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Using Docker to Run the Main Script

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 \
  biomero-converter:latest \
    --inputfile /data/input/input_file.tiff \
    --outputfolder /data/output \
    --outputformat omezarr2 \
    --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 version (default: omezarr2)
  • --show_progress: Show progress bar (flag)
  • --verbose: Enable verbose logging (flag)