scmorph.io.read_cellprofiler_batches

scmorph.io.read_cellprofiler_batches#

scmorph.io.read_cellprofiler_batches(path, output_file, file_pattern='Nuclei.csv', n_headers=1, meta_cols=None, sep=',')#

Read CellProfiler data from directories

Parameters:

  • path (str) – Path to a directory containing .csv files

  • output_file (str) – Path to output file, will create a .h5ad file. This is needed to prevent large memory allocations.

  • file_pattern (str (default: 'Nuclei.csv')) – re.Pattern to match .csv files.

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

  • meta_cols (Optional[list[str]] (default: None)) – Names of metadata columns. None for automatic detection.

  • feature_delim – Feature deliminator.

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

  • progress – Show progress bar.

Return type:

AnnData

Returns:

adata

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