usv-playpen v0.7.2

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GUI to facilitate conducting experiments with multi-probe e-phys (Neuropixels), multi-channel audio (Avisoft) and multi-camera video (Loopbio) acquisition. Developed for behavioral recording purposes at the Princeton Neuroscience Institute 2021-25 (Falkner/Murthy labs). Due to proprietary software design and limitations, recordings can only be performed on OS Windows. The data processing branch of the GUI is platform-independent.

Prerequisites

• Helvetica (download and install)
• Python 3.10 (and add it to top of PATH)
• git (and add it to PATH)
• ffmpeg (and add it to PATH)
• sox (and add it to PATH)
• sleap
• das
• CoolTerm

Installation and updating

Set up a new virtual environment with Python 3.10 and give it any name, e.g., usv.

python -m venv usv

Activate the virtual environment with:

source ./usv/bin/activate

or, on OS Windows:

.\usv\Scripts\activate

Install GUI with command below. Also, rerun the same command to check for and install updates.

pip install git+https://github.com/bartulem/usv-playpen --use-pep517

Add the python-motifapi package to your virtual environment:

pip install git+https://github.com/loopbio/python-motifapi.git#egg=motifapi --use-pep517

Test installation

Navigate to the main repo directory (example below).

cd /.../usv/lib/site-packages/usv-playpen
python -m unittest -v _tests.recording_tests
python -m unittest -v _tests.processing_tests

Example features

• behavioral_experiments.ExperimentController --> run behavioral experiments with Loopbio/Avisoft software
• extract_phidget_data.Gatherer --> extract data measured by illumination and temperature/humidity phidgets
• file_manipulation.Operator --> (1) break from multi to single channel, band-pass filter and temporally concatenate Avisoft-generated audio (e.g., WAV) files, (2) concatenate Motif-generated video (e.g., mp4) files and re-encode them to correct sampling rate (fps)
• synchronize_files.Synchronizer --> cut WAV file to video file (e.g., mp4) length and perform A/V synchronization check
• preprocessing_plots.SummaryPlotter --> generate summary figure for data preprocessing (i.e., metadata and sync quality)

Usage

Locate the pip installed package:

pip show usv-playpen

Navigate to the directory w/ the "usv_playpen_gui.py" file (example path listed below).

cd /.../usv/lib/site-packages/usv-playpen

Run the GUI.

python usv_playpen_gui.py

Developed and tested in PyCharm Pro 2024.3, on macOS Sequoia 15.1 / Pop!_OS 22.04 / Windows 11.