QBI 2020 Videos

Click on the links below to the see the videos of sessions from each of the conference days:

Monday, 6-Jan-2020

Workshops:

Spatial Statistics – Edward Cohen, Imperial College London (video : part A, part B, part C, part D)

Cluster analysis of single-molecule localization microscopy data – Dylan Owen, University of Birmingham (video)

Quantitative super-resolution imaging with DNA-PAINT – Christian Soeller, University of Exeter (video)

Quantitative super-resolution imaging in biology – Melike Lakadamyali, University of Pennsylvania (no video available)

Counting by photon statistics – Johan Hummert, Heidelberg University (video)

Quantitative imaging using super-resolution optical fluctuation imaging – Kristin Gruẞmayer, Laboratory of Nanoscale Biology (video)

Counting by photobleaching: a Bayesian nonparametric approach – Steve Pressé, Arizona State University (video)

–

Challenge Session:

Quantitating endolysosomal trafficking behavior for the design of therapeutics – Raimund Ober and Sally Ward, University of Southampton / Texas A&M University (video)

Sterol trafficking through the yeast vacuole – Challenges of imaging and phenotype classification – Daniel Wüstner, University of Southern Denmark (video)

Extracellular lysosomal digestion of large objects (Digestive Exophagy) – Fredrick Maxfield, Weill Cornell Medical College (video)

The challenges of imaging at multiple scale – Marino Zerial, Max Planck Institute of Molecular Cell Biology and Genetics (no public release)

A zoo of GFP-based imaging techniques in cell biology today – Jennifer Lippincott-Schwartz, HHMI Janelia Research Campus (video)

Challenges in designing brighter dyes for advanced fluorescence microscopy – Luke Lavis, HHMI Janelia Research Campus (video)

Consideration of optical aberrations and image artifacts they cause in 3D fluorescent microscopy – Chrysanthe Preza, University of Memphis (video)

–

Plenary Discussion:
Uses and misuses of machine learning – Florian Jug and Alexander Krull, Max Planck Institute of Molecular Cell Biology and Genetics (video)

–

–

Tuesday, 7-Jan-2020

Keynote Lecture 1:

Eukaryotic organelles: deciphering their interdependency, structure and dynamics with new imaging technologies – Jennifer Lippincott-Schwartz, HHMI Janelia Research Campus (video)

–

Past Chair Lecture:

Statistical and computational methods for intracellular trajectory analysis in fluorescence microscopy – Charles Kervrann, Inria – Rennes (video)

–

Poster Award Lecture:

DeepSTORM3D: Deep learning for dense 3D single molecule localization microscopy – Elias Nehme, Technion – Israel Institute of Technology (video)

–

Minisymposium: Volumetric Imaging

3D parallelized RESOLFT optical nanoscopy  – Ileria Testa, KTH SciLifeLab (preliminary video)

A bolt-on single-objective light-sheet design with uncompromised numerical aperture – Andrew York, Calico Labs (no public release)

Mesoscale imaging with the Mesolens – Gail McConnell, University of Strathclyde (no public release)

–

Session: Advanced Imaging Techniques

Quantitating light sheet microscopy – James Manton, MCR Laboratory of Molecular Biology (video)

Label-free live-cell imaging at 150nm and 100Hz by ROCS-microscopy – Alexander Rohrbach, University of Freiburg (video)

–

Session: Applications in Cell Biology

Multiplex Single Molecule Pull-down (SIMPull) measurements of EGFR site-specific phosphorylation – Diane Lidke, University of New Mexico (no public release)

Quantitative analysis of EGF receptor dynamics, confinement and interaction with the cytoskeleton using nanoparticle labeling, single-molecule tracking and hydrodynamic force application – Antigoni Alexandrou, Ecole Polytechnique (no public release)

Condensation of endoplasmic reticulum membrane domains – Konstantin Speckner, University of Bayreuth (preliminary video)

Super-resolution microscopy elucidates curvature generation by endocytic clathrin coats in live cells and tissues – Comert Kural, Ohio State University (video)

Nanoscale cellular dynamics with super-resolution spectroscopy – Erdnic Sezgin, University of Oxford (video)

Quantitative imaging of intracellular receptors in cardiac myocytes using DNA-PAINT – Anna Meletiou, University of Exeter (video)

Novel intensity-based approach to characterize astrocyte calcium signals – Andre Zeug, Hannover Medical School (no public release)

–

Minisymposium: Imaging in Immunology

Supramolecular attack particles: a new cytotoxic biomaterial – Michael Dustin, University of Oxford (video)

Superresolution microscopy images: what they tell us about protein clusters – and what they don’t – Gerhard Schütz, Vienna University of Technology (video)

Applications of single-molecule localization microscopy to studying negative regulators of T cell activation – Dylan Owen, University of Birmingham (video)

Quantitative analyses of T cell signaling – Christoph Wuelfing, University of Bristol (video)

–

Session: Advances in Optical Approaches

Towards quantum enhanced quantitative superresolution microscopy – Dan Oron, Weizmann Institute of Science (video)

Metal-induced energy transfer – Jörg Enderlein, Georg August University (video)

Homogenous multifocal excitation for high-throughput super-resolution imaging – Dora Mahecic, Ecole Polytechnique Federale de Lausanne (video)

Mulitconjugate adaptive optics for microscopy – Karen Hampson, University of Oxford (no public release)

Random Illumination Microscopy (RIM): nanoscopy in living tissues with neither calibration nor adaptive optics – Thomas Mangeat, CBI, Toulouse (video)

Thermophoretic trap for single amyloid fibril and protein aggregation studies – Tobias Thalheim, Peter Debye Institute for Soft Matter Physics (video)

–

Minisymposium: Bioimage Informatics

Machine Learning for Computational Phenotyping: how to overcome the need for massive imaging annotation – Thomas Walter, Mines Paris Tech (video)

Statistical analysis and modeling of single particle trajectories to reveal the flow and dynamics of the ER – David Holcman, ENS (video)

Quantitative multicolor super-resolution microscopy – Jean-Baptiste Sibarita, Interdisciplinary Institute for NeuroScience (video)

–

Session: Bioimage informatics

Quantifying the robustness of topological defects in orientation fields from bio-images – Karl Hoffmann, Max Planck Institute of Molecular Cell Biology and Genetics (video)

KDML: a Knowledge-Driven Machine Learning for analyzing high throughput imaging data – Heba Sailem, University of Oxford (video)

–

Session: Advanced Microscopy Techniques

Measuring diffusion dynamics at high photon-count rates with FCS and STED-FCS – Falk Schneider, University of Oxford (video)

Automated, user-independent correction of artefacts in fluorescence correlation spectroscopy measurements using convolutional neural networks – Alexander Seltmann, Friedrich Schiller University Jena (video)

Optimization of experimental and acquisitional parameters for improved SOFI super-resolution – Dario Cevoli, Umiversité de Lille (video)

Simultaneous multicolor single-molecule imaging using discrete PSF engineering – Win Vandenberg, KU Leuven (preliminary video)

Fluorescence speckle correlation spectroscopy – Antoine Delon, Université Grenoble Alpes (video)

–

Workshop: Single molecule localization microscopy flight simulator

SMLM flight simulator – Juliette Griffie, EPFL and Daniel Sage, EPFL (no public release)

–

–

Wednesday, 8-Jan-2020

Minisymposium: New Frontiers in Single Molecule Microscopy

Single molecule localization microscopy with modulated excitation – Sandrine Leveque-Fort, ISMO-CNRS (no public release)

–

Session: New Frontiers in Single Molecule Microscopy

Isotropic 3D molecular resolution in cells with MINFLUX nanoscopy – Francisco Balzarotti, Research Institute for Molecular Pathology (video)

Bayesian grouping of localizations: sub-nanometer precision, counting and resolution doubling – Keith Lidke, University of New Mexico (no public release)

Uniting structured illumination and localization microscopy (SIMLFUX) – Carlas Smith, TU – Delft (no public release)

Quantifying localization accuracy in single-molecule super-resolution microscopy – Matthew Lew, Washington University – St. Louis (video)

–

Session: Imaging in Immunology

Leukocyte mech(n)anobiology: super-resolution microscopy reveals actin nanoscale architecture at cell protrusions – Alessandra Cambi, Radboud UMC, RIMLS (preliminary video)

Thermoregulation of immune cell dynamics – Stefan Wieser, ICFO – The Institute of Photonic Sciences (no public release)

Lipid membrane sensing and remodeling during the immune synapse – Jorge de la Serna, Imperial College London (no public release)

Quantitative analysis of micropinocytosis in Dictyostelium captured with light-sheet microscopy – Josiah Lutton, University of Warwick (video)

Single-molecule approach to study mechanical control of B cell recognition – Anna Bajur, King’s College London (video)

Quantifying binding affinities and kinetics of biomolecular complexes with mass photometry – Fabian Soltermann, Oxford University (video)

–

Minisymposium: Modern Machine Learning Approaches to Image Analysis Uncertainty Quantification in Microscopy

Deep learning based Phase Microscopy with Uncertainty Quantification – Lei Tian, Boston University (video)

Using machine learning to design intelligent computational microscopes – Roarke Horstmeyer, Duke University (video)

Comprehensive in-situ profiling of brain cellular alterations in the injured brain for accelerating drug discovery – Badri Roysam, University of Houston (video)

–

Session: Modern machine learning approaches to image analysis uncertainty quantification in microscopy

Leveraging self-supervised denoising for image segmentation – Mangal Prakash, MPI-CBG/CSBD (preliminary video)

–

Session: Software

3Dscript: animating 3D/4D microscopy data using a natural-language-based syntax – Ralph Palmisano, Friedrich-Alexander University Erlangen – Nürnberg (preliminary video)

PhenoPlot-Web for visualizing microscopy data – Heba Sailem, University of Oxford (video)

CLIJ: GPU-accelerated real-time image analysis is the key to smart microscopy – Robert Haase, Max Planck Institute for Molecular Cell Biology and Genetics (video)

Virtual reality for quantification of multidimensional single-molecule data – Thomas Blanc, Institut Curie (no public release)

Developing microscope software with Python – David Pinto, University of Oxford (no public release)

Metadata and performance tracking for fluorescent microscopes – Maximiliaan Huisman, UMass Medical School (preliminary video)

–

Minisymposium: Spatial Statistics in Microscopy

Inferring correlation in inhomogenous and multitype point patterns – a review and new contributions – Rasmus Waagepetersen, Aalborg University (video)

Toward Bayesian inference of the spatial distribution of intracellular proteins from FRET data – Jan-Otto Hooghoudt, Aalborg University (no public release)

Quantitative analysis of molecular coupling with SODA – Thibault Lagache, Institut Pasteur (video)

QuantEv: a quantitative approach for analyzing the spatio-temporal distribution of 3D events in fluorescence microscopy – Thierry Pécot, Medical University of South Carolina (video)

–

Session: Applications in BioPharma

Machine learning and airy-light-sheet microscopy reveals morphometric indicators in organoid for informed anti-cancer drug discovery – Craig Russell, EBL EMBL (video)

Multiplexed imaging of lung tissue using a macroscopic light sheet fluorescent microscope with uniform axial resolution – Douglas Shepherd, Arizona State University (preliminary video)

Quantification of bone tissue heterogeneity and cell distribution patterns from digital histology: application in osteosarcoma – Anthony Mancini, IMFT (no public release)

Leveraging automated blood cell morphology for myelodyplastic syndrome diagnosis and prognosis prediction – Jose de Almeida, European Bioinformatics Institute (video)

Image-based nanoparticle characterization to aid drug design – Shoh Asano, Pfizer (video)

Automating FLImP – macromolecular structure fingerprints for personalizing cancer therapy – Daniel Rolfe, Rutherford Appleton Laboratory (video)

–

Session: Spatial Statistics and Clustering

Functional summary statistics for Poisson process on bound convex three dimensional shapes – Scott Ward, Imperial College London (video)

Generalized Statistical Object Distance Analysis (GSODA) for object colocalization in quantitative microscopy – Suvadip Mukherjee, Institut Pasteur (no public release)

Cluster analysis of localization microscopy data with machine learning – David Williamson, King’s College London (video)

FOCAL3D: a 3D clustering algorithm for single-molecule localization microscopy – Daniel Nino, University of Toronto (video)

Toward absolute molecular numbers in DNA-PAINT – Johannes Stein, Max-Planck institute of Biochemistry (video)

Molecular counting with calibrated fluorescent labeling and photobleaching step analysis – Klaus Yserentant, Heidelberg University (video)

Stoichiometric quantification of spatially dense assemblies with qPAINT – Daniel Nieves, University of Birmingham (video)

Statistical modeling of spatial interactions in biological patterns with application to plant nuclear organization – Philippe Andrey, INRIA (video)

–

Session: 3D methods

Consideration of optical aberrations and image artifacts they cause in 3D fluorescent microscopy – Chrysanthe Preza, University of Memphis (video)

4Pi-SMLM and the 3D architecture on the nuclear pore complex – Mark Bates, Max Planck Institute for Biophysical Chemistry (no public release)

Off-focus imaging exploits supercritical-angle fluorescence emission for precise SMLM – Alexander Jesacher, Medical University of Innsbruck (video)

Analysis of relative positions in 3D PALM and dSTORM provides high-resolution information on ordered biological complexes – Alistair Curd, University of Leeds (video)

Selective volumetric microscopy for single molecule imaging in living cells – Bassam Hajj, CNRS (no public release)

3D multicolor nanoscopy at 10,000 cells a day – Andrew Barentine, Yale University (video)

High-throughput multicolor 3D localization in live cells by depth-encoding imaging flow cytometry – Lucien Weiss, Techion – Israel Institute of Technology (video)

3D-SRRF: real-time live-cell-compatible volumetric super-resolution microscopy – Romain Laine, UCL (preliminary video)

–

Workshop:  Introduction to programming for microscopy image analysis

Introduction to programming for microscopy image analysis –  Anish Abraham, Texas A&M University (no public release)

–

–

Thursday, 9-Jan-2020

Keynote Lecture 2:

Structural biology in situ: The promise and challenges of cryo-electron tomography -Wolfgang Baumeister, Max Planck Institute of Biochemistry (video)

–

Tutorial: Quantitative Phase Imaging

Quantitative phase imaging – Alexander Jesacher, Medical University of Innsbruck (preliminary video)

–

Minisymposium: Correlative Microscopy

Imaging the nanoscale structure of endocytosis with correlative super-resolution light and electron microscopy – Justin Taraska, National Institutes of Health (video)

Live-cell correlative microscopy of single organelles – Nalan Liv, University Medical Center Utrecht (preliminary video)

Towards quantitative correlative microscopy – Lucy Collinson, Francis Crick Institute (no public release)

–

Session: Correlative/multimodal microscopy

Quantitative 3D super-resolution imaging of chromatin ‘blobs’ – Lothar Schermelleh, University of Oxford (video)

Cryo-CARE facilitates sub-tomogram averaging in cryo transmission electron microscopy – Tim-Oliver Buchholz, MPI-CBG/CSBD (video)

Towards correlative multimodal nanospectroscopy – Iztok Urbancic, Jozef Stefan Institute (video)

–

Session: Tracking

Novel particle tracking approach with CNN-based candidate selection and two-step linking by Bayesian network – Mariia Dmitrieva, University of Oxford (no public release)

Precise mapping of intracellular diffusion and drift from SPT data analysis – Antoine Salomon, Inria Rennes (video)

Probabilistic overall reconstruction of membrane-associated molecular dynamics from partial observations in rod-shaped bacteria – Yunjiao Lu, INRIA (preliminary video)

A 2-step algorithm for the estimation of time-varying Single Particle Tracking models – Boris Godoy, Boston University (preliminary video)

Single-particle diffusion characterization by deep learning – Yoav Shechtman, Techion – Israel Institute of Technology (preliminary video)

Faster FLImP – Towards high throughput image acquisition and tracking selection – Ben Davis, STFC (video)

Quantitative comparison of single particle tracking algorithms across different signal and noise levels – Sean Andersson, Boston University (video)

Effect of pixilation on the parameter estimation of single molecule trajectories – Raimund Ober, Texas A&M University / University of Southampton (video)

–

Minisymposium: Tissue Multiplexing Techniques and Applications in Oncology I

Introduction to the minisymposium on tissue multiplexing – Is more the merrier or messier? – Sripad Ram, Pfizer, Inc. (video)

Multiplex immunohistochemistry and transcriptomic data – Robert West, Stanford University Medical Center (video)

Implementation of multiplexing and image analysis to support drug discovery and development – Shanon Seger, Roche (video)

Deep learning approaches for reliable quantification of multi-omics cell imaging datasets to interrogate RNA and protein spatial and temporal subcellular interactions – Emmanuel Bouihol, CNRS (video)

Understanding and modeling inflammation induced immunosuppression in tumors using multi-plex immunofluorescence and live cell microscopy – Stephen Lockett, National Cancer Institute (no public release)

Highly multiplexed imaging in health and disease by imaging mass cytrometry – Bernd Bodenmiller, University of Zurich (no public release)

Multimodal mass spectrometry imaging of tumors – Josephine Bunch, National Physical Laboratory (no public release)

–

Session: Methods for Single Molecule Analysis

Single Molecule Localization Microscopy using time modulated illumination – Pierre Jouchet, CNRS (no public release)

Identifying analysis algorithm induced artefacts in localization microscopy – Richard Marsh, King’s College London (preliminary video)

SIMPLE: Structured Illumination based Point Localization Estimator with enhanced precision – Loïc Reymond, ICFO – The Institute of Photonic Sciences (video)

Spatiotemporial resolution as an information theoretical property of stochastic optical localization nanoscopy – Yi Sun, The City College of City University of New York (video)

Haste makes waste – Slow imaging increases resolution and labeling efficiencies in SMLM – Robin Diekmann, EMBL (no public release)

Towards Bayesian based smart microscopy – Juliette Griffie, EPFL (no public release)

Single molecule localization lightfield microscopy – Leila Muresan, University of Cambridge (preliminary video)

–

Minisymposium: Tissue Multiplexing Techniques and Applications in Oncology II

Multiplex immune cell profiling to gain insights into progression in early cancer – Natalia Martin, University of Oxford (video)

Towards computational multiplex fluorescence microscopy: machine learning-based integrated prediction of morphological and molecular tumor profiles – Frederick Klauschen, Charite University Hospital Berlin (no public release)

Multiplex imaging of lung tumors with CODEX technology – Marta Trüb, University of Basel/University Hospital Basel (no public release)

–

Session: Probe Development

Mechanical investigations of mEos4b blinking: longer single particle tracking with less track interruptions – Siewert Hugelier, KU Leuven (no public release)

Separation of cell signaling responses based on a new model for photoswitching in FRET biosensors – Thijs Roebroek, KU Leuven (video)

Innovative buffer for long-lived fluorescence imaging for 2D and 3D dSTORM – Karine Monier, CRCL (preliminary video)

–

Session: Point Spread Function Analysis

PSF-broadening due to fluorescence emission: principle and implications on imaging – Jan Becker, Leibniz Institute for Photonic Technology (video)

Simultaneous multicolor single-molecule imaging using discrete PSF engineering – Win Vandenberg, KU Leuven (preliminary video)

Measurement of the depth-dependence of point spread functions near the glass-water interface in high numerical aperture microscopy – Petar Petrov, Stanford University (video)

A general framework for fitting an arbitrary model to SMLM data – Jonas Ries, EMBL (video)

ZOLA-3D: a software for optimal 3D SMLM with arbitrary PSF – Benoit Lelandais, Institut Pasteur (preliminary video)

–

Session: Machine Learning

DeepFocus: a near one-shot micro-manager auto-focus plugin using convolutional neural networks – Adrian Shajkofci, Idiap Research Institute (preliminary video)

Probabilistic Noise2Void: unsupervised content-aware denoising – Alexander Krull, MPI-CBG/CSBD (video)

Bootstrapping unsupervised image denoising with parametric noise models – Mangal Prakash, MPI-CBG/CSBD (preliminary video)