Zephyr

CNN + TCN network that predicts a mouse's breathing trace from video.

This repository is a uv workspace of two packages:

Package	Import	Command	What it is
zephyr	zephyr	zephyr	The network: clip lists, preprocessing, training, evaluation, inference. The only released package.
zephyr-benchmarks	zephyr.benchmarks	zephyr-benchmarks	Benchmarks on our dataset and the methods zephyr is compared against (TS-CAN, PhysNet, pixel, Facemap-style). Workspace only.

zephyr never imports zephyr.benchmarks; a test enforces it.

git clone https://github.com/AllenNeuralDynamics/zephyr
cd zephyr
uv sync --locked --all-packages --extra cpu     # or --extra gpu for CUDA

Data

The dataset (face-camera videos, frame timestamps and thermistor traces) is on a public S3 bucket; no AWS credentials are needed. The download commands are in the benchmarks README, under Dataset. Everything goes into data/ at the repository root.

• examples/ has one clip list, fold and experiment to start from; the zephyr README walks through them.
• packages/zephyr-benchmarks/configs/ holds the benchmark's configs; its README covers downloading the data and reproducing the published results.
• data/ (inputs), benchmarks/ (reference runs) and runs/ (outputs) live at the repository root and are ignored by Git.