photon_mosaic.cli#
Command line interface for photon-mosaic.
Functions
|
Run the photon-mosaic Snakemake pipeline for automated and reproducible analysis of multiphoton calcium imaging datasets. |
- photon_mosaic.cli.main()[source]#
Run the photon-mosaic Snakemake pipeline for automated and reproducible analysis of multiphoton calcium imaging datasets.
This pipeline integrates Suite2p for image registration and signal extraction, with a standardized output folder structure following the NeuroBlueprint specification. It is designed for labs that store their data on servers connected to HPC clusters and want to batch-process multiple imaging sessions in parallel.
Command Line Arguments#
- –configstr, optional
Path to your config.yaml file. If not provided, uses ~/.photon_mosaic/config.yaml.
- –raw_data_basestr, optional
Override raw_data_base in config file (path to raw imaging data).
- –processed_data_basestr, optional
Override processed_data_base in config file (path for processed outputs).
- –jobsstr, default=”1”
Number of parallel jobs to run.
- –dry-runbool, optional
Perform a dry run to preview the workflow without executing.
- –forcerunstr, optional
Force re-run of a specific rule (e.g., ‘suite2p’).
- –rerun-incompletebool, optional
Rerun any incomplete jobs.
- –unlockbool, optional
Unlock the workflow if it’s in a locked state.
- –latency-waitint, default=10
Time to wait before checking if output files are ready.
- –log-levelstr, default=”INFO”
Log level.
- –reset-configflag, optional
Reset the config file to the default values.
- extralist
Additional arguments to pass to snakemake.
Notes
The pipeline will: 1. Create a timestamped config file in derivatives/photon-mosaic/configs/ 2. Save execution logs in derivatives/photon-mosaic/logs/ 3. Process all TIFF files found in the raw data directory 4. Generate standardized outputs following NeuroBlueprint specification