Align miniscope data with behavior
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
calcium_behavior_alignment.py [-h] [-n NUM_PROCESSES] [-v] exp_path id_path beh_path experiment
- exp_path: The path to the experiment directory.
- Example:
/scratch/09117/xz6783/minian/Satiation/
- Example:
- id_path: The path to the animal ID directory.
- Example:
/scratch/09117/xz6783/minian/Satiation/Session Combined/
- Example:
- beh_path: The path to the behavioral data directory.
- Example:
/scratch/09117/xz6783/minian/Behavior_Files/
- Example:
- experiment: The name of the experiment.
- Example:
Satiation
- Example:
-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.
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
- Ensure that you are running the python script on an environment with minian installed, e.g.
conda activate minian