Run the Main Script

Using Docker

You can use Docker to run the conversion process by mounting your input and output folders and passing the required arguments.

Example

docker run --rm \
  -v /local/input_folder:/data/input \
  -v /local/output_folder:/data/output \
  cellularimagingcf/biomero-converter:latest \
    --inputfile /data/input/input_file.tiff \
    --outputfolder /data/output \
    --outputformat omezarr04 \
    --show_progress \
    --verbose

Replace /local/input_folder and /local/output_folder with your actual local paths.
Adjust the image name (biomero-converter:latest) as needed.

Arguments

Refer to the main script for all available arguments:

--inputfile: Path to the input file (required)
--outputfolder: Path to the output folder (required)
--altoutputfolder: Alternative output folder (optional)
--outputformat: Output format: omezarr04, omezarr05, omezarr06 (OME-Zarr version) or ometiff (default: omezarr04)
--show_progress: Show progress bar (flag)
--verbose: Enable verbose logging (flag)
--plateid: Incucyte plate ID (optional, default: all plates)
--image_uuid: Leica image UUID (optional, default: all images in the file)

Alternatively install the Python package

Install the package from PyPI using pip install biomero-converter (or, from a clone of the repository, pip install -e .).
Run the biomero-converter command with the required arguments.

biomero-converter \
    --inputfile /data/input/input_file.tiff \
    --outputfolder /data/output \
    --outputformat omezarr04 \
    --show_progress \
    --verbose

usage: biomero-converter [-h] --inputfile INPUTFILE --outputfolder OUTPUTFOLDER [--altoutputfolder ALTOUTPUTFOLDER] [--outputformat OUTPUTFORMAT] [--show_progress] [--verbose] [--plateid PLATEID] [--image_uuid IMAGE_UUID]
biomero-converter: error: the following arguments are required: --inputfile, --outputfolder