ThermoKourt Documentation

A modular pipeline for analysing Drosophila courtship and aggression under thermal manipulation.

User guide

• Getting started
  • Installation
  • Verifying the installation
  • Your first extraction
• Pipeline guide
  • Stage 1 — Arena extraction
  • Stage 2 — Identity tracking
  • Stage 3 — Identity overlay
  • Stage 4 — Manual ethogram annotation
  • Stage 5 — Automated scoring
• Architecture & design rationale
  • 1 — Motivation
  • 2 — Design principles
  • 3 — Stage 1: Arena extraction
  • 4 — Stage 2: Identity tracking
  • 5 — Stage 3: Identity overlay
  • 6 — Stage 4: Manual ethogram annotation
  • 7 — Stage 5: Automated behavioural classification
  • 8 — Data flow and file formats
  • 9 — Development roadmap
  • 10 — References

Development

• Contributing
  • Development setup
  • Running the test suite
  • Linting
  • Building the docs locally
  • Commit conventions
  • Pull request workflow
• Continuous integration
  • tests.yml
  • docs.yml
  • release.yml
  • Branch protection
• Release process
  • 1. Pre-release checks
  • 2. Update version metadata
  • 3. Update the changelog
  • 4. Tag and push
  • 5. Post-release
  • Rolling back a broken release

API reference

• thermokourt.extract
  • thermokourt.extract.arena_extractor
• thermokourt.track
  • thermokourt.track.posttrack
  • thermokourt.track.cli
• thermokourt.overlay
  • thermokourt.overlay.cli
• thermokourt.score
• thermokourt.utils

Project

• Changelog

Overview

ThermoKourt chains together arena extraction, identity tracking, manual ethogram annotation, and automated behavioural classification into a single reproducible pipeline. See the Architecture & design rationale document for design rationale and the Pipeline guide guide for step-by-step usage.

Quick links

• Source: github.com/zerotonin/thermokourt

• Issues: GitHub Issues

• GameThogram: github.com/zerotonin/GameThogram

• idtracker.ai: idtracker.ai