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Open hardware and software for modular, automated microscopy

  • Full or part time
  • Application Deadline
    Sunday, February 09, 2020
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

The University of Bath is inviting applications for the following PhD project supervised by Dr Richard Bowman https://researchportal.bath.ac.uk/en/persons/richard-bowman/ in the Department of Physics.

Modern microscopy relies extensively on automation; high-throughput screening of many samples, monitoring of processes over time, and the integration of light sources, detectors, cameras, spectroscopy, and positioning systems is vital to these increasingly complex experiments. Traditionally, microscopes would be purchased, along with their accessories and upgrades, from a single vendor who would also supply the software. This proprietary model greatly restricts choice in the components of an experiment, makes it harder to understand sources of error in the system, and makes both hardware and software very hard to modify.

Open source hardware and software offer an alternative model; components can be added or modified freely, and missing features can be added to either hardware or software thanks to the openly available designs and source code. However, such systems are often seen as too complicated, clunky, or unreliable by many scientists. Our research group works on open hardware and software for scientific research, including the OpenFlexure Microscope – a lab-quality microscope complete with high precision translation stage and focus mechanism. As part of this, we have a strong research theme on enabling technology – including 3D printed optomechanical systems, and software for instrument control.

This project will use the same software tools that power today’s internet to make hardware control simpler and more intuitive. This includes both the final interface that biologists or medical technicians might use, but also the lower-level code that runs each piece of hardware and, most critically, the communication between all the different parts of the experimental software. This will include extending the emerging standards for “internet of things” devices to cater for the demands of scientific experiments and working with collaborators around the world to help different projects communicate with each other.

Instrumentation control is only useful when combined with instrumentation, and the student will also be involved with hardware development in our research group. We use both dedicated scientific hardware, and components produced primarily for consumer electronics, to create high-performance sensors, actuators, and scientific instruments. Together with the more advanced, generalised software, there will be opportunities for the student to get involved with developing the hardware for more advanced imaging in the OpenFlexure Microscope, building and integrating accessories such as micromanipulators and spectrometers, and exploring the use of more advanced image sensors.

This PhD project addresses a vital challenge that is common to almost all experimental science projects, which is that of combining different instruments together to work as one experiment. It will involve difficult software and hardware challenges but has the potential to benefit laboratories all around the world, especially our collaborators in Low and Middle Income Countries who are particularly excited about the prospect of high quality open laboratory instrumentation. The work of our research group has a strong focus on applications in the Global South, currently funded by several Global Challenges Research Fund projects, and we would be delighted to involve the student in this work.

Candidate requirements:

Applicants should hold, or expect to receive, a First Class or good Upper Second Class Honours degree (or equivalent) in Physics, Computer Science or a relevant Engineering discipline. A master’s level qualification would be advantageous. Strong programming skills and an appetite to learn and develop new web frameworks, interfaces and hardware control code will be required. Opportunities may well arise to work with biologists or clinicians, so some experience of biological work would also be an advantage, though a willingness to learn is sufficient.

Enquiries and applications:

Informal enquiries are welcomed and should be directed to Dr Richard Bowman, .

Formal applications should be made via the University of Bath’s online application form for a PhD in Physics:
https://samis.bath.ac.uk/urd/sits.urd/run/siw_ipp_lgn.login?process=siw_ipp_app&code1=RDUPH-FP01&code2=0014

More information about applying for a PhD at Bath may be found here:
http://www.bath.ac.uk/guides/how-to-apply-for-doctoral-study/

Anticipated start date: 28 September 2020.

Funding Notes

Research Council funding is available for an excellent UK or EU student who has been ordinarily resident in the UK since September 2017. For more information on eligibility: View Website.

Funding will cover UK/EU tuition fees, maintenance at the UKRI doctoral stipend rate (£15,009 per annum tax-free in 2019/20, increasing annually in line with the GDP inflator) and a training support grant (£1,000 per annum) for a period of up to 3.5 years.

We also welcome all-year-round applications from self-funded candidates and candidates who can source their own funding.

References

See https://openflexure.org/ for more details on the OpenFlexure project, which is one of our group’s main outputs.

How good is research at University of Bath in Physics?

FTE Category A staff submitted: 23.00

Research output data provided by the Research Excellence Framework (REF)

Click here to see the results for all UK universities

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