scmorph.io.read_cellprofiler_csv

scmorph.io.read_cellprofiler_csv#

scmorph.io.read_cellprofiler_csv(filename, n_headers=1, meta_cols=None, feature_delim='_', sep=',', backup_url=None)#

Read a matrix from a .csv file created with CellProfiler

Note

Depending on the CellProfiler version, you may have one or two header rows. Before using this function, do check the csv file to see if feature names are contained only in the first row or split over two and set n_headers accordingly.

Parameters:

  • filename (str) – Path to .csv file

  • n_headers (int (default: 1)) – Number of header rows.

  • meta_cols (list) – Names of metadata columns. None for automatic detection.

  • feature_delim (str (default: '_')) – Feature deliminator.

  • backup_url (Optional[str] (default: None)) – Retrieve the file from an URL if not present on disk.

  • sep (str (default: ',')) – Column deliminator.

Return type:

AnnData

Returns:

The read in AnnData object

Note

Depending on the size of the input matrix, this function can take a lot of memory. If needed, try exporting CellProfiler in batches of smaller csv files and read them in using io.read_cellprofiler_batches().

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