .csv(.gz) and .parquet files, are supported.

  • z_scale (float) – Factor to scale z-plane index to um, i.e. distance between z-planes.

  • remove_genes (Collection[str], optional) – List of regex patterns to filter the ‘gene’ column, ovrlpy.io.MERSCOPE_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