Knowbella Tech

[Anthropoid]

A New Open Source Imaging System

The open source movement has facilitated the development of low cost and easy-to-use technologies for scientific settings. A study published in PLOS ONE describes the creation of a novel multi-fluorescence imaging system from readily available, low cost components.

The study has just been awarded the 2018 PLOS Open Source Toolkit Channel Prize, and I was lucky to interview via email study authors Isaac Nuñez and Tamara Matute, of Pontificia Universidad Católica de Chile, who both contributed to the answers below.

What drew you to study bioengineering?

As engineers, we are always very interested in the development of technologies and tools for solving problems. Often engineers leave aside the biological perspective, but the ability of biological systems to solve problems is unique and carries a huge advantage compared to any tool invented by man. So we think it is vital to learn and seek solutions from this perspective.

What does the term “open source” mean, and how do open source tools benefit your research community?

There exist many good definitions of open source technologies, but for us, it refers to the freedom to use, study, replicate, modify, improve and redistribute technology without restrictions. As an investigator or developer, you work to make everything generated from your work generally available to be re-done, modified or mixed.

The GOSH (Global Open Science Hardware) movement and OpenPlant work to promote open source technology. We believe that openly shared technologies, such as open scientific hardware and open genetic tools, are crucial for technology development and knowledge production, particularly in low income countries.

In your study, you developed an open source imaging tool using cheap LEDs, filters and a Raspberry Pi camera in combination with fluorescent proteins. What gave you the idea?

We were inspired by the open source IO Rodeo transilluminator, which images electrophoresis gels, and the FlyPi microscope. We started to think how to evolve it to accomplish more sophisticated tasks for our daily research as well as for educational applications. So we combined the transilluminator with other existing advances such as long stokes shift fluorescent proteins, raspberry pi cameras and python programing resources.

Tell us about the development process.

When starting a project of this kind you have some ideas of what you want, but it really is an ongoing process. You have to prototype the different components in parallel and problem solve along the way. Our design also mutated along the way thanks to conversations with people such André Chagas (neuroscientist and co-editor of the PLOS Open Source Toolkit Channel) and information we found in online forums. It’s a continuous learning process and the final solution comes from the whole team.

Could you describe your tool and how it works?

It is a low cost multi fluorescence imaging station to study the dynamic genetic responses of cells. It uses blue light and an orange acrylic filter and excites different fluorescent proteins to emit a detectable fluorescent signal. The system is easy and cheap to build and uses only common available resources. Furthermore, we combined development of the equipment with testing of fluorescent proteins under blue light excitation to find which best fit the system as well as to adapt them to a set of modular genetic resources to use on it. The image recording mechanism is versatile, because you can use a raspberry pi system or simply a cell phone camera to take images or perform timelapse experiments. Finally, we included software resources to perform image processing, data analysis and teaching

Who do you hope might use your tool, and for what?

We hope that this tool will be used by researchers, educators and students of all ages.

For researchers, it can be used to obtain quantifiable cell data, such as growth and interaction dynamics in different experimental configurations, and to visualize the expression of fluorescent proteins and electrophoresis results.

For students and educators, we believe the tool can demonstrate experiments of quantitative biological behavior, something that we believe is lacking in biology education. Since the tool is inexpensive, it is possible to manufacture and use it in educational contexts where there is generally little or no access to technology. We hope that this is not a final product but just the first of a series of variations adapted for specific needs. We are currently exploring ways to openly distribute the required genetic resources.

Working with a potentially reconfigurable open device allows for more informative data acquisition, which increases our ability to propose new experiments or adaptations.

You have just been awarded the 2018 PLOS Open Source Toolkit Prize for this work. How did you feel when you found out that you’d won?

We were really happy and very honored. In our local context, open source is not well understood or simply unknown. Unfortunately, many institutions focus only on traditional proprietary development of technology, without giving space to other types of development. This award helps to get more attention for open technology in our institutions and also for the OpenPlant mini grants that were crucial for this work. We hope that winning the prize will contribute to advancing the understanding of open technologies and their great potential for both the scientific community and society.

What do you plan to do with your $500 prize money?

We are considering using the prize to develop new workshops about open technologies in the community, or to manufacture more equipment to realize these workshops and as gifts for schools.

Research Article: Nuñez I, Matute T, Herrera R, Keymer J, Marzullo T, Rudge T, et al. (2017) Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering. PLoS ONE 12(11): e0187163. https://doi.org/10.1371/journal.pone.0187163

Project page: https://osf.io/dy6p2/

Images Credits: Nuñez et al., 2017; Isaac Nuñez, Tamara Matute.

http://researchnews.plos.org/2018/07/04/shedding-light/