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Quickstart

Both pipelines can be tried on synthetic ("mock") data that the repository generates: no real videos, no models and no GPU are needed. Run the commands from the repository root after pip install -e ".[dev]".

STRIDE T-maze on mock data

python tests/mock/make_mock_dataset.py --out tests/mock/_data --only core
stride tmaze tests/mock/_data/core/videos --roi-dir tests/mock/_data/core/roi_yml \
    --metadata tests/mock/_data/core/meta_trials.csv --metadata tests/mock/_data/core/metadata.csv \
    --out mock_output/tmaze --skip-inference

The mock set comes with its pose and ROI files, so the two inference steps are skipped (--skip-inference). The run writes mock_output/tmaze/SUMMARY.md, the decision tables under decisions/ and the gait tables under gait/. The mock maze is drawn at 16 px/cm, so the gait step prints its "below 20 px/cm" warning.

STRIDE Gait on mock data

python tests/mock/make_mock_gait.py --out tests/mock/_data_gait --only runway
stride gait tests/mock/_data_gait/runway/videos --px-per-cm 24 \
    --metadata tests/mock/_data_gait/runway/metadata.csv --out mock_output/gait

A synthetic mouse walking a straight line, with its pose files. The tables are under mock_output/gait/gait/.

On your own recordings

Replace the placeholder paths with yours.

stride tmaze /data/videos \
    --pose-model /models/pose/centroid --pose-model /models/pose/centered_instance \
    --roi-model  /models/roi/centroid  --roi-model  /models/roi/centered_instance \
    --out /data/stride_out

# pose files (<video name>.slp) next to the videos or in --pose-dir; scale measured by you
stride gait /data/videos --px-per-cm 26.1 --out /data/gait_out

# no pose files yet: your trained pose model makes them; scale from the ChArUco board in view
stride gait /data/videos \
    --pose-model /models/pose/centroid --pose-model /models/pose/centered_instance \
    --out /data/gait_out

stride calibrate /data/videos --out /data/calibration

Or from a config file

stride init-config tmaze -o my_tmaze.yaml     # commented template: videos, models, output, steps ...
stride tmaze --config my_tmaze.yaml

stride init-config gait -o my_gait.yaml
stride gait --config my_gait.yaml

Anything given on the command line overrides the file. Every key is described in the Configuration reference.

What you get

decisions.csv, decisions_clean.csv, events.csv and metrics.csv for the task; gait_per_stride.csv, gait_per_stride_filtered.csv, gait_per_step.csv and gait_per_video.csv for gait; SUMMARY.md, a run log and run manifests. Column by column: Outputs and column glossary.

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