New paper out in MEE on potential of Raspberry Pi’s in biology

Single-board computers like the Raspberry Pi have taken the world by storm and are being used in almost any situation imaginable. In a new open-access paper I published in the journal Methods in Ecology and Evolution, I now show these low-cost open-source computers are also increasingly being used in science and highlight how the Raspberry Pi can play a fundamental role to further revolutionise biological research.

By reviewing the biological literature, I found over a hundred empirical studies across the biological domain that implemented the Raspberry Pi in some way, both in the lab, the field, and in the classroom. The list of applications is almost endless, and ranges from weather stations, and automated bird feeders, to closed-loop learning devices, deep-sea recording systems, environmental monitoring tools, and wild-life camera traps.

The broad capabilities of the Raspberry Pi, combined with its low cost, ease of use and large user community make it a great research tool for almost any project. But despite its increasing uptake by the scientific community, the Raspberry Pi is not the common research tool that it actually could be.

To stimulate its uptake and help researchers integrate the Raspberry Pi in their work, I provide detailed recommendations, guidelines, and considerations, and developed a dedicated website (raspberrypi-guide.github.io) with over 30 easy-to-use tutorials.

I believe low-cost micro-computers like the Raspberry Pi are a powerful tool that can help transform and democratize scientific research, and will ultimately help push the boundaries of science. I therefore hope my paper will help generate more awareness about the Raspberry Pi among scientists and help advance our understanding of biology, from the micro- to the macro-scale.

Source
Jolles, J. W. (2021). Broad‐scale applications of the Raspberry Pi: A review and guide for biologists. Methods Ecol. Evol. 12, 1562–1579. doi:10.1111/2041-210X.13652

Update: My paper has been picked up by the Raspberry Pi Blog (link), scidev.net (link), and Niche magazine of the British Ecological Society (link, p12), among others!

New paper and software package: pirecorder!

Paper screenshot

My latest paper has just been published in the Journal of Open Source Software! It is the paper that accompanies my Python package pirecorder, which facilitates controlled and automated image and video recordings with optimal settings for the raspberry pi, specifically developed for biological research.

So far, researchers have often relied on writing their own recordings scripts to take still photographs and videos from the command line.

Although some specific software solutions exist, what was missing is a complete solution that helps researchers, especially those with limited coding skills, to easily set up and configure their raspberry pi to run large numbers of controlled and automated image and video recordings.

pirecorder was developed to overcome this need. You can get a quick overview of the package and what it is capable of in the video below:


Pirecorder is open source via GitHub, https://github.com/JolleJolles/pirecorder, easy to install using pip (pip install pirecorder), and comes with its own dedicated documentation website: https://jollejolles.github.io/pirecorder/.

The accompanying paper is published in the Journal of Open Source Software:

Jolles, J.W. (2020). pirecorder: controlled and automated image and video recording with the raspberry pi. Journal of Open Source Software 5(54), 2584. doi: 10.21105/joss.02584.

Organised ASAB workshop on Raspberry Pi’s for animal behaviour research

At the ASAB Summer Conference in Konstanz this year, which was focused on new frontiers in the Study of Animal Behaviour, I gave a half-day workshop about automating behavioural experiments with Raspberry Pi’s.

After a general introduction, I discussed its use in animal behaviour research, how to set up, work with, and remotely control a raspberry pi, how to work with the rpi camera system, and finally how to automate recording, including via my own pirecorder software.

I started working with these amazing machines during my PhD, which where then still quite difficult to set up and quite slow, but now with the newest model for almost the same low price, so much is possible!

It was great to see so many people (120) interested in this great open-source technology for their own work, and many told me soon afterwards they immideately started setting-up their own systems.

Due to the interest and enthusiasm I am planning to give more and more hands-on workshops in the near future. Stay tuned!

 

Easy install OpenCV for python on Mac, Ubuntu, and Raspberry Pi

Installing OpenCV has never been easy and always required a lot of careful usage of the command line to build from source. This was especially painful when working with a Raspberry Pi as building and installing OpenCV took a lot of time on the RPi, especially on the older models. Luckily this has changed very recently as it is now possible to install OpenCV with pip!

Below I guide you through the basic steps that I think are necessary to get opencv to work nicely on Mac, Ubuntu and Raspberry Pi. If you want more background information, see the excellent article by Adrian Rosebrock from PyImageSearch.com.

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