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 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)

Alternatively Run the main script directly

1. Clone the repository and navigate to the project directory.
2. Install the required dependencies using pip install -r requirements.txt.
3. Run the main script with the required arguments.

python main.py \
    --inputfile /data/input/input_file.tiff \
    --outputfolder /data/output \
    --outputformat omezarr2 \
    --show_progress \
    --verbose

usage: main.py [-h] --inputfile INPUTFILE --outputfolder OUTPUTFOLDER [--altoutputfolder ALTOUTPUTFOLDER] [--outputformat OUTPUTFORMAT] [--show_progress] [--verbose] [--plateid PLATEID]
main.py: error: the following arguments are required: --inputfile, --outputfolder