Animals In Motion
Preface
Animals in Motion is an online handbook that introduces free, open-source tools for tracking animal motion from videos and extracting quantitative descriptions of behaviour from motion tracks.
Versions of this handbook have been taught as hands-on workshops in the following settings:
- the Neuroinformatics Unit Open Software Summer School
- the Sainsbury Wellcome Centre’s (SWC) Systems Neurscience PhD Programme.
Whether you are attending a workshop in person, or following along the materials at your own pace, be sure to check out Appendix A — Prerequisites.
All materials are shared under the CC-BY-4.0 license so you are welcome to use and adapt them for your own workshops. There is no need to ask for permission, but we’d love to hear about it if you do! Feedback and contributions to the handbook are always welcome, see Appendix B — Contributing.
Schedule
The workshop starting on August 17th, 2026, as part of the Neuroinformatics Unit Open Software Summer School, will cover the following chapters of this handbook:
| Time | Topics |
|---|---|
| Day 1: morning | 1 Introduction 2 Deep learning for computer vision primer |
| Day 2: morning | 3 Pose estimation with SLEAP |
| Day 2: afternoon | 4 Analysing tracks with movement |
| Day 3: morning | 7 Behaviour annotation with BORIS 8 Training a supervised behaviour classifier |
| Day 3: afternoon | 5 A mouse in the elevated plus maze 6 Zebra escape trajectories |
Versions
The latest release version is always available at the following URL:
https://animals-in-motion.neuroinformatics.dev/latest/
To view other versions, replace latest in the URL with one of the following version names:
| Version | Description |
|---|---|
| dev | development version, corresponding to the main branch. |
| v2026.08 | version used during the 2026 Open Software Summer School. |
| v2025.10* | version taught as part of the 2025 SWC Systems Neurscience PhD Programme. |
| v2025.08* | version used during the inaugural 2025 Open Software Week. |
*A companion -answers build, containing solutions to exercises, is also available for these versions, e.g. v2025.10-answers. Solutions are now included at the end of each chapter instead.
Funding & acknowledgements
The Open Software Summer School is funded by the Sainsbury Wellcome Centre, the Society for Research Software Engineering, AIBIO-UK, and The Neuro – Irv and Helga Cooper Foundation Open Science Prize.
The inaugural 2025 event, which inspired the creation of this handbook, was made possible by a Software Sustainability Institute fellowship to Niko Sirmpilatze
We thank the Sainsbury Wellcome Centre and the Gatsby Computational Neuroscience Unit for providing facilities for the workshops.
