PyCon UK 2019

Robotic Microscopy for Everyone
2019-09-14, 11:30–12:00, Assembly Room

The OpenFlexure Microscope is an open-source, 3D-printed motorised microscope targeted towards medical applications in sub-Saharan Africa. This talk will introduce our work with local innovation hubs, research institutions, and clinics to develop control software that encourages contributions across all communities, from school pupils to professors.


The OpenFlexure Microscope has applications ranging from a low-cost educational tool all the way up to a research-grade laboratory instrument. Previously, everyone used their own set of hastily-written control scripts, leading to duplicated effort and an interface that was difficult for non-programmers to use.

In response, we have been rebuilding our Python-based control software from the ground up, with our collaborators in Cambridge and Tanzania. By introducing a new common core, a comprehensive plugin system, and a Flask-based web API, we have been able to draw on the expertise of a diverse community to create a highly customisable software stack for controlling the device in any setting.

Our work has particularly focused on low-cost Malaria diagnosis, allowing automated analysis on a network of microscopes. Where trained microscopists are in short supply, this automation helps existing technicians diagnose more patients, and facilitates better training. Our developments have also enabled school pupils to develop microscope control scripts as part of outreach projects, and will soon see the microscope used in university-level teaching labs.

Open-source hardware is poised to revolutionise countless industries such as research, local manufacturing, and education. However, developing scientific instrumentation poses a unique set of challenges revolving around synchronisation, data transmission, and resource management. By building a software stack designed from the start to be extensible, we are building a strong community across each of these areas, where every contribution can directly benefit all applications around the globe.


Is your proposal suitable for beginners? – yes

I am a post-doctoral research associate in the Centre for Photonics and Photonic Materials at the University of Bath. Following my PhD in nano-photonics, I moved to the Bath Open Instrumentation Group, leading development of the OpenFlexure Microscope software. Now specialising in scientific instrumentation control, I'm working with collaborators in Tanzania and Cambridge to bring our open-source microscope platform to a wide global community of scientific researchers, medical experts, and hobbyists.