"FlyPi": an affordable do-it-yourself microscope system

It is portable, cheap and can be adapted to many individual experiments – Tom Baden and André Maia Chagas developed the "FlyPi", a modular labware system, based on 3D printing, an open-source manual and self-programmed electronics. Do these open source solutions and the current maker-movement have the potential to transform science?

André M. Chagas and Dr. Tom Baden explain in this interview with COMPAMED-tradefair.com how their labware system is organized. Furthermore, they point out the differences to regular lab systems and reflect on the question, what open labware systems could do for emerging countries.

Dr. Baden and Mr. Chagas, you designed a do-it-yourself lab system. How exactly is the FlyPi-system organized? Which components does it consist of?

Dr. Tom Baden: There is basically a 3D-printed frame holding everything in place. At its core, there is a Raspberry Pi, which is a single board computer, and a camera with an M12 lens. So basically, it is a webcam held in a 3D-printed frame that gives you a very high zoom.

André Chagas: On top of the basic unit, modules can be added independently. They are mainly built with off-the-shelf components and electronic parts used by hobbyists. So far, we have built an optogenetics module, based on strong LEDs, a thermogenetics module based on a peltier element, two other illumination modules, and a motor module. We use an Arduino microcontroller (an open-source platform for electronic prototypes) to control these. We then basically connect a monitor, a keyboard and a mouse to the Raspberry Pi and use the user interface we wrote in Python, an open source language, to control the physical components.

What is the difference to regular lab equipment?

Baden: The main thing is the price. If you wanted to buy a commercial solution, it would be substantially more expensive. In most cases people end up using commercial systems, but almost never use all options they offer. Individual experiments tend to use more or less individual options. Tailoring your design more specifically to what you actually need can help you save a lot of money.

Chagas: On one hand, our system cannot do everything that a lot of the modern systems can do, but on the other hand, it can do some things other systems cannot. For example, the “FlyPi“ has a very wide zoom range. The same lens can be used to image small animals and cells. You cannot do this with a regular microscope as they are finely tuned to magnify very small things. Furthermore, our device is portable. It fits on the palm of a hand and can be powered with a battery. It can be powered with 12 volts, which we either obtain from a battery or even from a car’s lighter output. We can control the device via the internet (wirelessly or via cable), using a laptop. So in principle, the system can be used anywhere, either in environmental studies to do sampling directly in the field, or in remote areas, or places with faulty infrastructure, such as regions in conflict.

For which other kinds of lab studies would it be suitable? Could you give another specific example?

Baden: It was originally designed for neurogenetic research, to do behavioral studies of very small animals like fruit flies and zebrafish. In neuroscience, a lot of tools from protein engineering have come up which can be specifically expressed inside nerve cells of animals to render them sensitive to for example light or heat. You can activate or deactivate specific sets of neurons and simultaneously observe what the animal does and how it responds. Thus, you can basically study the neurons’ function. The microscope is also designed to do fluorescence microscopy.

Chagas: You could also use it for diagnostics of human parasites for instance, or to conduct experiments in the field of plant physiology. With small modifications, it can also be used for observing the behavior of larger animals. The whole project is already available online, so people could adapt it to their specific needs. There is for example a Professor in Chile who has adapted it to image bacterial colonies. Also because of its low cost, you could have ten of them and thus automate the processes in the lab, and perform several experiments in parallel. Since the “FlyPi“ is open for everyone, we hope that at least a small community will gather around it and help develop it further.

Who could hold a particular interest in these systems?

Baden: We hope that it is generally interesting for people in the biological sciences. We can think of education in a school or in a university teaching lab. It is a digital microscope, so it can just be connected to a projector screen and the class can watch everything on screen. Of course, you can also use it for your own research. These open source labware systems are quite cheap to build, so you might be able to afford quite a few of them. If someone is very limited in funding, they might at least be able to get a single one.

What would be the greatest opportunities worldwide, for example for emerging countries, in your opinion?

Chagas: The greatest opportunity for people in those countries would be to learn from this and the many other designs available online, so that they also start creating their own equipment. In this way, development can come from inside out, rather than rely on external contributions. They would join a vibrant online community of makers and DIYers. We have been running workshops under the NGO TReND in Africa where we teach researchers basic electronics, 3D printing, and how to use open source solutions which are available online in order to build laboratory equipment. For readers interested in contributing, we are always looking for volunteers from all fields!

Baden: The developing nations angle is certainly very valid, but even for richer countries it is interesting to have cost-effective labware.

Which new possibilities do you think open labware can create for Neuroscience or science in general?

Chagas: With open labware anyone can take any project that is available online and study, modify, improve them. In this way, these projects evolve, becoming more complex and useful. If enough people pick this up, open source scientific hardware will be the norm and not the exception, leveling the playing field for researchers and health care professionals worldwide.