LSFM2019
Dec 4-6, 2019 : The Light Sheet Microscopy Conference : Frankfurt am Main
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New Generation
Light Sheet Microscopes
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New applications and models
Dec 4-6, 2019
Campus Riedberg
Frankfurt am Main, Germany
Discuss with top experts how Light Sheet Microscopy meets the future challenges in Biology.
Light sheet microscopy allows observing the development of live three-dimensional organoids and organisms over a long time up to several days. This massive amount of multi-dimensional microscopy data poses significant challenges in both data management and modelling. Tackling these challenges is fundamental to advance scientific discovery in biological and biomedical research. LSFM2019 fosters the exchange between top researchers working to the development of new light sheet microscopes, new three-dimensional cellular systems and model organisms, as well as in artificial intelligence and mathematical modelling. We aim to bridge the gap among different disciplines, paving the way to disruptive approaches.
Supported by
Francesco Pampaloni
Goethe Universität Frankfurt
(Germany)
Ernst H.K. Stelzer
Goethe Universität Frankfurt
(Germany)
STAY UPDATED
The SPEAKERS of LSFM2019
The invited speakers represent the most relevant developments in Light Sheet Microscopy: imaging of live organoids, screening of tumor spheroids, histopathology on whole biopsies, developmental biology of mouse, plants, and insects. Our speakers will also illustrate the newest technical developments, including light sheet shaping and innovative LSFM geometries.
Laura Batti
The Wyss Center, Genève (Switzerland)
Talk: "Advanced Light sheet Imaging Center (ALICe)"
Laura joined the Wyss Center in September 2016 as Microscopy Facility Manager bringing expertise in bioimaging and neuroscience. She worked closely with the Preclinical Neuroscience Platform (PNP) Manager to establish the new resource and now manages the microscopy facility which offers both technical support and innovation in imaging technology.
In conjunction with the Scientific Coordinator (Stéphane Pagès), she also manages the newly developed Advanced Lightsheet Imaging Center.
Talk: "Advanced Light sheet Imaging Center (ALICe)"
Laura joined the Wyss Center in September 2016 as Microscopy Facility Manager bringing expertise in bioimaging and neuroscience. She worked closely with the Preclinical Neuroscience Platform (PNP) Manager to establish the new resource and now manages the microscopy facility which offers both technical support and innovation in imaging technology.
In conjunction with the Scientific Coordinator (Stéphane Pagès), she also manages the newly developed Advanced Lightsheet Imaging Center.
Julien Colombelli
IRB, Barcelona, (Spain)
Talk: "Innovating under ultra-low-cost requirements: Open lightsheet device for very large cleared organisms"
Julien Colombelli earned a Physics degree at the universities of Paris XI (France) and Edinburgh (Scotland), and a MSc in Optical Engineering at “École Central Marseille” (France) and “Politecnico di Milano” (Italy). He worked as a research engineer (2002-2008) in the Light Microscopy Group at the European Molecular Biology Laboratory (EMBL-Heidelberg, Germany) where he developed Laser photomanipulation technology. He moved on to implement and head the Advanced Digital Microscopy Core Facility at the Institute for Research in Biomedicine (IRB Barcelona, Spain), where he currently works. His research interests involve lightsheet microscopy, tissue clearing, laser photomanipulation, intelligent imaging, high-throughput applications, open source tools for Open Science, cancer imaging, label-free imaging. JC is a founding member of REMOA (Spanish network of Advanced Optical Microscopy) and NEUBIAS (Network of European Bioimage Analysts, COST Action CA15124) that he currently chairs.
Talk: "Innovating under ultra-low-cost requirements: Open lightsheet device for very large cleared organisms"
Julien Colombelli earned a Physics degree at the universities of Paris XI (France) and Edinburgh (Scotland), and a MSc in Optical Engineering at “École Central Marseille” (France) and “Politecnico di Milano” (Italy). He worked as a research engineer (2002-2008) in the Light Microscopy Group at the European Molecular Biology Laboratory (EMBL-Heidelberg, Germany) where he developed Laser photomanipulation technology. He moved on to implement and head the Advanced Digital Microscopy Core Facility at the Institute for Research in Biomedicine (IRB Barcelona, Spain), where he currently works. His research interests involve lightsheet microscopy, tissue clearing, laser photomanipulation, intelligent imaging, high-throughput applications, open source tools for Open Science, cancer imaging, label-free imaging. JC is a founding member of REMOA (Spanish network of Advanced Optical Microscopy) and NEUBIAS (Network of European Bioimage Analysts, COST Action CA15124) that he currently chairs.
Gustavo Quintas Glasner de Medeiros
Friedrich Miescher Institute for Biomedical Research, Basel (Switzerland)
Talk: "Mechanisms driving symmetry-breaking in intestinal organoids"
Bachelor in Physics at the Federal University of Rio de Janeiro.
Masters degree at the Karlsruhe Institute of Technology, with focus on the determination of extinction coefficients for novel polymer-fullerene blends for organic solar cells with higher efficiencies.
PhD work at EMBL Heidelberg in the lab of Lars Hufnagel, working on ways to image and perturb live samples deep in the tissue.
Now postdoctoral fellow in the lab of Prisca Liberali, focusing on studying the dynamics behind symmetry-breaking during single intestinal organoid development, and on the development of imaging tools around light-sheet microscopy tailored for organoid imaging.
Talk: "Mechanisms driving symmetry-breaking in intestinal organoids"
Bachelor in Physics at the Federal University of Rio de Janeiro.
Masters degree at the Karlsruhe Institute of Technology, with focus on the determination of extinction coefficients for novel polymer-fullerene blends for organic solar cells with higher efficiencies.
PhD work at EMBL Heidelberg in the lab of Lars Hufnagel, working on ways to image and perturb live samples deep in the tissue.
Now postdoctoral fellow in the lab of Prisca Liberali, focusing on studying the dynamics behind symmetry-breaking during single intestinal organoid development, and on the development of imaging tools around light-sheet microscopy tailored for organoid imaging.
Chris Dunsby
Imperial College London (UK)
Talk: "High-speed 3D and high-content light sheet fluorescence microscopy"
Dr Chris Dunsby works on the development of quantitative fluorescence imaging techniques for applications in biomedicine, including Förster resonant energy transfer microscopy, automated multiwell plate imaging and fluorescence lifetime imaging (FLIM). He has also worked on super-resolution fluorescence imaging techniques and collaborates with colleagues in Bioengineering to translate optical methods to achieve super-resolved ultrasound imaging. He invented, patented and licensed oblique plane microscopy, which is a form of light sheet fluorescence microscopy that can be implemented on a conventional microscope frame to provide high speed 2-D and 3-D imaging. He has also led projects to develop and apply multiphoton imaging and FLIM for clinical applications and developed novel multiphoton endoscopes.
Talk: "High-speed 3D and high-content light sheet fluorescence microscopy"
Dr Chris Dunsby works on the development of quantitative fluorescence imaging techniques for applications in biomedicine, including Förster resonant energy transfer microscopy, automated multiwell plate imaging and fluorescence lifetime imaging (FLIM). He has also worked on super-resolution fluorescence imaging techniques and collaborates with colleagues in Bioengineering to translate optical methods to achieve super-resolved ultrasound imaging. He invented, patented and licensed oblique plane microscopy, which is a form of light sheet fluorescence microscopy that can be implemented on a conventional microscope frame to provide high speed 2-D and 3-D imaging. He has also led projects to develop and apply multiphoton imaging and FLIM for clinical applications and developed novel multiphoton endoscopes.
Reto Fiolka
UT Southwestern, Dallas (USA)
Talk: "Cleared tissue imaging at subcellular resolution"
Reto Fiolka is an assistant Professor at UT Southwestern in the Department of Cell Biology and Bioinformatics in Dallas, TX. He conducted post-doctoral research under the guidance of the late Dr. Mats Gustafsson on 3D structured illumination microscopy and under Dr. Meng Cui on adaptive optics. His current research is focused on improving spatiotemporal resolution in fluorescence microscopy and translating new technologies to biological research. Recently his lab has also started work on cleared tissue imaging with subcellular resolution.
Talk: "Cleared tissue imaging at subcellular resolution"
Reto Fiolka is an assistant Professor at UT Southwestern in the Department of Cell Biology and Bioinformatics in Dallas, TX. He conducted post-doctoral research under the guidance of the late Dr. Mats Gustafsson on 3D structured illumination microscopy and under Dr. Meng Cui on adaptive optics. His current research is focused on improving spatiotemporal resolution in fluorescence microscopy and translating new technologies to biological research. Recently his lab has also started work on cleared tissue imaging with subcellular resolution.
Sabine Fischer
University of Würzburg (Germany)
Talk: “Image-based mathematical modelling of spatial cell-cell interactions”
Sabine Fischer is a Professor at the Centre for Computational and Theoretical Biology (CCTB) of the University of Würzburg. Her group studies spatial interactions of cells with their neighbours. Current projects investigate interactions of cells in complex tissues as well as interactions of moving cells. A major emphasis is on developing data-informed models. Therefore, all projects are based on close collaborations with experimental groups. The techniques applied comprise image analysis, spatial statistics and agent-based modelling.
Sabine Fischer received a PhD in Mathematical Biology from Nottingham University (UK) in 2009. Seeking closer interactions with experimentalists as well as quantitative experimental data with spatial resolution, she spent two years as a postdoc at the University of Cambridge (UK) and six years as a postdoc at the Goethe University Frankfurt (Germany). During these years, she studied cell-cell interactions in the Drosophila embryo as well as in three-dimensional in vitro cell cultures such as tumour spheroids and stem cell organoids. After a fruitful year as a developmental engineer in industry, Sabine Fischer joined the University of Würzburg in 2018, where she is now one of the directors of the CCTB.
Talk: “Image-based mathematical modelling of spatial cell-cell interactions”
Sabine Fischer is a Professor at the Centre for Computational and Theoretical Biology (CCTB) of the University of Würzburg. Her group studies spatial interactions of cells with their neighbours. Current projects investigate interactions of cells in complex tissues as well as interactions of moving cells. A major emphasis is on developing data-informed models. Therefore, all projects are based on close collaborations with experimental groups. The techniques applied comprise image analysis, spatial statistics and agent-based modelling.
Sabine Fischer received a PhD in Mathematical Biology from Nottingham University (UK) in 2009. Seeking closer interactions with experimentalists as well as quantitative experimental data with spatial resolution, she spent two years as a postdoc at the University of Cambridge (UK) and six years as a postdoc at the Goethe University Frankfurt (Germany). During these years, she studied cell-cell interactions in the Drosophila embryo as well as in three-dimensional in vitro cell cultures such as tumour spheroids and stem cell organoids. After a fruitful year as a developmental engineer in industry, Sabine Fischer joined the University of Würzburg in 2018, where she is now one of the directors of the CCTB.
Adam Glaser
University of Washington, Seattle (USA)
Talk: "A bigger and better picture of clinical specimens: open-top light-sheet microscopy for 3D pathology"
Talk: "A bigger and better picture of clinical specimens: open-top light-sheet microscopy for 3D pathology"
Peter Horvath
Biological Research Center, Szeged (Hungary)
Talk: "Life beyond the pixels: Image analysis and machine learning techniques in single cell 2 and 3D microscopy"
Peter Horvath (1980) is currently a group leader in the Biological Research Center of the Hungarian Academy of Sciences in Szeged and holds a Finnish Distinguished Professor (FiDiPro) Fellow position in the Institute for Molecular Medicine Finland (FIMM), Helsinki. He graduated as a software engineer and mathematician, and received his Ph.D. from INRIA and University of Nice, Sophia Antipois, France in satellite image analysis. Between 2007 and 2013 he was a senior scientist at the ETH Zurich, in the Light Microscopy Centre. Peter Horvath is interested in solving computational cell biology problems related to light microscopy and is involved in three main research fields; 2/3D biological image segmentation and tracking; development of microscopic image correction techniques; machine learning methods applied in high-throughput microscopy. He is the co-founder of the European Cell-based Assays Interest Group and the councillor of the Society of Biomolecular Imaging and Informatics.
Talk: "Life beyond the pixels: Image analysis and machine learning techniques in single cell 2 and 3D microscopy"
Peter Horvath (1980) is currently a group leader in the Biological Research Center of the Hungarian Academy of Sciences in Szeged and holds a Finnish Distinguished Professor (FiDiPro) Fellow position in the Institute for Molecular Medicine Finland (FIMM), Helsinki. He graduated as a software engineer and mathematician, and received his Ph.D. from INRIA and University of Nice, Sophia Antipois, France in satellite image analysis. Between 2007 and 2013 he was a senior scientist at the ETH Zurich, in the Light Microscopy Centre. Peter Horvath is interested in solving computational cell biology problems related to light microscopy and is involved in three main research fields; 2/3D biological image segmentation and tracking; development of microscopic image correction techniques; machine learning methods applied in high-throughput microscopy. He is the co-founder of the European Cell-based Assays Interest Group and the councillor of the Society of Biomolecular Imaging and Informatics.
Florian Jug
MPI-CBG and Center for System Biology Dresden (CSBD), Dresden (Germany)
Talk: "Content-Aware Image Restoration for Light and Electron Microscopy – a progress report!"
Abstract:
In recent years, fluorescent light microscopy and cryo-electron microscopy saw tremendous technological advances. Using light microscopes, we routinely image beyond the resolution limit, acquire large volumes at high temporal resolution, and capture many hours of video material showing processes of interest inside cells, in tissues, and in developing organisms. Cryo-electron microscopes, at the same time, are capable of visualizing cellular building-blocks in their native environment at close to atomic resolution. Despite these possibilities, the analysis of raw images is usually non-trivial, error-prone, and cumbersome.
In my talk, I will show how machine learning can help to tap the full potential of raw microscopy data by applying so called content-aware image restoration (CARE) techniques.
Since our first CARE method was published, tremendous technological progress was made, allowing us today to train competitive denoising models without requiring high SNR (ground truth quality) images to be available. Hence, the application of such CARE approaches to virtually all microscopy datasets is now easier than ever before.
Florian Jug is a research group leader at the Center for System Biology Dresden (CSBD) and the Max-Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG). The overarching goal of his research is to push the boundaries of what image analyses and machine learning can do to quantitatively analyze biological (image)-data. Research in the Jug Lab aims at finding novel ways to efficiently analyze large amounts of microscopy data, while avoiding impossible amounts of manual analyses and curation tasks – often a major bottleneck in biomedical research. Besides finding novel algorithms and machine learning methods, the Jug Lab is also critically involved in the development of Fiji, a popular and widely applicable open software platform for biomedical image analysis and an ideal way to disseminate newly developed methods and tools.
Talk: "Content-Aware Image Restoration for Light and Electron Microscopy – a progress report!"
Abstract:
In recent years, fluorescent light microscopy and cryo-electron microscopy saw tremendous technological advances. Using light microscopes, we routinely image beyond the resolution limit, acquire large volumes at high temporal resolution, and capture many hours of video material showing processes of interest inside cells, in tissues, and in developing organisms. Cryo-electron microscopes, at the same time, are capable of visualizing cellular building-blocks in their native environment at close to atomic resolution. Despite these possibilities, the analysis of raw images is usually non-trivial, error-prone, and cumbersome.
In my talk, I will show how machine learning can help to tap the full potential of raw microscopy data by applying so called content-aware image restoration (CARE) techniques.
Since our first CARE method was published, tremendous technological progress was made, allowing us today to train competitive denoising models without requiring high SNR (ground truth quality) images to be available. Hence, the application of such CARE approaches to virtually all microscopy datasets is now easier than ever before.
Florian Jug is a research group leader at the Center for System Biology Dresden (CSBD) and the Max-Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG). The overarching goal of his research is to push the boundaries of what image analyses and machine learning can do to quantitatively analyze biological (image)-data. Research in the Jug Lab aims at finding novel ways to efficiently analyze large amounts of microscopy data, while avoiding impossible amounts of manual analyses and curation tasks – often a major bottleneck in biomedical research. Besides finding novel algorithms and machine learning methods, the Jug Lab is also critically involved in the development of Fiji, a popular and widely applicable open software platform for biomedical image analysis and an ideal way to disseminate newly developed methods and tools.
Ulrich Kubitscheck
University of Bonn (Germany)
Talk: "Light-sheet fluorescence expansion microscopy: fast mapping of neural circuits at super resolution"
Ulrich Kubitscheck is the department head of Biophysical Chemistry at the Institute of Physical and Theoretical Chemistry of the University of Bonn in Germany. Having obtained his academic degrees from the University of Bremen, Germany, he spent his career working at The Weizmann Institute of Science and the Institute of Medical Physics and Biophysics of the University of Münster, Germany, before taking up his present appointment at the University of Bonn. Professor Kubitscheck is interested in supra-molecular complexes and neural circuits and develops single molecule and light sheet imaging techniques.
Talk: "Light-sheet fluorescence expansion microscopy: fast mapping of neural circuits at super resolution"
Ulrich Kubitscheck is the department head of Biophysical Chemistry at the Institute of Physical and Theoretical Chemistry of the University of Bonn in Germany. Having obtained his academic degrees from the University of Bremen, Germany, he spent his career working at The Weizmann Institute of Science and the Institute of Medical Physics and Biophysics of the University of Münster, Germany, before taking up his present appointment at the University of Bonn. Professor Kubitscheck is interested in supra-molecular complexes and neural circuits and develops single molecule and light sheet imaging techniques.
Anna Kreshuk
EMBL Heidelberg (Germany)
Talk: "Image segmentation with machine learning"
Abstract:
Recent technological advances in light and electron microscopy allow for image acquisition at a very large scale. I will talk about the next step of the pipeline: automatic large-scale volume segmentation and the challenges of insufficient training data, biological variability and overall image size. I will also show the latest developments in making such methods more accessible to scientists without computational expertise.
Talk: "Image segmentation with machine learning"
Abstract:
Recent technological advances in light and electron microscopy allow for image acquisition at a very large scale. I will talk about the next step of the pipeline: automatic large-scale volume segmentation and the challenges of insufficient training data, biological variability and overall image size. I will also show the latest developments in making such methods more accessible to scientists without computational expertise.
Elena Martinez
IBEC, Barcelona, Spain
Talk: “Biofabrication light-based strategies to generate complex geometries in hydrogels for intestinal tissue modeling”
Dr. Elena Martínez holds a PhD in Physics by the University of Barcelona (2001). After postdoctoral stages at the EPFL and Imperial College, she settled in the Institute for Bioengineering of Catalonia (IBEC). At IBEC, she was senior researcher at Prof. Samitier’s group, where she was investigating the cellular response to substrates with topographical and chemical micro and nanopatterns. In 2014 she was appointed as Junior Group leader at IBEC to develop new systems that mimic 3D tissue microfeatures for biomimetic in vitro assays. During this period, she was able to obtain funding from prestigious entities (ERC-Consolidator 2014) and consolidate a research group attracting excellent young researchers (a Ramon y Cajal researcher among them). During her scientific career, she has supervised 9 PhD students, published 106 papers and participated in national and international projects. She has also established fruitful collaborations at the international and national level. She got promoted to Group leader in 2018. Her group is currently composed by 12 people from a diverse scientific background. Current projects deal with the in vitro modeling of drug-induced arrythmias in cardiac engineered constructs and the in vitro modeling of intestinal tissue using adult stem cells derived from intestinal organoids for the study of intestinal development and diseases.
Talk: “Biofabrication light-based strategies to generate complex geometries in hydrogels for intestinal tissue modeling”
Dr. Elena Martínez holds a PhD in Physics by the University of Barcelona (2001). After postdoctoral stages at the EPFL and Imperial College, she settled in the Institute for Bioengineering of Catalonia (IBEC). At IBEC, she was senior researcher at Prof. Samitier’s group, where she was investigating the cellular response to substrates with topographical and chemical micro and nanopatterns. In 2014 she was appointed as Junior Group leader at IBEC to develop new systems that mimic 3D tissue microfeatures for biomimetic in vitro assays. During this period, she was able to obtain funding from prestigious entities (ERC-Consolidator 2014) and consolidate a research group attracting excellent young researchers (a Ramon y Cajal researcher among them). During her scientific career, she has supervised 9 PhD students, published 106 papers and participated in national and international projects. She has also established fruitful collaborations at the international and national level. She got promoted to Group leader in 2018. Her group is currently composed by 12 people from a diverse scientific background. Current projects deal with the in vitro modeling of drug-induced arrythmias in cardiac engineered constructs and the in vitro modeling of intestinal tissue using adult stem cells derived from intestinal organoids for the study of intestinal development and diseases.
Paola Perin
University of Pavia (Italy)
Talk: "Vascular districts in the intact 4th ventricle of the rat: do we have the whole picture on circumventricular organs?"
My scientific interest has been focused on signal transmission in sensory systems, and in particular signal encoding and synaptic transmission in the auditory and vestibular system.
For the first part of my career, I mainly studied signal processing by vestibular hair cells, especially as regards the influence of ion channels and Ca2+ on response dynamics. Subsequently, my main research topic shifted to the central vestibular and auditory system, and in particular neuroimmune interactions affecting it in health and pathology. Currently I am on a pretty interesting detour following the ins and outs of brain macrophages in the choroid plexus, and where they move upon neuroinflammation. The main question I would like to solve is what are the signals that say that a neural activity pattern is “wrong” in the auditory system and trigger plastic changes (helpful or maladaptive) in the neuronal circuits. Answering this question will help treating disorders such as tinnitus, where maladaptive plasticity appears to be key.
Talk: "Vascular districts in the intact 4th ventricle of the rat: do we have the whole picture on circumventricular organs?"
My scientific interest has been focused on signal transmission in sensory systems, and in particular signal encoding and synaptic transmission in the auditory and vestibular system.
For the first part of my career, I mainly studied signal processing by vestibular hair cells, especially as regards the influence of ion channels and Ca2+ on response dynamics. Subsequently, my main research topic shifted to the central vestibular and auditory system, and in particular neuroimmune interactions affecting it in health and pathology. Currently I am on a pretty interesting detour following the ins and outs of brain macrophages in the choroid plexus, and where they move upon neuroinflammation. The main question I would like to solve is what are the signals that say that a neural activity pattern is “wrong” in the auditory system and trigger plastic changes (helpful or maladaptive) in the neuronal circuits. Answering this question will help treating disorders such as tinnitus, where maladaptive plasticity appears to be key.
Karel Riha
CEITEC Masaryk University, Brno
(Czech Republic)
Talk: "Imaging plant germline differentiation in the context of developing flower by light sheet microscopy"
Talk synopsis:
In higher plants, germline differentiation occurs in relatively short time window within developing flowers. This process involves a number of spectacular cellular events such as fate acquisition of archesporial cells, male and female meiosis, asymmetric cell division of microspores to form vegetative and sperm pollen nuclei, and postmeiotic divisions of a megaspore to form embryo sack. Despite undisputable importance of plant sexual reproduction in agriculture and food production, our understanding of mechanisms that govern germline differentiation still lags behind other plant developmental processes. This is largely because these events take place in relatively few cells that are buried deep within floral tissues, which makes them notoriously difficult to study. In my presentation I will report on our effort to overcome this limitation by establishing methodology for live imaging of germ cell lineage differentiation within developing floral organs by light sheet microscopy. I believe that this methodology opens new avenues of research into plant sexual reproduction.
Karel Riha is a research group leader at the Central European Institute of Technology (CEITEC) in Brno, Czech Republic. His group studies processes that govern genome stability and chromosome segregation in plants. Karel Riha received PhD in genetics at Masaryk University in Brno, Czech Republic in 1998. He then spent four years as postdoctoral fellow at Texas A&M University where he studied telomeres in plants. In 2003 he joined newly established Gregor Mendel Institute in Vienna as a research groupleader. In 2014 he returned to Brno, where he currently serves as a deputy director for science at CEITEC, Masaryk University.
(Czech Republic)
Talk: "Imaging plant germline differentiation in the context of developing flower by light sheet microscopy"
Talk synopsis:
In higher plants, germline differentiation occurs in relatively short time window within developing flowers. This process involves a number of spectacular cellular events such as fate acquisition of archesporial cells, male and female meiosis, asymmetric cell division of microspores to form vegetative and sperm pollen nuclei, and postmeiotic divisions of a megaspore to form embryo sack. Despite undisputable importance of plant sexual reproduction in agriculture and food production, our understanding of mechanisms that govern germline differentiation still lags behind other plant developmental processes. This is largely because these events take place in relatively few cells that are buried deep within floral tissues, which makes them notoriously difficult to study. In my presentation I will report on our effort to overcome this limitation by establishing methodology for live imaging of germ cell lineage differentiation within developing floral organs by light sheet microscopy. I believe that this methodology opens new avenues of research into plant sexual reproduction.
Karel Riha is a research group leader at the Central European Institute of Technology (CEITEC) in Brno, Czech Republic. His group studies processes that govern genome stability and chromosome segregation in plants. Karel Riha received PhD in genetics at Masaryk University in Brno, Czech Republic in 1998. He then spent four years as postdoctoral fellow at Texas A&M University where he studied telomeres in plants. In 2003 he joined newly established Gregor Mendel Institute in Vienna as a research groupleader. In 2014 he returned to Brno, where he currently serves as a deputy director for science at CEITEC, Masaryk University.
Alexander Rohrbach
IMTEK, University of Freiburg (Germany)
Talk: „Has guiding of light through biological material in light-sheet microscopy reached it’s limit?”
Short Biosketch:
PhD and Habilitation in Physics in 1998 and 2005, Full professor since 2006
Research areas: Microscopy, Trapping&Tracking, Biophysics
Talk: „Has guiding of light through biological material in light-sheet microscopy reached it’s limit?”
Short Biosketch:
PhD and Habilitation in Physics in 1998 and 2005, Full professor since 2006
Research areas: Microscopy, Trapping&Tracking, Biophysics
Saiedeh Saghafi
Vienna University of Technology-TU Wien, Bioelectronics department, Vienna (Austria)
Talk: "Non-diffractive light sheets: A novel approach in static light sheet microscopy"
SAIEDEH SAGHAFI received her B.Sc. degree in Applied Physics from the University of Tehran. In 1996, she started her M.Sc. degree in Optical Physics at University of Sydney studying Gaussian beam propagation in and beyond the paraxial approximation. In 1998, she won Overseas Postgraduate award to attend the Ph.D. program in Physics Department /Macquarie University/Australia. In year 2000, she won two research awards, IEEE/LEOS Graduate Fellowship and Australian Optical Society award. In 2001, she received her Ph.D. in modal analysis of lasers employing unstable resonators. Her thesis was nominated for the AIP Bragg Gold medal for the best PhD thesis. She held a postdoctoral position for one year in CLA- Centre for Lasers and Applications. Then, she worked as an assistant professor at Biophotonics group at IAU working on the medical applications of laser beam. She has been an academic member of Vienna University of Technology, FKE, Bioelectronics Department developing new system for Ultramicroscopy imaging techniques since 2008.
Talk: "Non-diffractive light sheets: A novel approach in static light sheet microscopy"
SAIEDEH SAGHAFI received her B.Sc. degree in Applied Physics from the University of Tehran. In 1996, she started her M.Sc. degree in Optical Physics at University of Sydney studying Gaussian beam propagation in and beyond the paraxial approximation. In 1998, she won Overseas Postgraduate award to attend the Ph.D. program in Physics Department /Macquarie University/Australia. In year 2000, she won two research awards, IEEE/LEOS Graduate Fellowship and Australian Optical Society award. In 2001, she received her Ph.D. in modal analysis of lasers employing unstable resonators. Her thesis was nominated for the AIP Bragg Gold medal for the best PhD thesis. She held a postdoctoral position for one year in CLA- Centre for Lasers and Applications. Then, she worked as an assistant professor at Biophotonics group at IAU working on the medical applications of laser beam. She has been an academic member of Vienna University of Technology, FKE, Bioelectronics Department developing new system for Ultramicroscopy imaging techniques since 2008.
Gopi Shah
EMBL Barcelona (Spain)
Talk: "Uncovering cell dynamics in developing embryos, embryoids and organoid models"
Abstract: Recent trends in developmental biology and clinical research have introduced a variety of embroid and organoid models that resemble the in vivo 3D environment. However, these models are extremely sensitive to the imaging environment and are more variable in their morphology as compared to embryos/organs. Hence, a larger sample size is required to obtain a reliable understanding of the system, posing challenges in terms of imaging throughput, data handling, and visualization of numerous big datasets and integration of information therein. We are addressing these by implementing robust incubation systems and multi-sample imaging and analysis. I will present time-lapse imaging of organoids derived from mouse intestinal tissue as well as of embryoid models derived from zebrafish and mouse embryonic stem cells which recapitulate events from embryonic development.
Gopi Shah is the Project Manager for Advanced Mesoscopy Applications at the Mesoscopic Imaging Facility (MIF) at EMBL Barcelona. MIF provides imaging and data processing services for visualizing large, chemically cleared as well as live biological tissues with commercial and custom implementations of light sheet microscopy and optical projection tomography.
Gopi obtained her PhD in 2016, from the Max Planck Institute for Cell Biology and Genetics (MPI-CBG) in Dresden, Germany, where she worked with an interdisciplinary team to develop light sheet microscopes capable of long-term, high-throughput imaging and real-time data-processing. Thereafter, she joined the Cancer Research UK Cambridge Institute (CRUK CI) in Cambridge, UK, as a Senior Scientific Associate in the light microscopy core facility. Here she established light sheet microscopy as a tool for imaging various human and mouse tumour-derived organoid and co-culture models for observing tumor biology in 4D. Her current work focuses on enabling live imaging of a variety of in vitro 3D models of animal development and diseases in collaboration with scientists at EMBL and beyond.
Talk: "Uncovering cell dynamics in developing embryos, embryoids and organoid models"
Abstract: Recent trends in developmental biology and clinical research have introduced a variety of embroid and organoid models that resemble the in vivo 3D environment. However, these models are extremely sensitive to the imaging environment and are more variable in their morphology as compared to embryos/organs. Hence, a larger sample size is required to obtain a reliable understanding of the system, posing challenges in terms of imaging throughput, data handling, and visualization of numerous big datasets and integration of information therein. We are addressing these by implementing robust incubation systems and multi-sample imaging and analysis. I will present time-lapse imaging of organoids derived from mouse intestinal tissue as well as of embryoid models derived from zebrafish and mouse embryonic stem cells which recapitulate events from embryonic development.
Gopi Shah is the Project Manager for Advanced Mesoscopy Applications at the Mesoscopic Imaging Facility (MIF) at EMBL Barcelona. MIF provides imaging and data processing services for visualizing large, chemically cleared as well as live biological tissues with commercial and custom implementations of light sheet microscopy and optical projection tomography.
Gopi obtained her PhD in 2016, from the Max Planck Institute for Cell Biology and Genetics (MPI-CBG) in Dresden, Germany, where she worked with an interdisciplinary team to develop light sheet microscopes capable of long-term, high-throughput imaging and real-time data-processing. Thereafter, she joined the Cancer Research UK Cambridge Institute (CRUK CI) in Cambridge, UK, as a Senior Scientific Associate in the light microscopy core facility. Here she established light sheet microscopy as a tool for imaging various human and mouse tumour-derived organoid and co-culture models for observing tumor biology in 4D. Her current work focuses on enabling live imaging of a variety of in vitro 3D models of animal development and diseases in collaboration with scientists at EMBL and beyond.
Pavel Tomancak
MPI-CBG, Dresden (Germany)
Talk: "Insights into gastrulation morphogenesis of insects enabled by in toto light sheet imaging"
Pavel Tomancak studied Molecular Biology and Genetics at the Masaryk University in Brno, Czech Republic. He then did his PhD at the European Molecular Biology Laboratory in the field of Drosophila developmental genetics. During his post-doctoral time at the University of California in Berkeley at the laboratory of Gerald M. Rubin, he established image-based genome scale resources for patterns of gene expression in Drosophila embryos. Since 2005 he leads an independent research group at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden where he became senior research group leader in 2013.
His laboratory continues to study patterns of gene expression during development by combining molecular, imaging and image analysis techniques. The group has lead a significant technological development aiming towards more complete quantitative description of gene expression patterns using light sheet microscopy. The emphasis on open access resulted in establishment of major resources such as OpenSPIM (http://openspim.org) and Fiji (http://fiji.sc). The Tomancak lab is expanding the systematic analysis of gene expression patterns to other Drosophila tissues and employing the comparative approach in other Drosophilids and invertebrate species.
Talk: "Insights into gastrulation morphogenesis of insects enabled by in toto light sheet imaging"
Pavel Tomancak studied Molecular Biology and Genetics at the Masaryk University in Brno, Czech Republic. He then did his PhD at the European Molecular Biology Laboratory in the field of Drosophila developmental genetics. During his post-doctoral time at the University of California in Berkeley at the laboratory of Gerald M. Rubin, he established image-based genome scale resources for patterns of gene expression in Drosophila embryos. Since 2005 he leads an independent research group at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden where he became senior research group leader in 2013.
His laboratory continues to study patterns of gene expression during development by combining molecular, imaging and image analysis techniques. The group has lead a significant technological development aiming towards more complete quantitative description of gene expression patterns using light sheet microscopy. The emphasis on open access resulted in establishment of major resources such as OpenSPIM (http://openspim.org) and Fiji (http://fiji.sc). The Tomancak lab is expanding the systematic analysis of gene expression patterns to other Drosophila tissues and employing the comparative approach in other Drosophilids and invertebrate species.
Raju Tomer
Columbia University, NY (USA)
Talk: "Quantitative imaging of large cleared samples with Light Sheet Microscopy"
Raju Tomer joined Columbia University in 2016 as an Assistant Professor in the Department of Biological Sciences with affiliations to the Data Science Institute and Neuro Technology Center. Dr. Tomer completed his undergraduate studies at Indian Institute of Technology (IIT) Delhi, and his Ph.D. at European Molecular Biology Laboratory (Heidelberg), where he developed and applied novel methods to unravel the deep evolutionary origins of cell-types in higher-order brain centers. In his postdoctoral studies in the lab of Prof. Karl Deisseroth at Stanford University, Dr. Tomer developed pioneering microscopy and histological technologies for high-resolution mapping of brain structure and function. Currently in his lab at Columbia University, Dr. Tomer continues to develop new approaches required for systematically understanding the brain structural and functional plasticity in the normal and diseased brains.
Talk: "Quantitative imaging of large cleared samples with Light Sheet Microscopy"
Raju Tomer joined Columbia University in 2016 as an Assistant Professor in the Department of Biological Sciences with affiliations to the Data Science Institute and Neuro Technology Center. Dr. Tomer completed his undergraduate studies at Indian Institute of Technology (IIT) Delhi, and his Ph.D. at European Molecular Biology Laboratory (Heidelberg), where he developed and applied novel methods to unravel the deep evolutionary origins of cell-types in higher-order brain centers. In his postdoctoral studies in the lab of Prof. Karl Deisseroth at Stanford University, Dr. Tomer developed pioneering microscopy and histological technologies for high-resolution mapping of brain structure and function. Currently in his lab at Columbia University, Dr. Tomer continues to develop new approaches required for systematically understanding the brain structural and functional plasticity in the normal and diseased brains.
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Open Lightsheet Tools session
Be inspired by the open resources community for light sheet microscopy and beyond.
Talks, demonstrations, discussions contributed by Julien Colombelli, Benedict Diederich, Emmanuel Reynaud, Pavel Tomancak.
Session Moderator: Emmanuel Reynaud
University College Dublin, Ireland
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Andor Technology - Oxford Instruments
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Okolab
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CONTACT US
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Acknowledgement:
This LSFM4LIFE project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 668350.
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F. Pampaloni, 2019