Murine Shift Work

Behavioural task acquisition with hardware support.

msw run --setup rig-a --subject mouse001 --task sequence

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What it does

• Behavioural tasks — sequence learning, probabilistic switching, optotagging, calibration routines
• Hardware abstraction — interchangeable backends for behaviour controllers, cameras, stage, scale, stimulators
• Config system — layered YAML overrides: bundled defaults → rig overlay → task mode → subject → CLI
• Session files — structured .msw.session.yaml + JSONL trial data; reader API for analysis
• Live plot — per-task online performance display during acquisition
• TTL barcodes — unique per-trial barcodes on BNC output for alignment with parallel recordings

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Installation

Requires Python ≥ 3.12 and uv.

pip install murineshiftwork

First-time setup

msw init --config-dir /path/to/msw_configs
msw setup create rig-a
msw subject add -s mouse001

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Development

git clone https://github.com/larsrollik/murineshiftwork.git
cd murineshiftwork
uv sync --group dev
uv run pytest tests/

Pre-commit hooks (ruff, mypy, secrets scan):

pre-commit install

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Docs

See docs/ for CLI reference, config system, session files, and task guides. Key architecture decisions are in docs/MASTER_PLAN.md.

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License

Copyright © 2021–2026 Lars B. Rollik. See LICENSE for terms.