The majority of my work in this space happens by collaborating on pre-existing projects - I put tools to the test, provide feedback to developers and engage in discussions; open science is team science, and “lone wolf” projects too often whither away. I also maintain a couple of recipes on conda-forge related to tracking tools. And then I develop some projects of my own. I’m particularly proud of animovement, an R toolbox for analysing animal movement; I collaborate with developers of the movement Python package to create community around the packages and ensure high quality.
And everything I do is open science, whether it’s open hardware or open software, it’s open and freely available to use and to tinker with.
| Title | Description | Categories |
|---|---|---|
| animovement | 📈 An R toolbox for analysing animal movement across space and time | r, movement, animal behaviour |
| respirometr | 📈 An R toolbox for analysing respirometry data | r, respirometry, metabolism |
| rpix | 🌳 An R interface for pixi | pixi, conda, r, software |
| AniScope | ⚙️ A modular ethoscope for customised behavioural experiments with tiny animals | hardware, 3D printing, experiment |
| TinyTrackball | ⚙️ A small trackball adapted for respirometry experiments | hardware, 3D printing, experiment |
| BeeHive | ⚙️ A flexible platform for connecting different sensors and actuators | hardware, microcontroller, micropython |
| LaPreprint | 📝 A nicely formatted LaTeX preprint template | typesetting, LaTeX, preprint |
| academicv | 📝 A clean, flexible curriculum vitae (CV) template using Typst and YAML | typesetting, typst, cv |
Here’s some of the tools developed by others that I have tested extensively, reported bugs and suggested features:
- movement: a Python toolbox for analysing animal body movements across space and time
- autopilot: a Python framework to perform behavioral experiments with one or many Raspberry Pis
- belay: a Python Library for Rapid Hardware Development with MicroPython and CircuitPython
- TRex: a fast multi-animal tracking system with markerless identification, and 2D estimation of posture and visual fields
- idtracker.ai: tracks groups of up to 100 unmarked animals from videos recorded in laboratory conditions
- FreeMoCap: a free-and-open-source, hardware-and-software-agnostic, minimal-cost, research-grade, motion capture system and platform for decentralized scientific research, education, and training
- SLEAP: an open source deep-learning based framework for multi-animal pose tracking
- DeepLabCut: a toolbox for state-of-the-art markerless pose estimation of animals performing various behaviors
- performance: an R Package for Assessment, Comparison and Testing of Statistical Models