CLI Batch Processing#

Process an entire directory of plate images using the PhenoTypic command-line interface.

Basic Usage#

python -m phenotypic pipeline.json /path/to/plates/ /path/to/output/

Arguments:

  1. pipeline.json — Pipeline configuration (created with pipeline.to_json())

  2. Input directory — Folder containing plate images

  3. Output directory — Where results are saved

Grid Plates#

python -m phenotypic pipeline.json /plates/ /output/ \
    --image-type GridImage --nrows 8 --ncols 12 --ext .png

Parallelism#

python -m phenotypic pipeline.json /plates/ /output/ --n-jobs 4

Omit --n-jobs to use all available CPU cores.

Resume After Interruption#

python -m phenotypic pipeline.json /plates/ /output/ --resume

Add --retry-failures to reprocess only failed images.

Testing#

# Dry run: validate pipeline and list images without processing
python -m phenotypic pipeline.json /plates/ /output/ --dry-run

# Process 5 random images as a test
python -m phenotypic pipeline.json /plates/ /output/ --sample 5