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Ethoscope manual

An ethoscope platform records the behaviour of many animals at once, in real time. It has four parts:

  • Ethoscopes: Raspberry Pi computers with a camera, held above an arena of flies and lit with infrared light. Each ethoscope tracks its own animals and writes the results to a database on its card.
  • The node: an ordinary Linux PC that finds the ethoscopes on the network, starts and stops experiments from a web interface, and collects their data.
  • The network: a dedicated Wi-Fi network that connects ethoscopes and node.
  • Analysis software: ethoscopy in Python or rethomics in R, which read the databases the node collects.

Optional modules plug into an ethoscope over USB to deprive flies of sleep, deliver odours or light, or record the environment of the incubator.

Before building a platform, read the paper that describes it:

Geissmann Q., Garcia Rodriguez L., Beckwith E.J., French A.S., Jamasb A.R. and Gilestro G.F. (2017). Ethoscopes: an open platform for high-throughput ethomics. PLoS Biology 15(10): e2003026. doi:10.1371/journal.pbio.2003026

The analysis tools are described in Geissmann et al. 2019 (rethomics) and Blackhurst and Gilestro 2023 (ethoscopy). BibTeX for all three is on the publications page.

What you need

Section titled “What you need”
  • One or more ethoscopes: a 3D printer, a Raspberry Pi, a NoIR camera and a few electronic parts each (see Building an ethoscope).
  • A Wi-Fi router or access point reserved for the ethoscopes.
  • A PC to act as the node, with two network ports.
  • Some familiarity with Linux. Once running, the platform is easy to use and maintain, but building it from scratch takes time.

How this manual is organised

Section titled “How this manual is organised”

The manual is a continuous work in progress. If something is wrong or unclear, please open an issue or ask in GitHub Discussions.