cibrrig.preprocess.preproc_pipeline

This module runs the preprocessing pipeline for a session. It extracts sync, video frame, opto, and physiology information from the session.

Attributes

_log

Functions

plot_QC(ephysQC)	Plot the quality control figures for the ephys data.
run_ephys_qc_session(session_path)	Run ephysQC on all probes in the session.
run(session_path[, skip_ephysqc])	Run the preprocessing pipeline for a session.
cli(session_path, skip_ephysqc)	Command-line interface for running the preprocessing pipeline.
runQC(session_path)

Module Contents

cibrrig.preprocess.preproc_pipeline._log

cibrrig.preprocess.preproc_pipeline.plot_QC(ephysQC)

Plot the quality control figures for the ephys data. Saves images to the raw ephys folder

Parameters:

ephysQC (EphysQC) – EphysQC object containing the quality control data computed by IBL

cibrrig.preprocess.preproc_pipeline.run_ephys_qc_session(session_path)

Run ephysQC on all probes in the session.

Parameters:

session_path (str or Path) – Path to the session directory.

Returns:

None

cibrrig.preprocess.preproc_pipeline.run(session_path, skip_ephysqc=False)

Run the preprocessing pipeline for a session. 1) Extract sync times (digital signals from the SpikeGLX NIDQ signal) 2) Extract video frame times (from the digital line on the NIDQ input) 3) Extract opto times (From either digital or analog signals, looks for “laser” in the wiring dictionary) 4) Extract physiology data (emgs, ekgs, pressure differential, temperature) 5) Run ephysQC (optional)

Parameters:

• session_path (str or Path) – Path to the session directory.

• skip_ephysqc (bool, optional) – If True, skip the ephysQC step. Defaults to False.

Returns:

None

cibrrig.preprocess.preproc_pipeline.cli(session_path, skip_ephysqc)

Command-line interface for running the preprocessing pipeline.

Parameters:

• session_path (str) – Path to the session directory.

• skip_ephysqc (bool) – If True, skip the ephysQC step.

Returns:

None

cibrrig.preprocess.preproc_pipeline.runQC(session_path)