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converter.convert() Usage

The convert() function in biomero_converter/converter.py is used to convert an input file to OME format and write the result to one or more output folders.

Example Usage

from biomero_converter.converter import convert

input_filename = "path/to/input_file"
output_folder = "path/to/output_folder"
alt_output_folder = "path/to/alternative_output_folder"

result_json = convert(
    input_filename,
    output_folder,
    alt_output_folder,
    output_format="omezarr04",
    show_progress=False,
    verbose=False
)

print(result_json)

Arguments

  • input_filename (str): Path to the input file.
  • output_folder (str): Output folder path.
  • alt_output_folder (str, optional): Alternative output folder path.
  • output_format (str): Output format: 'omezarr04', 'omezarr05', 'omezarr06' (OME-Zarr version) or 'ometiff' (default: 'omezarr04').
  • show_progress (bool): If True, prints progress.
  • verbose (bool): If True, enables verbose logging.
  • **kwargs: Source specific parameters, e.g.:
  • plate_id (str): Incucyte plate ID (default: all plates).
  • image_uuid (str) or image_index (int): Leica image to convert (default: all images in the file).

Returns

A JSON string containing an array with conversion result info, e.g.:

[
  {
    "name": "experiment_name",
    "full_path": "path/to/output_folder/experiment_name.ome.zarr",
    "alt_path": "path/to/alternative_output_folder/experiment_name.ome.zarr"
  }
]