w2t-bkin 0.0.1

Mouse wiskers body kinematics and behaviour

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post_title: "W2T Body Kinematics Pipeline (Design Phase)" author1: "Project Team" post_slug: "readme-w2t-bkin" microsoft_alias: "na" featured_image: "/assets/og.png" categories: ["pipeline", "docs"] tags: ["overview", "design", "nwb"] ai_note: "Draft produced with AI assistance and reviewed by maintainers." summary: "Overview, goals, architecture, development workflow, and roadmap for the modular W2T body kinematics pipeline." post_date: "2025-11-08"

Overview

Modular, reproducible Python pipeline turning multi-camera rodent behavior recordings plus sync and optional pose/facial/event logs into a validated NWB dataset with QC and provenance.

Status: Phase 4 Complete (NWB Assembly with pynwb) ✅
Test Coverage: 255 tests passing (13 skipped)
Latest: Real NWB file assembly with external video links, rate-based timing, and provenance embedding

Key Features

• Explicit per-frame timestamps from hardware sync (TTL or counters)
• Optional mezzanine transcoding (idempotent)
• Pose harmonization (DLC/SLEAP) with skeleton mapping and confidence retention
• Facemap facial metric integration
• Bpod behavioral data parsing with multi-file session support (glob patterns, ordering, merging)
• Trials & events import from NDJSON (not used for sync)
• Single NWB output with external video links (no embedded heavy binaries)
• QC HTML: drift, drops, pose confidence, facial previews
• Deterministic, config-driven (TOML + Pydantic)

High-Level Flow

ingest → sync → (transcode) → pose / facemap / events → nwb → validate → qc

Package Modules (Planned)

Module	Purpose	Status
config	Load & validate settings	✅ Complete
ingest	Discover assets, produce manifest	✅ Complete
sync	Generate timestamps, drift/drop stats	✅ Complete
transcode	Optional stable mezzanine videos	✅ Complete
pose	Import/harmonize pose outputs	✅ Complete
facemap	Import/compute facial metrics	✅ Complete
events	Normalize NDJSON → trials/events	✅ Complete
nwb	Assemble NWB file & provenance	✅ Complete
qc	Build HTML report from summaries	🔲 Planned
validate	Run nwbinspector validation	🔲 Planned
cli	Typer CLI entry points	🔲 Planned
utils	Shared primitives	✅ Complete
domain	Shared typed domain models	✅ Complete

Configuration Snippet (Example)

[project]
name = "w2t-bkin"
n_cameras = 5

[paths]
raw_root = "data/raw"
intermediate_root = "data/interim"
output_root = "data/processed"
models_root = "models"

[video]
pattern = "cam{index}.mp4"

[sync]
primary_clock = "cam0"
tolerance_ms = 2.0

[nwb]
link_external_video = true

CLI (Planned Subcommands)

• ingest — build manifest
• sync — compute timestamps & stats
• transcode — optional mezzanine outputs
• pose — import/harmonize pose outputs
• infer — run pose inference when configured
• facemap — facial metric stage
• events — normalize NDJSON logs
• to-nwb — assemble NWB
• validate — run nwbinspector
• report — generate QC HTML

Development Setup

python -m venv .venv
source .venv/bin/activate
pip install -e .[dev]
pre-commit install
pytest -q

Testing Strategy (Summary)

• Unit: timestamp math, skeleton mapping, event derivation
• Integration: synthetic mini-session end-to-end
• CLI: artifact presence & exit codes
• Type: mypy on core modules; style: ruff

Artifact Locations

Path	Description
data/raw/<session>	Source videos + logs
data/interim/<session>/sync	Timestamps + summaries
data/interim/<session>/pose	Harmonized pose
data/interim/<session>/facemap	Facial metrics
data/interim/<session>/events	Trials/events tables
data/interim/<session>/video	Mezzanine videos
data/processed/<session>	NWB + validation report
data/qc/<session>	QC HTML

Quality Gates

• Timestamps monotonic per camera
• Drift within configured threshold
• No critical nwbinspector issues
• Pose confidence distributions reasonable
• Trials table non-overlapping

Roadmap

✅ Completed (Phases 0-4)

• Configuration loading and validation (Phase 0)
• File discovery and manifest building (Phase 1)
• Timebase synchronization and alignment (Phase 2)
• Behavioral events from Bpod .mat files (Phase 3)
• Video transcoding to mezzanine format (Phase 3)
• Pose import and harmonization (DLC/SLEAP) (Phase 3)
• Facemap facial metrics computation (Phase 3)
• NWB file assembly with pynwb (Phase 4)
  • Real pynwb Device and ImageSeries objects
  • External video file links
  • Rate-based timing (no per-frame timestamps)
  • Provenance metadata embedding
  • Security validations and deterministic output

🔲 Planned (Phase 5+)

• NWB validation with nwbinspector
• QC HTML report generation
• CLI interface with Typer
• Optional modalities integration in NWB (pose, facemap, Bpod events)
• Full end-to-end pipeline orchestration

Out of Scope

• Camera calibration & 3D reconstruction
• Embedding raw video in NWB by default

Contributing (Early Phase)

Open an issue describing proposed functionality. Keep PRs small and focused (single stage or feature). Add/adjust tests and update documentation sections touched.

License

Apache-2.0 (see LICENSE).

Summary Sentence

Design-phase repository for a modular, timestamp-faithful, NWB-centric behavioral pipeline with explicit synchronization, optional analytics stages, and transparent QC.