Virtual Super-Resolution Workshop - Friday 9 July

12:30 - 17:00 hours BST

Scientific Organisers: Professor Michelle Peckham and Dr Hari Shroff

Designed to talk about the current challenges in developing and using super-resolution microscopy with short talks and lots of time for discussion, this year the workshop will be split into 2 sessions, focussing on the topics of ‘using machine learning and AI in super-resolution imaging’ and the other will be ‘expansion microscopy’.  Thoughts and ideas are encouraged to help define what is good/best practice around these challenges, and give an insight into future potential developments.

Invited Speakers will include:

Machine learning

Dr Aubrey Weigel

Janelia Research Campus

Aubrey Weigel is currently a Project Scientist of the Cellular Organelle Segmentation in Electron Microscopy (COSEM) Project Team at HHMI – Janelia Research Campus. The team uses advanced imaging technologies to study the ultrastructure and dynamics of subcellular organelles under both healthy and pathological conditions. Aubrey’s previous research background is in biophysics, with an emphasis in microscopy. Her formal training is in physics and engineering. During her graduate work Aubrey was the co-discoverer of ergodicity breaking in cells along with Diego Krapf, driving a pivotal shift in the field of diffusion analysis in living systems. Throughout her postdoctoral career under the guidance of Jennifer Lippincott-Schwartz, she applied her training in physics and microscopy directly to answer biological questions. Here, Aubrey unraveled the underlying structure of the endoplasmic reticulum and revealed its complex dynamics. She also uncovered the nano-anatomy of early secretory compartments and discovered a new, dynamic organelle, responsible for delivering newly synthesized cargo from the endoplasmic reticulum to the Golgi. Aubrey’s recent work as the leader of the COSEM project includes developing an invaluable tool for cell biology - an analysis pipeline based on deep learning architectures for segmentation - allowing comprehensive reconstruction and analysis of organelles within entire cells imaged by volumetric electron microscopy. Aubrey is committed to integrating her multi-disciplinary training into facilitating large-effort, collaborative, team projects to take on challenging scientific problems and sharing these resources with the broader scientific community.

Professor Dong Li

Chinese Academy of Science

Dr. Dong Li received Ph.D. in electronic and computer engineering at Hong Kong University of Science and Technology in 2011. He completed postdoctoral training in Dr. Eric Betzig’ group at Janelia Research Campus, Howard Hughes Medical Institute, after that he joined Institute of Biophysics, Chinese Academy of Sciences as principal investigator in 2015. Dr. Dong Li’s group focuses on developing super-resolution microscopy (SIM) for high-speed and long-term live imaging, and exploring their applications in biological research. Recently, Dong has made advances in patterned activation nonlinear SIM (PA NL-SIM) that breaks the 100 nm resolution barrier of conventional SIM for live-cell imaging; grazing incidence SIM (GI-SIM) that optimizes the 2D illumination depth while suppressing out-of-focus background; deep Fourier channel attention network SIM (DFCAN-SIM) that achieved robust SIM reconstruction at the challenging imaging conditions. These techniques enable us interrogate the dynamics of biological processes in live status at ultrahigh resolution in space and time.

Professor Dylan Owen

University of Birmingham 

I am a joint appointment between the Institute of Immunology and Immunotherapy and the School of Mathematics at the University of Birmingham, and am the deputy-director of the Centre of Membrane Proteins and Receptors (COMPARE). My lab focusses on developing new fluorescence microscopy methods, especially post-processing routines for single-molecule localisation microscopy (SMLM) and applying these to learn more about membrane biophysics and immunology. We are especially interested in the role of nanoscale protein clustering at the T cell immunological synapse. Prior to joining Birmingham in 2019, I was a lecturer at King’s College London joint between the Department of Physics and Randall Division of Biophysics, a post-doc in the Australian Centre for Nanomedicine at the University of New South Wales and a PhD student at Imperial College London, joint between the Department of Physics and the National Heart and Lung Institute supervised by Profs. Tony Magee and Paul French.

Dr Florian Jug

MPI Dresden 

 

Dr. Florian Jug holds a PhD in Computational Neuroscience from the Institute of Theoretical Computer Science at ETH Zurich. His research aims at pushing the boundary of what AI and machine learning can do to better analyse and quantify biological data. At HT, Dr. Jug covers the full breadth of bio-image computing, from research on novel methods for computer vision and machine learning, all the way to offering bio-image analysis as a service.

Florian Jug is a strong proponent of open access science, open AI and ML methods, and open source software. His team is a core contributor to  Fiji (~100,000 active users)  and collaboratively develops open methods such as CARENoise2VoidPN2VDivNoising, etc. He organizes scientific conferences (e.g. the I2K conference), workshops (e.g. the BIC workshops at top-tier computer vision conferences) and various practical courses on machine learning for bio-image analysis (e.g. [email protected] in Woods Hole) or microscopy (e.g. Quantitative Imaging at Cold Spring Harbour).

Dr Susan Cox

King's College London


Susan works at the Randall Centre for Cell and Molecular Biophysics, developing fluorescence microscopy techniques and applying them to discover new cell biology at the nanoscale. In 2011 she was awarded a Royal Society University Research Fellowship, which she used to develop a substantial research program based around localisation microscopy, and methods to extract more information from super-resolution image data. SC is best known as the developer of Bayesian analysis of blinking and bleaching (3B), a method for analysing extremely dense localisation microscopy image series. Its importance has been recognised with the award of the Royal Microscopical Society light microscopy medal and the Society of Experimental Biology Presidents Medal. More recently, she has explored the limits of localisation in terms of speed and accuracy. She mathematically described the role of the size of the point spread function size in limiting information transmission speed and developed a machine learning based approach to remove poor fits from the super resolution image. Since it is obviously more desirable to avoid poor fits in the first place, she developed Haar Wavelet Kernel analysis (HAWK), an approach to localisation microscopy data analysis which avoids artifacts and ensures the results reflect the underlying structure of the sample.

Expansion Microscopy

Dr Gerti Beliu

University of Würzburg

Gerti Beliu studied Biology (BSc & MSc) and earned his Ph.D in Biology at the University of Würzburg in the department of Prof. Markus Sauer, where he characterized clickable tetrazine-derivatives for their use in super-resolution microscopy. By combining genetic code expansion (GCE) and click chemistry, his research focused on building biochemical tools for better protein labeling and visualization with highest spatiotemporal resolution. Currently, he is developing fluorogenic biosensors for protein-protein interaction assays and site-specific biomolecule-tagging, where he applies novel biochemical strategies to immune cells for better translational bioimaging. In September 2021 he will start his independent Junior Research Group at the Rudolf-Virchow-Center (Würzburg/Germany).

Dr Helge Ewers

Free University Berlin

Helge Ewers studied Biochemistry in Hannover/Germany and New York City, USA and got his PhD from ETH Zurich, Switzerland where he worked with Ari Helenius. After a short postdoc with Daniel Choquet at the CNRS in Bordeaux, France, he started his group at ETH Zurich, Switzerland. From 2013 to 2014 he moved his lab to King’s College London where he was Senior Lecturer in the Randall Division before he accepted a full professorship at Free University Berlin. His laboratory develops microscopy assays for Cell Biology. The biological interest lies in the membrane cytsoskeleton, specifically the septins and the organization and compartmentalization of mammalian cell membranes.

Dr Izzy Jayasinghe

University of Sheffield
Izzy is a Senior Research Fellow and a UKRI Future Leader Fellow in the Department of Molecular Biology & Biotechnology in the University of Sheffield. Her research has focused on developing new optical microscopy techniques for studying the organisation of the molecules of life, particularly proteins, within the heart. Currently, she is developing a series of methodologies which enable super-resolution microscopy in the broader Life Sciences such as clinical and environmental research. Prior to moving to Sheffield, Izzy completed a PhD in Physiology in Auckland (New Zealand) and two postdoctoral fellowships in Queensland (Australia) and Exeter where she established a track record in developing and applying new optical imaging methods. She established her independent research group in the University of Leeds in 2015 where developed adaptations of optical imaging methods such as DNA-PAINT and Expansion microscopy to study pathological nanoscale remodelling in the failing heart.

Dr Joshua Vaughan

University of Washington, Seattle

Josh grew up near San Francisco, California and had an interest in science from an early age. He studied chemistry at Reed College in Portland, Oregon and then earned a Ph.D. in physical chemistry at MIT in the lab of Keith Nelson working on applications of adaptive optics to ultrafast spectroscopy. For his postdoctoral research in Xiaowei Zhuang's lab at Harvard, Josh developed tools for super-resolution fluorescence microscopy and studied virus transport. His current interests include developing new tools to extract molecular detail from intact biological specimens and applying these tools to important biological questions. Outside of work, he enjoys music, sailing, hiking, and spoiling his two daughters.

Professor Dr Silvio Rizzoli

The Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (GGNB)


Silvio O. Rizzoli, PhD, completed a BSc in biochemistry in 2000 at the University of Bucharest, Romania. He then carried out graduate training, until 2004, in the laboratory of Dr. William Betz at the University of Colorado. Dr. Rizzoli studied synaptic function for his PhD, and then trained as a postdoctoral fellow in the laboratory of Dr. Reinhard Jahn at the Max-Planck-Institut for Biophysical Chemistry in Göttingen, Germany, again focusing on synaptic function. Since 2007, he has led his own laboratory, first as a group leader and then as a professor at the University of Göttingen Medical Center.

Silvio’s laboratory has a dual focus – high-end imaging and cutting edge research in synaptic physiology. All projects that are run make use of advanced imaging techniques, including STED and electron microscopy.

The cost to attend this workshop is £20, you can add it to your schedule when registering to attend.


Sponsorship opportunities are available, if you are interested in sponsoring this meeting please contact Dawn Hopkins ([email protected])



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