CLI Batch Processing#

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

Basic Usage#

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

Required path options:

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

  2. --input /path/to/plates/ — Folder containing plate images

  3. --output /path/to/output/ — Where results are saved

Grid Plates#

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

Parallelism#

python -m phenotypic --mode full --pipeline pipeline.json --input /plates/ --output /output/ --njobs 4

Omit --njobs to use all available CPU cores.

Resume After Interruption#

python -m phenotypic --mode full --pipeline pipeline.json --input /plates/ --output /output/ --resume

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

Testing#

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

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