Open Lab Instrumentation

Lead Research Organisation: University of Cambridge
Department Name: Physics

Abstract

Everyday gadgets contain an impressive range of technology; very high quality sensors, cameras, and microprocessors are now incredibly cheap - making it possible to build lab equipment very cheaply. Doing this would make a big difference in developing countries, as it enables better screening for diseases like malaria or TB, and makes it possible to study science in the lab as well as in theory. The biggest challenge with this approach is often mounting the different parts together: good quality mechanical mounts are very expensive. We will measure and develop micro-mechanical properties of printed plastic parts, and understand how the structure of the prints affects their strength and flexibility. This will allow us to improve the way parts are printed, and create stronger, better mechanisms using only low-cost plastic. Together with readily available parts, we will then design, build and test a number of optical lab instruments, including microscopes, spectrometers, and sample preparation equipment.

The 3D printers that are now found all over the world work by extruding plastic through a hot nozzle, and drawing shapes by moving the nozzle over a print bed. 3D objects can be made by stacking multiple layers on top of each other. This layer-by-layer approach means that the exact path taken by the nozzle as it prints the object strongly affects the mechanical properties of the part, and it is this effect that we particularly want to understand and control. Once we have fully understood the relationship between the path taken by the nozzle and the properties of the final part, we will be able to create much better toolpaths to make objects that are stronger, weaker, stiffer or more flexible - and to balance these properties as we need them in different parts of a design.

This new printing process will allow us to create parts that move very precisely, which is a crucial part of building precision instruments such as microscopes, spectrometers, and more. These instruments can be produced anywhere with a printer - including in many of the least developed countries in the world. Our partners in Tanzania will pilot this, and work with local clinics, universities and schools to explore how these better, cheaper instruments can help improve education and healthcare.

Planned Impact

A new capacity for technological innovation in the developing world is the main impact of this project: while the instruments we develop will quickly find applications in healthcare and sanitation, the deeper and longer impact comes from the central role of STICLab, our Tanzanian partners, in this work. Through co-development with them of improved printing methods, we will both advance what current 3D printers are capable of and ensure that the skills and knowledge to use and continue this work are embedded in the developing countries that can benefit most from such innovation.

Better microscopes, and in particular ones that can be automated with high-quality translation stages and tracking of biological objects such as cells, have the capacity to greatly improve diagnosis of many conditions prevalent in sub-Saharan Africa, such as Malaria, Tuberculosis, and many other parasitic diseases. We will create microscope designs that can be produced in the countries where they are needed, using commodity parts and 3D printed frames. STICLab will co-develop these designs, and as a registered company in Tanzania are perfectly placed to supply them to clinics and hospitals, as well as universities and schools. 3D printing and other digital manufacturing technologies are spreading across the world - together with STICLab, we will document and learn from our experience of supplying instruments in Tanzania, developing ways that the model can be replicated at many "digital blacksmiths" in other ODA countries.

Low cost instrumentation is also key to our not-for-profit start-up WaterScope, which uses our early prototype microscope to detect bacteria in drinking water faster, more simply, and at lower cost than existing tests. Our higher-performance designs will enable them to use sample-scanning to detect bacteria the essential large sample areas, which is one of the current limiting factors for the test's efficiency. We will continue to support WaterScope's activities and to develop instrumentation that will help their new water test become reality.

Our instruments, while of high enough quality to be useful in research and medical laboratories, will also be able to be produced cheaply enough for use in schools and university teaching labs. A significant impact will be the provision of high quality equipment for education and outreach to the general public. We have already run workshops and given demonstrations to a wide range of ages and backgrounds; we will build on this to make microscopy accessible, and inspire the next generation of scientists. By making the instruments open, it becomes possible for students to automate, construct, and modify their equipment, building valuable practical skills that they can take into research or transfer to many other technical career paths.

Publications

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Aitchison H (2017) Analytical SERS: general discussion. in Faraday discussions

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Baumberg J (2018) Reality science in Physics World

 
Title Microscope Folk comic 
Description As well as being exhibited at the "visions of science" exhibition, Tom Armstrong's comic book about a visit to our lab, "the microscope folk" has been distributed in print and online to many interested parties, collaborators, and colleagues. 
Type Of Art Artwork 
Year Produced 2018 
Impact This output was exhibited at an exhibition on campus, and has also provided imagery that we have used to illustrate talks - particularly to non scientific audiences, where the comic book style helps to make our content more approachable. 
 
Description What have you discovered or developed through the research funded on this grant? Please explain for a non-specialist audience.
We have developed several instruments, including a micromanipulator, a mechanical tester, and a microscope suitable for clinical use. We have also worked on documentation standards and "slicer" methods to 3D print objects with optimised toolpaths, though this work is still very much in progress.
Exploitation Route Our instruments have already been replicated by academic and non-academic organisations around the world. We are working with Ifakara Health Institute, supported by a different project, to evaluate and improve the microscope in a clinical setting with patient samples, with the eventual goal of automating the diagnosis of malaria.
Sectors Education,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

 
Description We are working with a non profit startup, Waterscope, to make cheap, reliable water testing for developing world countries. This has included a field trip to India in early 2019 where we evaluated how trained and untrained users were able to use the prototype test we developed. This has informed our development of the test, and will lead to a project that will be marketed in the coming years. The same field trip also allowed us to run workshops on assembly of our open-source microscope design, which engaged with >20 people at each workshop and will feed into ongoing science outreach programmes, for example in association with Miranda House, a nationally-recognised womens' college. We have developed instruments including the OpenFlexure Microscope (see associated output in "research tools and methods") and a related micromanipulation stage. These have been reproduced by hobbyists and scientists around the globe, and an active community has formed on Github.com using and building the instruments.
First Year Of Impact 2017
Sector Healthcare
Impact Types Societal

 
Description URF Enhancement Award
Amount £200,000 (GBP)
Organisation The Royal Society 
Sector Academic/University
Country United Kingdom
Start 10/2018 
End 03/2021
 
Description University Research Fellowship
Amount £600,000 (GBP)
Organisation The Royal Society 
Sector Academic/University
Country United Kingdom
Start 10/2018 
End 09/2023
 
Title OpenFlexure Microscope v5.20 
Description The OpenFlexure Microscope is a 3D printable design for a microscope, equipped with a high quality motorised stage for automatic focus and sample translation. It includes a range of options for the optics, from a very simple webcam-based design (suitable for use in schools, for example) to a lab-ready design with condenser optics on the transmission illumination, and a conventional microscope objective for high resolution imaging. As well as being inexpensive to produce, this microscope is designed parametrically, which makes it simple to customise for different use cases. By integrating all of the control electronics, including an embedded Raspberry Pi computer, into a portable, low cost, low power device, we have created a research tool that will enable long-running experiments, or multiple experiments in parallel, without the need to tie up expensive microscopy equipment that is often in high demand by multiple users. These same advantages make our tool particularly appropriate for healthcare and research scenarios in the developing world, or for use in education scenarios where budgets are limited. NB the date below relates to the most recent "release" of the project which represents a step change in performance and functionality. An earlier version of the microscope has been in circulation since 2015. 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? Yes  
Impact Our microscope design is in use across the world, in countries including Kenya, Tanzania, Ghana, Paraguay, and Chile - mostly in research labs and schools. It has also been reproduced in research labs in the UK, Germany, the US, and more for use in research projects. 
URL https://github.com/rwb27/openflexure_microscope/
 
Title Raspberry Pi camera lens shading code 
Description The Raspberry Pi camera module is a popular image sensor in many open source scientific hardware projects due to its low cost and high performance. One major limitation is in the firmware that applies a "lens shading correction" to images, which is problematic when using the camera with custom optics. We have improved an open source library, to allow the use of custom calibrations and manual gain settings with the camera. 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? Yes  
Impact Our improvements have been acknowledged by the original authors of the libraries and will be incorporated "upstream". 
URL https://github.com/rwb27/picamera/releases
 
Company Name WaterScope 
Description No-for-profit social entreprenuer company making cheap water testing kits 
Year Established 2017 
Impact RAE Fellowship for Waterscope developments, £30k GCRF funding from University, supported £1M EPSRC funded open Open Instrumentation, competition wins include: EPOC Business Plan Competition, Cambridge University Entrepreneurs Competition, and Downing Enterprise Competition. Organised a successful field trial to Nyarugusu refugee camp, one of the largest refugee camps in the modern world, with our collaborator Oxfam, during which we obtained user data on our system. Nyarugusu camp, based in Tanzania, is home to over 150,000 refugees from Congo, Burundi and Rwanda, with Oxfam supplying the water from boreholes and shallow wells.
Website http://www.waterscope.org/
 
Description Exeter Festival of Physics workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact 15 school, pupils and members of the public attended a workshop where we build and then used 3D printed microscopes to view a number of samples, and explore physical computing concepts by writing an autofocus routine in Python.
Year(s) Of Engagement Activity 2018
 
Description Nature 3D printing article 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Dr Julian Stirling was interviewed for an article on the use of 3D printing in science
Year(s) Of Engagement Activity 2018
 
Description Royal Society Summer Exhibition 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Massive event at Royal Society, for 1 week in July 2018; reaching >13000 of the public. Also many radio, TV, and newspaper interviews
Year(s) Of Engagement Activity 2018
URL http://nanogap.nanodtc.cam.ac.uk/
 
Description Science Festival talks 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Talks and exhibits at the Cambridge Science Festival
Year(s) Of Engagement Activity 2018
 
Description Stoner lecture, Leeds 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact JJB gave the Stoner lecture on translating research
Year(s) Of Engagement Activity 2017
 
Description Visions of Science exhibit 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact We participated in the Edge Arts "Visions of Science" scheme, where we collaborated with a comic book artist to produce a comic book about our lab. This started as an exposition of "Brightening the dim modes of plasmonic nanostructures" but broadened into an exploration of all the work we do in our lab.
Year(s) Of Engagement Activity 2018