Raspberry Pi: a versatile tool for biological sciences
Over the nine-ish years since the release of our first model, we’ve watched grow a thriving global community of Raspberry Pi enthusiasts, hobbyists, and educators. But did you know that Raspberry Pi is also increasingly used in scientific research?
Dr Jolle Jolles, a behavioural ecologist at the Center for Ecological Research and Forestry Applications (CREAF) near Barcelona, Spain, and a passionate Raspberry Pi user, has recently published a detailed review of the uptake of Raspberry Pi in biological sciences. He found that well over a hundred published studies have made use of Raspberry Pi hardware in some way.
How can Raspberry Pi help in biological sciences?
The list of applications is almost endless. Here are just a few:
- Nest-box monitoring (we do love a good nest box)
- Underwater video surveillance systems (reminds us of this marine conservation camera)
- Plant phenotyping (These clever people made a ‘Greenotyper’ with Raspberry Pi)
- Smart bird-feeders (we shared this one, which teaches pigeons, on the blog)
- High-throughput behavioural recording systems
- Autonomous ecosystem monitoring (you can listen to the Borneo rainforest with this project)
- Closed-loop virtual reality (there are just too many VR projects using Raspberry Pi to choose from. Here’s a few)
Onwards and upwards
Jolle’s review shows that use of Raspberry Pi is on the up, with more studies documenting the use of Raspberry Pi hardware every year, but he’s keen to see it employed even more widely.
“It is really great to see the broad range of applications that already exist, with Raspberry Pi’s helping biologists in the lab, the field, and in the classroom. However, Raspberry Pi is still not the common research tool that it could be”.Jolle Jolles
How can I use Raspberry Pi in my research?
To stimulate the uptake of Raspberry Pi and help researchers integrate it into their work, the review paper offers guidelines and recommendations. Jolle also maintains a dedicated website with over 30 tutorials: raspberrypi-guide.github.io
“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.”Jolle Jolles
The paper, Broad-scale Applications of the Raspberry Pi: A Review and Guide for Biologists, is currently under review, but a preprint is available here.
‘Pirecorder’ for automating image and video capture
Jolle has also previously published a very handy software package especially with biological scientists in mind. It’s called pirecorder and helps with automated image and video recording using Raspberry Pi. You can check it out here: https://github.com/JolleJolles/pirecorder.
You can keep up with Jolle on Instagram, where he documents all the dreamy outdoor projects he’s working on.
Drop a comment below if you’ve seen an interesting scientific application of Raspberry Pi, at work, on TV, or maybe just in your imagination while you wait to find the time to build it!
I’m currently using a modified mostly printed CNC machine for changing over sediment toxicity tests. I would love to add a Pi and the new camera to help make observations. Using AI to make observation on the visibility of organisms and to capture images. I’m just a bit under skilled to do it just yet.
I just got a raspberry pi I have it all Connected to my TV I want to learn how to use python what’s the best programs to use for a beginner?
A bit off-topic. I think Thonny and Geany are included pre-installed in Raspberry Pi OS. But many tutorials will use IDLE which is part of a normal Python installation.
If you want a powerful and good IDE (text editor), then I would definitely reccomend using Visual Studio Code: https://code.visualstudio.com/
To install it, just use the “sudo apt install code -y” command, or check out this article: https://www.raspberrypi.org/blog/visual-studio-code-comes-to-raspberry-pi/
Next, to use Python, you’ll have to use the VS Code Python extension, available here: https://marketplace.visualstudio.com/items?itemName=ms-python.python
Stuart Andrew Jones
I have a particular interest in potential Raspberry Pi applications in biomedicine. The current models provide enough computing power for potential applications, including:
1. Medical image storage and viewing. There are several DICOM compatible viewing and storage programs that have been ported to Raspberry Pi OS.
2. Patient monitoring for critical care. This might require the combination of Raspberry Pi and Arduino, but could provide improved performance compared to current products. Also, such products could be battery-powered and thus used in the field for emergency care, also providing monitoring equipment for medical care in less developed countries.
3. Medical record keeping (especially personal). There are open source medical record programs that could be ported and adapted for personal use, as well as for clinics in less developed countries.
4. Automated homeostasis systems. Raspberry Pi has already been adapted to manage blood glucose in brittle type I diabetes mellitus, and could be used to manage levels of other metabolites.
5. Patient localization, particularly of the demented and mentally ill, via Bluetooth or RFID. Also video patient monitoring.
6. Recording and tracking critical data in management of chronic diseases (e.g. weight in congestive heart failure, blood glucose in diabetes.
7. Pattern-matching medical diagnosis of rare diseases or unusual presentations of more common disorders. This does not involve ‘traditional’ AI or Bayesian statistics, but emulates the process of differential diagnosis performed by expert physicians. A medical school classmate of mine proved that this works, but this was never followed up.
8. In addition, a Raspberry Pi can provide computing power to monitoring all sorts of biological and medical laboratory operations too numerous to mention here. The referenced article mentions a few of these, but I believe barely scratches the surface of what is possible.
Thanks Stuart for your message. You are totally right that the Raspberry Pi has incredible potential to help in medicine and you give some great examples. By paper is specifically about applications for biological research and teaching so I did not include such practical applications as you mention. But might be nice to indeed at least mention some of this potential. Thanks!
Let me expand the list a bit. We are developing C4D system for capillary electrophoresis based on Raspberry Pi, using realtime Linux. Realtimeness is sufficient for our slow sampling rate (20 S/s). Target is – a mobile unit powered by batteries or a PSU, capable of doing analysis in the field. Applications range from water analysis to blood analysis, we are trying to make a realtime patient monitoring system, analysing analytes as time progresses, showing it in a 3D graph. Some of the analytes show how the patient reacts to various load conditions.
To keep the realtime properties right, Raspi must not overheat, downclock, or change frequency on the fly.
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