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Open, reproducible hardware for microscopy

Theo Murphy meeting organised by Dr Richard Bowman, Dr Caroline Müllenbroich, Dr Benedict Diederich, Dr Julieta Arancio, Dr Sanli Faez and Professor Gail McConnell. The organisers would like to acknowledge the contribution of Dr Kirti Prakash, who has since stepped down from the organising committee, for helping to set up this meeting.

Add to Calendar 05/22/23 09:00 AM 05/23/23 05:00 PM United Kingdom (GMT) Open, reproducible hardware for microscopy <p>This meeting will bring together researchers, manufacturers, and others involved in open microscopy to discuss recent developments, best practice, and goals for the future.</p> Crowne Plaza Glasgow
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Overview Organisers Programme

Overview

Theo Murphy meeting organised by Dr Richard Bowman, Dr Caroline Müllenbroich, Dr Benedict Diederich, Dr Julieta Arancio, Dr Sanli Faez and Professor Gail McConnell. The organisers would like to acknowledge the contribution of Dr Kirti Prakash, who has since stepped down from the organising committee, for helping to set up this meeting.

Reproducible experiments in microscopy require well-understood instruments that can be replicated independently. Open Source Hardware, the practice of sharing complete designs under an open license can make instrument development more reproducible, more accessible, and reduce duplicated effort. This meeting will bring together researchers, manufacturers, and others involved in open microscopy to discuss recent developments, best practice, and goals for the future.

The schedule of talks and speaker biographies will be available soon. Meeting papers will be published in a future issue of Philosophical Transactions of the Royal Society A.

Poster/demonstration session

  • There will be a poster session on Monday 22 May 2023. If you would like to apply to present a poster please submit your proposed title, abstract (not more than 200 words and in third person), author list, name of the proposed presenter and institution to the Scientific Programmes team no later than Monday 17 April 2023.
  • If you would like to bring a hardware demonstration, please mention if it would require power and/or table space.
  • The organisers may invite a small number of attendees who submit abstracts to join panel discussions, on the basis of those abstracts.
  • Please include the text 'Poster abstract submission - Open, reproducible hardware for microscopy' in the email subject line. Please note that places are limited, and posters are selected at the scientific organisers' discretion.

Attending this event

This event is intended for researchers in relevant fields.

  • Free to attend
  • Advance registration essential (please request an invitation)
  • This is an in-person meeting.

Enquiries: contact the Scientific Programmes team

Image credit: Joseph Knapper, University of Bath (A fluorescent micrograph of some plant cells)

 

Cells under microscope
A fluorescent micrograph of some plant cells. Image credit: Joseph Knapper, University of Bath

Organisers

Dr Richard Bowman, University of Glasgow, UK

Dr Richard Bowman, University of Glasgow, UK

Dr Richard Bowman is a Royal Society University Research Fellow and Reader at the University of Glasgow, specialising in optical instrumentation and laboratory automation. Over the last six years he has led the OpenFlexure Project, centred on open source designs for a laboratory microscope suitable for diagnostics, research, and teaching. It has been reproduced thousands of times by a diverse community in over 40 countries around the world, including research labs in many disciplines, pathology research and teaching, community groups looking at environmental samples, and companies using it as a basis for new products. He is a strong advocate of openness as a means to improve both the reproducibility and accessibility of modern scientific apparatus, and very much hopes this meeting helps to forge links between the microscopy and open hardware communities.

Dr Caroline Müllenbroich, University of Glasgow, UK

Dr Caroline Müllenbroich, University of Glasgow, UK

Dr Caroline Müllenbroich is a lecturer at the School of Physics and Astronomy at the University of Glasgow. She studied physics at the University of Heidelberg, Germany and obtained her PhD at the Institute of Photonics, University of Strathclyde, Glasgow in 2012. She then joined the European Laboratory for Nonlinear Spectroscopy (LENS) in Florence, Italy working on light-sheet microscopes for structural imaging of clarified mouse brains and functional imaging in Zebrafish. From 2016 on, she was a researcher with the Italian National Institute of Optics, National Research Council and focused her activities on the application of non-diffractive Bessel beams for the high-fidelity interrogation of neuronal structure and function. She obtained a Marie Curie Fellowship and a position at Glasgow University where her group now works on deep cardiac imaging, remote focusing and light-sheet microscopy. She is an advocate for increased inclusion and diversity in our the STEM (Science, Technology, Engineering, Maths and Medicine) community. 

Dr Benedict Diederich, Leibniz Institute of Photonic Technology, Germany

Dr Benedict Diederich, Leibniz Institute of Photonic Technology, Germany

After doing an apprenticeship as an electrician Benedict Diederich started studying electrical engineering at the University for Applied Science Cologne. A specialisation in optics and an internship at Nikon Microscopy Japan pointed him to the interdisciplinary field of microscopy. After working for Zeiss he started his PhD in the Heintzmann Lab at the Leibniz IPHT Jena, where he focusses on bringing cutting edge research to everybody by relying on tailored image processing and low-cost optical setups. Part of his PhD program took place at the Photonics Center at the Boston University in the Tian Lab. A recent contribution was the open-source optical toolbox UC2 (You-See-Too) which tries to democratise science by making cutting-edge affordable and available to everyone, everywhere.

Dr Julieta Arancio, University of Bath, UK

Dr Julieta Arancio, University of Bath, UK

Dr Julieta Arancio is a postdoctoral researcher at the Centre for Science, Technology and Society, Drexel University (USA), and an associated researcher at CENIT-UNSAM (Argentina). She holds a degree in environmental science from Universidad de Buenos Aires and a PhD in science and technology studies from Universidad Nacional de Quilmes. Julieta has followed the open science hardware movement since 2017, looking at its potential contributions to more equitable science. Her current work, funded by the Alfred P Sloan Foundation, explores how open hardware is enabling new research activities and agendas. She has written academic papers and policy briefs on the topic, having presented her research at venues such as University of Cambridge (UK) and MIT (US), and teaching seminars at Universidad Nacional de Rosario (Argentina) and TU Berlin (Germany). Beyond academia, Julieta co-founded the Open Science Hardware network in Latin America (reGOSH) and the mentorship program Open Hardware Makers.

Dr Sanli Faez, Utrecht University, the Netherlands

Dr Sanli Faez, Utrecht University, the Netherlands

Sanli Faez is a professor (UD) at the Physics department of Utrecht University, a member of KNAW De Jonge Akademie, and a fellow at the Centre for Unusual Collaborations. He studied Physics at the Sharif University of Technology in Iran, and recieved his master’s degree in Nanotechnology from the University of Twente. His doctorate research at the University of Amsterdam was on wave propagation in strongly scattering media and Anderson localization. After post-doctoral research at the Max Planck Institute for the Science of Light and Leiden Institute of Physics, focused on single-molecule optics and (cryogenic) microscopy, he became the principal investigator for the research direction nanoElectroPhotonics at the Nanophotonics section of the Debye Institute for Nanomaterials at Utrecht University. He has hosted and produced several podcasts about open science.

Professor Gail McConnell, Strathclyde Institute for Pharmacy and Biomedical Sciences at the University of Strathclyde, Glasgow, UK

Professor Gail McConnell, Strathclyde Institute for Pharmacy and Biomedical Sciences at the University of Strathclyde, Glasgow, UK

Gail McConnell is Professor of Biophotonics at the Strathclyde Institute for Pharmacy and Biomedical Sciences at the University of Strathclyde, Glasgow, UK. Following a first degree in Laser Physics and Optoelectronics (1998) and PhD in Physics from the University of Strathclyde (2002), she obtained a Personal Research Fellowship from the Royal Society of Edinburgh (2003) and a Research Councils UK Academic Fellowship (2005), securing a Readership in 2008 and Professorship in 2012. The work in Gail’s group involves the design, development and applications of linear and nonlinear optical instrumentation for biological and medical imaging, from the nanoscale to the whole organism. She is a Fellow of the Royal Society of Edinburgh, a Fellow of the Institute of Physics, and a Fellow of the Royal Microscopical Society, where she is the current Chair of the Light Microscopy Committee.

Schedule

09:00-12:30
Session 1: Open hardware reaches further
9 talks

Chair

Dr Sanli Faez, Utrecht University, the Netherlands

Dr Sanli Faez, Utrecht University, the Netherlands

Sanli Faez is a professor (UD) at the Physics department of Utrecht University, a member of KNAW De Jonge Akademie, and a fellow at the Centre for Unusual Collaborations. He studied Physics at the Sharif University of Technology in Iran, and recieved his master’s degree in Nanotechnology from the University of Twente. His doctorate research at the University of Amsterdam was on wave propagation in strongly scattering media and Anderson localization. After post-doctoral research at the Max Planck Institute for the Science of Light and Leiden Institute of Physics, focused on single-molecule optics and (cryogenic) microscopy, he became the principal investigator for the research direction nanoElectroPhotonics at the Nanophotonics section of the Debye Institute for Nanomaterials at Utrecht University. He has hosted and produced several podcasts about open science.


Chair

Dr Julieta Arancio, University of Bath, UK

Dr Julieta Arancio, University of Bath, UK

Dr Julieta Arancio is a postdoctoral researcher at the Centre for Science, Technology and Society, Drexel University (USA), and an associated researcher at CENIT-UNSAM (Argentina). She holds a degree in environmental science from Universidad de Buenos Aires and a PhD in science and technology studies from Universidad Nacional de Quilmes. Julieta has followed the open science hardware movement since 2017, looking at its potential contributions to more equitable science. Her current work, funded by the Alfred P Sloan Foundation, explores how open hardware is enabling new research activities and agendas. She has written academic papers and policy briefs on the topic, having presented her research at venues such as University of Cambridge (UK) and MIT (US), and teaching seminars at Universidad Nacional de Rosario (Argentina) and TU Berlin (Germany). Beyond academia, Julieta co-founded the Open Science Hardware network in Latin America (reGOSH) and the mentorship program Open Hardware Makers.

09:00-09:01
Session 1: Open hardware reaches further

Abstract

Sharing hardware openly both enables more people and labs to access it, but through encouraging replication it makes science more reproducible. In this session, we will hear from speakers who work with or develop open projects, that have achieved a much wider reach because of that openness. The discussion will touch on the benefits of openness applied to experimental hardware, particularly as applied to reducing the inequalities entrenched in modern scientific practice. We will discuss issues around how to make projects open, barriers we often face to doing so, and tools that can help.

09:00-09:05
Welcome by the lead organiser
09:05-09:45
Panel 1

Speakers

Dr Jenny Molloy, University of Cambridge, UK

Dr Jenny Molloy, University of Cambridge, UK

Dr Jenny Molloy is a Senior Research Associate at the University of Cambridge building technologies for an open, globally inclusive and equitable bioeconomy through the Open Bioeconomy Lab. She develops biomanufacturing tools and technologies that are sustainable by design and deployable in low-resource contexts. Her group also investigates the most effective ways that their research can make a positive impact in developing and emerging economies, particularly the effect of open licensing and collaborative development with end users. Jenny was a member of the World Economic Forum Global Future Council on Synthetic Biology,  chairs an independent multi-sectoral working group on Local Production and Diagnostics in Low and Middle Income Countries and has co-founded four social enterprises and non-profits supporting the development and deployment of open source tools for science. 

09:45-10:25
Panel discussion – Q&A
10:25-10:40
Introduction to the unconference format
10:40-11:10
Break
11:10-12:10
Unconference session 1 following on from the panel discussion
12:10-12:30
Plenary feedback and discussion
12:30-13:30
Lunch
13:30-18:15
Session 2: Faster, more reproducible instrument development
8 talks

Chair

Dr Caroline Müllenbroich, University of Glasgow, UK

Dr Caroline Müllenbroich, University of Glasgow, UK

Dr Caroline Müllenbroich is a lecturer at the School of Physics and Astronomy at the University of Glasgow. She studied physics at the University of Heidelberg, Germany and obtained her PhD at the Institute of Photonics, University of Strathclyde, Glasgow in 2012. She then joined the European Laboratory for Nonlinear Spectroscopy (LENS) in Florence, Italy working on light-sheet microscopes for structural imaging of clarified mouse brains and functional imaging in Zebrafish. From 2016 on, she was a researcher with the Italian National Institute of Optics, National Research Council and focused her activities on the application of non-diffractive Bessel beams for the high-fidelity interrogation of neuronal structure and function. She obtained a Marie Curie Fellowship and a position at Glasgow University where her group now works on deep cardiac imaging, remote focusing and light-sheet microscopy. She is an advocate for increased inclusion and diversity in our the STEM (Science, Technology, Engineering, Maths and Medicine) community. 

Session 2: Faster, more reproducible instrument development

Abstract

Many cutting-edge techniques are now being shared under open licenses. This enables us to build on each other's work without the need for licensing deals, which is good for reproducibility and also for the pace of innovation. This session will let us hear from speakers developing novel technologies and sharing them openly.

13:30-14:10
Panel 2

Abstract

Professor Paul French - openScopes: an open, modular platform for microscopy and high content analysis

Professor French and his collaborators are developing open multidimensional fluorescence imaging instrumentation, including high content analysis (HCA), super-resolved microscopy, quantitative phase imaging and optical projection tomography. For fluorescence microscopy, they are developing a modular open-source microscopy platform based on openFrame, a low-cost, modular, microscope stand that can be used for low-cost and sustainable instruments in lower resource settings or for rapidly prototyping of advanced microscopy concepts. For open HCA and slide scanning, the scientists have developed novel optical autofocus modules including a long-range (~200 micron) implementation utilising machine learning. This can be combined with easySTORM for cost-effective single molecule localisation microscopy (SMLM) including automated multiwell plate SMLM for super-resolved HCA. They have also developed a polarization differential phase contrast microscopy (pDPC) module providing single-shot quantitative phase imaging that we are applying to label-free single cell segmentation and tracking for long time-base assays.

 

Dr Johannes Hohlbein - Open microscopy in the life sciences: sharing is caring 

Together with other colleagues enthusiastic about open science, Dr Hohlbein recently published a comment on the past, presence and future potential of open microscopy. Here, the author will iterate on some of the key points with a focus on single-molecule localisation microscopy (SMLM). SMLM allows monitoring molecular interactions in live cells and other complex samples. A few years ago, the scientists developed the miCube microscopy framework to increase the general accessibility and affordability of SMLM. They were intrigued to see how quickly other groups came up with new ideas and improvements in addition to our own developments including new algorithms for fast data analysis, addition of adaptive optics for localising proteins in turbid media and a scheme for spectrally resolved SMLM. These few examples demonstrate the huge potential of open microscopy in enabling interdisciplinary science and lowering the threshold for researchers to find the best solutions for their scientific imaging challenges.

Speakers

Professor Paul French, Imperial College London, UK

Professor Paul French, Imperial College London, UK

Paul French received his BSc (Hons) degree in physics (1983) and PhD in laser optics (1987) from Imperial College London. He was a Royal Society University Research Fellow at Imperial from 1989 until 1994, when he joined the academic staff, having previously worked at AT&T Bell Laboratories, (1990/91). Today his research group is based in the Physics Department at Imperial and in a satellite laboratory at the Francis Crick Institute. His research has evolved from ultrafast dye and solid-state laser physics to biomedical optics for applications in cell biology, drug discovery and clinical diagnosis. Current interests include the development and application of multidimensional fluorescence imaging technology for assays of biomolecular interactions, super-resolved microscopy, automated high content analysis, endoscopy and tomography, with open-source approaches to instrumentation, including hardware, data acquisition and analysis.

Dr Johannes Hohlbein, Wageningen University, The Netherlands

Dr Johannes Hohlbein, Wageningen University, The Netherlands

Dr Johannes Hohlbein studied Medical Physics at the MLU Halle-Wittenberg (Germany). In 2008 he obtained his PhD in Physics working on single-molecule detection in nanoscale confinement at the MPI of Microstructure Physics (Halle, Germany). He then joined the ‘Gene Machines’ group of Professor Kapanidis at the University of Oxford (UK) to work on DNA polymerases and developing assays for DNA sequencing. In 2012 he accepted a position as an Assistant Professor in the Laboratory of Biophysics at Wageningen University & Research (The Netherlands). Since then, his lab has been working on studying DNA-protein interactions in vitro and advancing single-molecule detection schemes. In 2018, Dr Hohlbein obtained tenure followed by promotion to Associate Professor. The current research in the lab is focussed on exploring DNA-RNA-protein interactions in live bacteria and performing functional food imaging using super-resolution microscopy and related techniques.

14:10-14:40
Panel discussion - Q&A
15:10-15:40
Break
15:40-16:25
Unconference session 2
16:25-16:45
Plenary feedback and discussion
16:45-18:15
Poster/tabletop presentations
18:15-00:00
Close
09:00-12:20
Session 3: Interoperability and reproducibility for experiments
6 talks

Chair

Dr Richard Bowman, University of Glasgow, UK

Dr Richard Bowman, University of Glasgow, UK

Dr Richard Bowman is a Royal Society University Research Fellow and Reader at the University of Glasgow, specialising in optical instrumentation and laboratory automation. Over the last six years he has led the OpenFlexure Project, centred on open source designs for a laboratory microscope suitable for diagnostics, research, and teaching. It has been reproduced thousands of times by a diverse community in over 40 countries around the world, including research labs in many disciplines, pathology research and teaching, community groups looking at environmental samples, and companies using it as a basis for new products. He is a strong advocate of openness as a means to improve both the reproducibility and accessibility of modern scientific apparatus, and very much hopes this meeting helps to forge links between the microscopy and open hardware communities.

09:00-09:01
Session 3: Interoperability and reproducibility for experiments

Abstract

Any design can be shared, but when interoperability, openness, and reproducibility are included in a design from the start, it often has great results. We will have a discussion led by panellists who are experienced in working openly, and in designing interfaces between different systems. The utopia of a lab where different experiments can be designed and implemented by connecting standard components in a seamless and rapid way is still some way off, but we will discuss how we can achieve this using open tools.

09:00-09:40
Panel 3
09:40-10:20
Panel Discussion
10:20-10:50
Break
10:50-12:00
Unconference session 3
12:00-12:20
Unconference recap
12:20-13:20
Lunch
13:20-17:00
Session 4: Making open, reproducible hardware a reality
6 talks

Chair

Dr Benedict Diederich, Leibniz Institute of Photonic Technology, Germany

Dr Benedict Diederich, Leibniz Institute of Photonic Technology, Germany

After doing an apprenticeship as an electrician Benedict Diederich started studying electrical engineering at the University for Applied Science Cologne. A specialisation in optics and an internship at Nikon Microscopy Japan pointed him to the interdisciplinary field of microscopy. After working for Zeiss he started his PhD in the Heintzmann Lab at the Leibniz IPHT Jena, where he focusses on bringing cutting edge research to everybody by relying on tailored image processing and low-cost optical setups. Part of his PhD program took place at the Photonics Center at the Boston University in the Tian Lab. A recent contribution was the open-source optical toolbox UC2 (You-See-Too) which tries to democratise science by making cutting-edge affordable and available to everyone, everywhere.

09:00-09:01
Session 4: Making open, reproducible hardware a reality

Abstract

Open hardware is already possible in microscopy, and is increasingly being seen as good practice. If we're to make open hardware more widespread, we need to understand how to recognise this practice in ways that are picked up by academic metrics, and how to produce instruments commercially without exclusive licenses. Our panellists represent a variety of different stakeholders from the scientific ecosystem, including suppliers, funders, publishers, and a legal expert. The discussion will start focused on questions around how we can help open hardware become more widely practised, including how it's published, purchased, and funded.

13:20-14:20
Panel 4
14:20-15:00
Panel Discussion
15:00-15:30
Break
15:30-16:25
Unconference 4
16:25-16:45
Plenary discussion
16:45-17:00
Plenary wrap-up