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

10 25 50
 
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 We have developed several instruments, including a micromanipulator, a mechanical tester, and a microscope suitable for clinical use. We have also worked on "slicer" methods to 3D print objects with optimised toolpaths, which are shared as an open source code repository.

A significant barrier to many of our original objectives was the difficulty of working with a distributed team on an open hardware project. We have developed software and workflows that facilitate this, and a significant part of our contribution to the field of open hardware is sharing this know-how through publications, open software, and other dissemination activities.
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.

We have started an educational project, funded by the Royal Academy of Engineering and Royal Society, that aims to make the OpenFlexure Microscope a valuable educational resource in the UK and abroad.

We have written up our findings on best practice and supporting digital infrastructure for open hardware projects, and are working to engage with policymakers and key influencers to support open projects in the future.
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. We have created OpenFlexure Industries, a UK micro-business, to sell kits of these designs and enable educators, researchers, and hobbyists to access them more easily. The OpenFlexure Microscope is now the centre of a large open-source community, including scientists, hobbyists, and engineers around the world. It is also being assessed for medical use in Tanzania, and has been taken up by a number of community initiatives aiming to bring the benefits of deep learning to microscopy in resource-constrained settings. Finally, the workflows and practices we developed during this project, in particular our working relationship with STICLab, have helped us inform several collaborations in Cambridge, Bath, and beyond, as to how best to arrange an open hardware project as part of the global COVID-19 response. This has resulted in a conference paper, articles in the Design Journal and the Conversation, and media interest from a number of outlets.
First Year Of Impact 2018
Sector Healthcare
Impact Types Societal

 
Description UKRI Circular Economy Approaches to Eliminate Plastic Waste - University of Cambridge
Amount £1,010,067 (GBP)
Funding ID EP/S025308/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 01/2019 
End 06/2020
 
Description URF Enhancement Award
Amount £200,000 (GBP)
Organisation The Royal Society 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2018 
End 03/2021
 
Description University Research Fellowship
Amount £600,000 (GBP)
Organisation The Royal Society 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2018 
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
 
Title The OpenFlexure Block Stage 
Description A 3D printable micropositioning stage, with a step size of 12nm and a range of 2x2x2mm 
Type Of Material Technology assay or reagent 
Year Produced 2020 
Provided To Others? Yes  
Impact The block stage has not yet been widely adopted. 
URL https://gitlab.com/openflexure/openflexure-block-stage/
 
Title Dataset for "Flat-field and colour correction for the Raspberry Pi camera module" 
Description This repository contains the hardware (OpenSCAD/STL files) and build instructions, software (Python scripts and Arduino firmware), data analysis (iPython notebook), and manuscript describing how to calibrate the colour response of a Raspberry Pi camera module. It also includes the calibration images acquired during the preparation of the work. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://researchdata.bath.ac.uk/id/eprint/764
 
Title Dataset for "Robotic microscopy for everyone: the OpenFlexure Microscope" 
Description This dataset contains microscopy images collected to demonstrate imaging capabilities of the OpenFlexure Microscope. Images for bright-field transmission and reflection, polarisation contrast, and fluorescence imaging are provided. A set of images obtained from a large tile scan are provided, along with the Microsoft Image Composite Editor file used for tiling. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://researchdata.bath.ac.uk/id/eprint/734
 
Title Research data supporting "Controlling Optically-Driven Atomic Migration Using Crystal-Facet Control in Plasmonic Nanocavities" 
Description  
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://www.repository.cam.ac.uk/handle/1810/308195
 
Title Research data supporting "Detecting mid-infrared light by molecular frequency upconversion with dual-wavelength hybrid nanoantennas" 
Description This folder contains research data from every figure in the paper. Briefly, files contain the reflection of the nanoparticle-on-resonator (NPoR) in visible and mid-infrared regime. Further, we enclose experiment data of surface enhanced Raman spectroscopy (SERS) of the constructs under study, as described in the linked manuscript. Here, we perform power dependent frequency upconversion measurements while measuring SERS. We show upconversion with pump ON and OFF. Then we show detail upconversion measurements for 40 NPoRs where we focus in various Stokes and antiStokes peaks for clarity. Lastly, we examine the mid-infrared tuning dependence of the frequency upconversion. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
URL https://www.repository.cam.ac.uk/handle/1810/330223
 
Title Research data supporting "Eliminating irreproducibility in SERS substrates" 
Description Surface enhanced Raman spectroscopy (SERS) data from self-assembled gold nanoparticle to study how the reproducibility in SERS substrates can be improved. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
URL https://www.repository.cam.ac.uk/handle/1810/315936
 
Title Research data supporting "Single photon multiclock lock-in detection by picosecond time stamping" 
Description This folder contains research data of every figure in the paper. This includes histograms of the lock-in frequencies as well as time tracks of the optical signal locked-in to the laser repetition rate, the laser modulation and the sweep of a delay stage. Finally, we record time-resolved coherent anti-Stokes Raman scattering to determine the vibrational lifetime of molecules in a plasmonic nanocavity. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
URL https://www.repository.cam.ac.uk/handle/1810/330674
 
Description MakerNet Alliance 
Organisation MakerNet Alliance
Sector Charity/Non Profit 
PI Contribution Our work on how to document open hardware projects has led to participation in the MakerNet alliance, a network that aims to create open standards that will allow the sharing of hardware documentation between platforms such as Thingiverse, Github, and WikiFactory in an open way. This is fully aligned with our goals for the project, as we are committed to making it possible to share knowledge without relying on proprietary formats. We have contributed guidelines and specifications for a MarkDown-based hardware documentation standard, along with example implementation code to render documentation and automate bill-of-materials generation.
Collaborator Contribution Connecting with a wider network of platform developers, makers, and users of open hardware is precisely the sort of steer our work needs in order to be most useful. This user "pull" is an essential part of any project that aims to achieve serious societal or technological impact, and thus while it is difficult to estimate a financial value, its intangible value is very high indeed.
Impact This is a multidisciplinary collaboration between scientists, engineers, platform developers, and third sector organisations such as Field Ready who make use of hardware designs. Current outputs include collaboratively-developed draft specifications, e.g. https://github.com/bath-open-instrumentation/markdown_documentation_for_hardware/ but more formal outputs are expected later this year.
Start Year 2019
 
Description Trinity Dublin NanoPhotonics 
Organisation Trinity College Dublin
Country Ireland 
Sector Academic/University 
PI Contribution Expt progress on nanophotonics for low energy switches
Collaborator Contribution Theory progress on nanophotonics for low energy switches
Impact Many research papers under development
Start Year 2019
 
Title Chief Ray Angle Compensation for the Raspberry Pi Camera Module 
Description This repository contains the hardware (OpenSCAD/STL files and build instructions, software (Python scripts and Arduino firmware), data analysis (iPython notebook), and manuscript describing how to calibrate the colour response of a Raspberry Pi camera module. analysis contains the data analysis code. data contains the images that we used for the graphs in the manuscript. neopixel_driver is the arduino firmware. image_acquisition includes the Python code that acquired the images and controlled the neopixel. calibration_jig contains the printable files, source OpenSCAD files, and assembly instructions for the calibration jig. colour_test_sheet contains source Inkscape SVG files and PDF renders of the test target used in the experiments. manuscript contains the source files for the manuscript. This is an open project, run by the Bath Open Instrumentation Group, part of the University of Bath. Unless otherwise specified, all code is licensed under the GPL v3 or later, hardware is under the CERN open hardware license, and documentation/manuscript is CC-BY 3.0 or later. The repository will be archived along with a published paper once it has been peer reviewed. If you are viewing a static archive of these files, you may want to consult the working repository, which may receive updates in the future. 
Type Of Technology Software 
Year Produced 2020 
URL https://zenodo.org/record/3699731
 
Title Chief Ray Angle Compensation for the Raspberry Pi Camera Module 
Description This repository contains the hardware (OpenSCAD/STL files and build instructions, software (Python scripts and Arduino firmware), data analysis (iPython notebook), and manuscript describing how to calibrate the colour response of a Raspberry Pi camera module. analysis contains the data analysis code. data contains the images that we used for the graphs in the manuscript. neopixel_driver is the arduino firmware. image_acquisition includes the Python code that acquired the images and controlled the neopixel. calibration_jig contains the printable files, source OpenSCAD files, and assembly instructions for the calibration jig. colour_test_sheet contains source Inkscape SVG files and PDF renders of the test target used in the experiments. manuscript contains the source files for the manuscript. This is an open project, run by the Bath Open Instrumentation Group, part of the University of Bath. Unless otherwise specified, all code is licensed under the GPL v3 or later, hardware is under the CERN open hardware license, and documentation/manuscript is CC-BY 3.0 or later. The repository will be archived along with a published paper once it has been peer reviewed. If you are viewing a static archive of these files, you may want to consult the working repository, which may receive updates in the future. 
Type Of Technology Software 
Year Produced 2020 
URL https://zenodo.org/record/3699730
 
Title OpenFlexure eV 
Description OpenFlexure eV is a modern, Electron-based application that allows interactive control of the OpenFlexure Microscope. It was developed by our team to enable a wider range of users to work with the microscope. 
Type Of Technology Software 
Year Produced 2019 
Open Source License? Yes  
Impact The software is in use by a number of groups around the world, in Tanzania, Kenya, Ghana, Cameroon, the USA, Germany, Chile, Peru, Paraguay, and many more. The software enables our work at Ifakara Health Institute where we are trialling the microscope for malaria diagnostics. 
URL https://gitlab.com/openflexure/openflexure-microscope-jsclient
 
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/
 
Company Name OPENFLEXURE INDUSTRIES LTD 
Description OpenFlexure Industries supplies kits of open-source hardware projects to enable a greater number of people to engage with the project. 
Year Established 2019 
Impact As a recently-established microbusiness, OpenFlexure Industries has only just started selling products, but has been chosen as a case study by the Gathering for Open Science Hardware to study how sustainable businesses can be built on open hardware.
Website https://openflexure.com
 
Description Article in The Conversation 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Commissioned to write an article for The Conversation on open hardware, and how it might help to improve medical supply chains in the future.
Year(s) Of Engagement Activity 2021
URL https://theconversation.com/making-hardware-open-source-can-help-us-fight-future-pandemics-heres-how...
 
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