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Calcium-Behavior-Alignment

Align miniscope data with behavior

Command Line Interface (CLI) Overview

In addition to modulated functions for Jupyter notebook usage, there is also a CLI functionality for running on the terminal. Below is an overview of how to use the CLI for the calcium behavior alignment script.

  • The script can be executed from within the directory of calcium_behavior_alignment.py

Usage

calcium_behavior_alignment.py [-h] [-n NUM_PROCESSES] [-v] exp_path id_path beh_path experiment

Positional Arguments

  1. exp_path: The path to the experiment directory.
    • Example: /scratch/09117/xz6783/minian/Satiation/
  2. id_path: The path to the animal ID directory.
    • Example: /scratch/09117/xz6783/minian/Satiation/Session Combined/
  3. beh_path: The path to the behavioral data directory.
    • Example: /scratch/09117/xz6783/minian/Behavior_Files/
  4. experiment: The name of the experiment.
    • Example: Satiation

Optional Arguments

  • -h, --help: Display the help message and exit the program.
  • -n, --num_processes: The number of processes to use for multiprocessing (default: 2)
  • -v, --verbose: Whether to print verbose output. Helpful for debugging.

Example

python calcium_behavior_alignment.py /scratch/09117/xz6783/minian/Satiation/ /scratch/09117/xz6783/minian/Satiation/Session Combined/ /scratch/09117/xz6783/minian/Behavior_Files/ Satiation -n 5 -v

Important Note:

  • Ensure that you are running the python script on an environment with minian installed, e.g. conda activate minian