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Invited Speakers

We have invited the following speakers to the Laser Analytics Group:

13 August 2018

Andrew Barentine is a PhD student of Biomedical Engineering in the Bewersdorf lab at Yale University School of Medicine. 

'3D Nanoscopy at 10000 Cell a Day'

Single-Molecule-Switching (SMS) nanoscopy methods retrieve spatial information from within a cell at 20-80 nm resolution, about 10-fold better than conventional microscopy. However, the slow recording speed typical of SMSN imaging (tens of minutes) limits the number of cells which can be imaged, dramatically weakening the statistical power of quantitative SMS-based investigation. sCMOS cameras and high laser powers have recently enabled acquisition at speeds an order of magnitude faster than with EMCCD cameras. However, the large data volume produced by sCMOS cameras, ~70 TB/day, has prevented extended high-speed SMS. In addition to the difficulty of data storage, the localization analysis bottleneck is compounded for high-quality fits, as the non-negligible sCMOS read-noise requires a more complicated noise model. We developed a platform for high-speed and high-throughput SMSN, included in the Python Microscopy Environment (PYME), which enables automated super-resolution imaging of ~10000 3D fields of view a day. We leverage distributed storage and a fully GPU-accelerated sCMOS-specific routine to localize 49500 loc./s, which is real-time at 800 Hz for up to 62 emitters/frame. We demonstrated our advances using an automated biplanar-astigmatism microscope designed to produce high-volumes of 3D and two-color SMS data, allowing us to image entire nuclei in less than 10 seconds. In addition to real-time localization of full-bandwidth sCMOS data, we developed a distributed post-localization analysis architecture integrated in PYME. With our other advances, we can now quantify unprecedented numbers of SMS images, which we are using to investigate the organization of the interphase nucleus. 

 26 April 2018

Jonathan Powell is the Head of Biomineral Research and Fellow of Hughes Hughes.  John Wills is a Herchel Smith Fellow and Fellow of Girton College.

 'In Situ Cytometry Studies of the Endogenous Nano-chaperone Pathway for Gut Immune Cell Surveillance'

 In 2015 we reported on our discovery of an endogenous nanomineral that chaperones luminal antigen and bacterial MAMPs to intestinal immune cells, as a part of normal immunosurveillance (Nature Nanotechnology. 2015 Apr;10(4):361-9). We have since shown that this pathway is promiscuous, across species and operates far beyond the ileal lymphoid patches as we originally described it. We have also shown that in humans there is hijack of the pathway by engineered food additive and excipient nanoparticles, to which humans are so commonly orally exposed. The recipient immune cells for both the endogenous and exogenous nanoparticles normally express the immuno-modulatory receptor PD-L1, but we showed that this fails in Crohn’s disease (Sci Rep. 2016 May 26;6:26747). These and ensuing studies face marked technical challenges: the endogenous chaperone is friable and labile and destroyed by processing so in situ analyses of frozen or anhydrous tissues is required. Signals- such as cytokines and chemokines that diffuse from cells- provide strong clues as to whether recipient cells of particles are initiating cell-cell signalling so gradients must be established, again in situ and quantitatively. Quantitative cell content with precise locational data and nearest neighbour phenotypes are also required. All of these- and more- are addressed by our development of in situ cytometry (ISC). Like similar quantitative histology and histochemistry techniques, ISC utilises open source software to segment cells and analyse their content and location simultaneously. Through integration of carefully controlled sample preparation, imaging, image analysis and machine learning, we are able to provide fully quantitative cell-by-cell outputs for the complex tissue types and variable tissue regions that make up the gastrointestinal tract, and demonstrate detailed nanoparticle interactions in situ.  


26 April 2018

Studying Human Brain Development and Evolution in Cerebral Organoids

Dr Madeline Lancaster is a Group Leader in the Cell Biology Division of the Medical Research Council (MRC) Laboratory of Molecular Biology, part of the Cambridge Biomedical Campus in Cambridge, UK. Madeline studied biochemistry at Occidental College, Los Angeles, USA, before completing a PhD in 2010 in biomedical sciences at the University of California, San Diego, USA. She then joined the Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) in Vienna, Austria as a postdoctoral researcher, before joining the LMB in 2015.

Human brain development exhibits a number of unique characteristics, such as dramatic size expansion and variation in relative abundance of specific neuron populations. In an effort to better understand human brain development, we developed a human model system, called cerebral organoids. Cerebral organoids, or “mini-brains”, are 3D tissues generated from human pluripotent stem cells that allow modelling of brain development in vitro. We have been able to demonstrate that brain organoids are particularly powerful not only for examining human specific mechanisms, but also pathogenesis of neurological disease. More recently, we have developed improvements to better control their differentiation using micropatterning to guide their development while maintaining self-organization. Current findings reveal the timed generation of excitatory neurons and inhibitory interneurons as well as their proper migration and positioning. We are now using this system to perform the first functional tests of putative brain evolution genes in this human model system. These studies are revealing some interesting roles for these factors in regulation of human neurogenesis.

Research in the Lancaster lab focuses on human brain development using a new model system, called cerebral organoids. These ‘mini-brains’ are 3D tissues generated from stem cells that allow modelling of human brain development in vitro. The laboratory uses mini-brains to study the most fundamental differences between human brain development and that of other mammalian species – what makes us human. We are also studying neurodevelopmental disorders such as autism and intellectual disability, and the cellular mechanisms underlying neurodevelopmental disease progression and potential therapeutic avenues.

Lab webpage: http://www2.mrc-lmb.cam.ac.uk/madeline-lancaster/ 


20 March 2018

Imaging Luminescence Losses in Halide Perovskite Photovoltaics

Sam Stranks is a Royal Society URF in the Cavendish. He completed his PhD (DPhil) in Physics at Oxford University, followed by a JRF at Worcester College Oxford and a Marie Curie Fellowship at MIT. He received the 2017 European Physical Society Early Career award for his contributions to the perovskite field. 

Halide perovskites are generating enormous attention for their potential use in inexpensive yet high-performance photovoltaics and light-emitting diodes. However, device performance is still limited by non-radiative losses. In this work, I'll discuss our recent work revealing the origin of non-radiative decay in the bulk and at interfaces through imaging. I'll describe how we can tactically remove the losses through passivation approaches, which could push devices towards their limits. 


14 February 2018

Christian Eggeling

Dr Eggeling holds a PhD in Physics from the University of Göttingen. He worked as a research scientist at the biotech company Evotec and was as a senior scientist at the Max-Planck-Institute for Biophysical Chemistry in the department of Professor Stefan Hell. Since 2012, Christian Eggeling has been a principal investigator in the Human Immunology Unit and the scientific director of the newly established Wolfson Imaging Centre Oxford at the Weatherall Institute of Molecular Medicine. He has been appointed Professor of Molecular Immunology in 2014 and started as a Professor of Super-Resolution Microscopy in the Institute of Applied Optics of the Friedrich Schiller-University and the Leibniz Institute of Photonic Technologies in Jena in 2017. Christian Eggeling’s research is focused on the development of advanced microscopy for the investigation of molecular organization and dynamics in cells, especially on the cellular plasma membranes. He will be talking about tackling challenges and potentials in biomedical research with Super-resolution microscopy:

Understanding the complex interactions of molecular processes underlying the efficient functioning of the human body is one of the main objectives of biomedical research. Scientifically, it is important that the applied observation methods do not influence the biological system during observation. A suitable tool that can cover all of this is optical far-field fluorescence microscopy. Yet, biomedical applications often demand coverage of a large range of spatial and temporal scales, and/or long acquisition times, which can so far not all be covered by a single microscope and puts some challenges on microscope infrastructure. Taking immune cell responses and plasma membrane organization as examples, we outline these challenges but also give new insights into possible solutions and the potentials of these advanced microscopy techniques, e.g. for solving long-standing questions such as of lipid membrane rafts.


7 February 2018

Marcel Bruchez

Marcel Bruchez is Professor for Biological Sciences and Chemistry at Carnegie Mellon University and Director of the Molecular Biosensors and Imaging Center.

He will be talking about the "Fluorogen Switch":

Fluorogen activating proteins that activate the fluorescence of triarylmethane dyes have been demonstrated as practical tags for both cell surface and intracellular labelling, with applications ranging from single-molecule imaging to whole-animal optogenetics. The binding of a fluorogenic dye can result in thousands-fold activation, serving as a binding mediated optical switch, which activates fluorescence from otherwise dark molecules. Synthesis of various fluorescent donors linked to a far-red excitable fluorogen at distances far shorter than the Forster radius of the dyes has established a new family of FRET-based multi excitation fluorogenic dyes, with tunable excitation and emission properties suitable for use with a wide variety of conventional and superresolution microscopy methods. Use of environmentally sensitive donor dyes produces targeted and activated ratiometric fluorescent indicators, enabling optical physiology at and beyond the diffraction limit. I will discuss applications of pH sensors in living cells for measurement of endolysosomal trafficking and development and validation ROS generating and sensor dyes for use in live cells and model organisms.


 30 January 2018

George Malliaras

George Malliaras from the Department of Engineering will present his work on interfacing with the brain using organic electronics.

One of the most important scientific and technological frontiers of our time is the interfacing of electronics with the human brain. This endeavour promises to help understand how the brain works and deliver new tools for diagnosis and treatment of pathologies including epilepsy and Parkinson's disease. Current solutions, however, are limited by the materials that are brought in contact with the tissue and transduce signals across the biotic/abiotic interface. Recent advances in organic electronics have made available materials with a unique combination of attractive properties, including mechanical flexibility, mixed ionic/electronic conduction, enhanced biocompatibility, and capability for drug delivery. I will present examples of novel devices for recording and stimulation of neurons and show that organic electronic materials offer tremendous opportunities to study the brain and treat its pathologies.


22 January 2018

Thomas Huser

Professor Thomas Huser from the Biomolecular Photonics Group at the University of Bielefeld will present his latest efforts in unveiling and following structural changes of cellular nanopores in living cells by GPU-enhanced super-resolution structured illumination microscopy.

During the last decade a number of optical imaging techniques have been developed that utilize different physical or photochemical means to overcome the optical diffraction limit. Any single technique is, however, often not well suited to address all needs of a specific biomedical research problem. Single molecule localization microscopy, for instance, provides very high spatial resolution and quantification, but requires a considerable amount of time to conduct which is often not ideal for addressing imaging needs in live cell studies. Super-resolved structured illumination microscopy, on the other hand, is well suited for live cell imaging, but its spatial resolution improvement is, in most cases, limited to a factor of two. In my research group, much of the research interests are driven by specific biomedical needs, e.g. resolving the structure and dynamics of nanopores in the cellular plasma membrane, or investigating the mechanisms and specific sequence in the transmission of virus from infected cells to uninfected cells. To best address these issues from all perspectives, we typically utilize a suite of multimodal methods, e.g. the combination of optical tweezers with optical nanoscopy, or the combination of temporal and spatial methods of improving the spatial resolution and select the best possible method for each research question. 


16 January 2018

Melody Clark

Professor Melody Clark has a genetics degree and PhD from London University. After a string of short-term post doc contracts working on areas ranging from plant chromosomes to the high-profile Japanese pufferfish genome project, she finally landed a job as Project Leader at the British Antarctic Survey (BAS) in August 2003.

She currently leads the Adaptations group and will talk about how animals have adapted to life in freezing oceans and how they respond to climate change. In particular, the paradox of the incredible biodiversity in the Southern Ocean and the cellular level problems of protein folding at such low temperatures.


  •  Dr Balpreet Singh Ahluwalia

30 August 2017

Balpreet Singh

Dr. Ahluwalia is working on optimizing and fabricating high-refractive index contrast waveguides for lab-on-a-chip applications including optical trapping, propulsion, sensing, and superresolution microscopy.

He talked about Nanoscopy over millimeter scale using photonic chip” and provided us with an overview of photonics chip-based dSTORM, chip-based light fluctuating optical nanoscopy, and chip-based SIM (structured illumination microscopy). By retrofitting photonic chips to any standard optical microscope it is possible to convert it into an optical nanoscope (dSTORM, SIM, etc). Chip-based optical nanoscopy enables sub-100 nm optical resolution over extra-ordinary large field-of-view (millimetre scale). This will enable application of high-throughput chip-based optical nanoscopy in diagnostics and pathology.


  •  Dr Marcel Mueller

12 July 2017

Marcel Mueller

Marcel Müller studied physics and worked a post doc at Bielefeld University where he developed the widely known fairSIM plug-in for ImageJ. He then continued his work in Oxford to include 3D-SIM capabilities in software package and started a new post doc in the Dedecker lab in Leuven to work on Multifocus 3D-SIM.


  •  Professor Anatoly Grudinin

7 July 2017

Anatoly Grudinin

Anatoly Grudinin started his work in the area of fiber optics in 1980 as one of the first researchers who studied nonlinear properties of silica fibers and nonlinear dynamics of picosecond and femtosecond pulse evolution in single-mode optical fibers. In 2003 Anatoly left his professor's chair at the Optoelectronics Research Centre at University of Southampton and founded Fianium, a fiber laser company focused on development and volume manufacturing of ultrafast fiber lasers for bio-medical and industrial applications. 

In this talk “Ultrafast fiber lasers: the hunt for a killer application” he reviewed latest developments and applications of picosecond and femtosecond fiber lasers. Motivated by rapid improvement of performance and attractive features such as compactness and low ownership cost, ultrafast fiber lasers now challenge conventional DPSS ultrafast sources across numerous industrial sectors. They enable development of unique sources such as supercontinuum lasers capable of enabling scientific discovery and replace incumbent illumination technologies within industrial instruments and systems.


16 June 2017

Morten Bache

Morten Bache is associate professor in the Nonlinear Optics and Biophotonics Section at DTU Fotonik and Ultrafast Nonlinear Optics team leader. He is an expert in theoretical and numerical modeling of nonlinear optical phenomena with a vast experience in realistic numerical modeling of experiments. During his Ph.D. and a 3 year postdoc in Italy he worked on nonlinear and quantum optics and on ultra-fast spatial and temporal phenomena in quadratic nonlinear materials. His current research concerns ultra-fast femtosecond nonlinear optics in fibers and nonlinear crystals.


12 June 2017

Patrick Salter

Dr. Salter is a W.W. Spooner Research Fellow at New College in Oxford and conducts research into photonic engineering,    particularly adaptive optics systems, laser microfabrication and diamond technology. 

​He gave a talk entitled "​Adaptive optics for femtosecond laser writing inside transparent materials" in which he described methods of writing waveguides into CVD diamond materials and applications. 


22 May 2017

Emmanuel Derivery

Dr. Derivery is a group leader at the Laboratory of Molecular Biology in Cambridge. He pioneers ground breaking new imaging and biophysical tools to study symmetry breaking during development.

Dr. Derivery talked about polarized endosome dynamics by spindle asymmetry during asymmetric cell division. During asymmetric division, fate determinants at the cell cortex segregate unequally into the two daughter cells. It has recently been shown that Sara signalling endosomes in the cytoplasm also segregate asymmetrically during asymmetric division. Dr. Derivery and his group unravelled the molecular mechanism of this asymmetric dispatch of signalling endosomes.


11 May 2017

Ali Hassanali

Dr Hassanali is a senior investigator in the Condensed Matter and Statistical Physics section (CMSP) at the International Center for Theoretical Physics (ICTP) in Trieste, Italy.

Dr Hassanali talked about theoretical and computational investigations of quantum and microscopic interactions in molecular systems using ab initio molecular dynamics simulations. Dr Hasanali's team performed ground breaking molecular dynamics and DFT simulations to explain our intriguing discovery that the amyloid systems develop an intrinsic fluorescence in the UV-Vis range that is independent of aromatic residues.  His simulation demonstrated that frequent proton charge exchanges can take place between adjacent C- and N- Termini in amyloids.