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 list[str] | None (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:

The read in AnnData object.