Animals In Motion (with answers)
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.
Earlier 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 on October 8th, 2025, for students of the SWC Systems Neurscience PhD Programme will cover the following chapters of this handbook:
| Time | Topics |
|---|---|
| Morning | 1 Introduction 3 Pose estimation with SLEAP |
| Afternoon | 4 Analysing tracks with movement |
Students may also review the following chapters after the workshop, depending on their interests:
- 2 Deep learning for computer vision primer
- Case studies applying the
movementpackage to real-world datasets:
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 |
| v2025.10 | pre-release of the version taught as part of the SWC Systems Neurscience PhD Programme in October 2025 |
| v2025.10-answers | same as v2025.10 but with answers to exercises |
| v2025.08 | version used during the inaugural Open Software Week in August 2025 |
| v2025.08-answers | same as v2025.08 but with answers to exercises |
Funding & acknowledgements
The inaugural Open Software Week, which inspired the creation of this handbook, was made possible by a Software Sustainability Institute fellowship to Niko Sirmpilatze, as well as further funding support by the Sainsbury Wellcome Centre, the Society for Research Software Engineering and AIBIO-UK.
We thank the Sainsbury Wellcome Centre and the Gatsby Computational Neuroscience Unit for providing facilities for the workshops.
