CLI Reference#

PhenoTypic provides a command-line interface for batch processing plate images.

Usage#

python -m phenotypic PIPELINE_JSON INPUT_DIR OUTPUT_DIR [OPTIONS]

PIPELINE_JSON: Path to a pipeline configuration file created with pipeline.to_json().
INPUT_DIR: Directory containing plate images to process.
OUTPUT_DIR: Directory where results (overlays, measurements, checkpoints) are saved.

--image-type {Image,GridImage}: Image class to use for loading. Default: Image.
--nrows N: Number of grid rows (GridImage only). Default: 8.
--ncols N: Number of grid columns (GridImage only). Default: 12.
--bit-depth {8,16}: Force bit depth. Default: auto-detect.
--detect-mode MODE: Detection matrix source channel. Default: gray.
--ext EXT: File extension filter (e.g., .png, .jpg). Default: all supported formats.

--n-jobs N: Number of parallel worker processes. Default: all available CPUs.
--force-local: Run locally even if SLURM is available.
--dry-run: Validate pipeline and list images without processing.
--sample N: Process only N random images (for testing).
--random-seed SEED: Random seed for --sample reproducibility.

--resume: Continue from a previous run. Skips already-processed images.
--retry-failures: Re-process only images that failed. Requires --resume.
--restart: Clear all state and start fresh. Mutually exclusive with --resume.
--overwrite: Reprocess all images. Mutually exclusive with --resume.
--checkpoint-interval N: Save checkpoint state every N images. Default: 100.

--slurm-args KEY=VALUE: Pass SLURM scheduling parameters (e.g., time=04:00:00, partition=gpu).
--wait: Wait for SLURM jobs to complete before returning.

--overlay-alpha FLOAT: Opacity of detection overlay in saved images. Default: 0.3.
--include-dataset-column: Add a dataset column to measurement CSV output.
--metadata-csv PATH: Path to a CSV file with additional metadata to merge into results.
--skip-validation: Skip pipeline validation before processing.