Registration Desk Opens

Opening Remarks

Lecture (Machine Learning theme)

Session Chair: Charles Kervrann

Lecture (Machine Learning theme)

Session Chair: Charles Kervrann

Lecture (Single Molecule Microscopy theme)

Session Chair: Susan Cox

Coffee Break

Hamamatsu Photonics Workshop I

Minisymposium: Machine learning in bioimage analysis and microscopy

Session Chair: Christopher P Calderon

Session: Single Molecule Microscopy

Session Chair: Susan Cox

Session: Optical Methods Developments

Session Chair: Sjoerd Stallinga

Session: Biological Applications of Optical Developments

Session Chair: Sjoerd Stallinga

Lunch (provided)

Pair Talk

Session Chair: E. Sally Ward

Lecture (Software development theme)

Session Chair: Raimund J Ober

Lecture (Past chair lecture)

Session Chair: Raimund J Ober

Coffee Break

Poster Session: Single Molecule Microscopy Methods Development

Poster Session: Optical Methods Developments

Poster Session: Applications of Single Molecule Microscopy

Poster Session: Single Molecule Microscopy Experimental Approaches

Poster Session: Biological Applications of Optical Developments

Marketing Session: Oxford NanoImaging

Minisymposium: Software design for microscopy hardware control

Session Chair: Raimund J Ober

Session: Applications of Single Molecule Microscopy

Session Chair: Diane Lidke

Session: Single Molecule Microscopy Experimental Approaches

Session Chair: Bernd Rieger

QBI Student/Post-doc Chapter Inaugural Meeting

Opening Reception and Poster Viewing

Registration Desk Opens

Lecture (Quantitative tools for subcellular trafficking)

Session Chair: Daniel Wüstner

Tutorial (Correlative imaging)

Session Chair: Daniel Wüstner

Lecture (Imaging for BioPharma applications theme)

Session Chair: Sripad Ram

Poster Award Lecture

Session Chair: Susan Cox

Tribute to Maxime Dahan by Bassam Hajj (Institut Curie Paris)

Coffee Break

Hamamatsu Photonics Workshop II

Minisymposium: Quantitative tools to define subcellular trafficking processes

Session Chair: E. Sally Ward

Session: Machine Learning in Single Molecule Microscopy and Deconvolution

Session Chair: Christophe Zimmer

Lunch (provided)

Pair Talk

Session Chair: Diane Lidke

Session: Application of Image Analysis Approaches

Session Chair: Jean-Christophe Olivo-Marin

Session: Sample Methods Development

Session Chair: Dirk-Peter Herten

Coffee Break

Poster Session: Applications in Biopharma

Poster Session: Machine Learning

Poster Session: Application of Image Analysis Approaches

Poster Session: Sample Methods Developments

Poster Session: Instrument Characterization

Poster Session: Data Analysis Methods Development for Single Molecule Microscopy

Marketing Session: GE Healthcare

Marketing Session: QuantaCell

Minisymposium: Microscopy in BioPharma

Session Chair: Sripad Ram

Session: Data Analysis Methods Development for Single Molecule Microscopy

Session Chair: Yoav Shechtman

Dinner Break

QBI Society Meeting

Registration Desk Opens

Lecture (Structured Illumination theme)

Session Chair: Raimund Ober

Lecture (Optics theme)

Session Chair: Jörg Enderlein

Tutorial (Spatial Statistics)

Session Chair: Jean-Christophe Olivo-Marin

Coffee Break

Minisymposium: Structured illumination: a review of the state of the art

Session Chair: Rainer Heintzmann

Session: Applications in Cell Biology and Biophysics II

Session Chair: Daniel Wüstner

Lunch (provided)

Session: Structured Illumination

Session Chair: Sjoerd Stallinga

Session: Machine Learning in High Throughput Imaging

Session Chair: Patrick Bouthemy

Session: Spatial Statistics

Session Chair: Edward Cohen

Session: Single Molecule Counting and Cluster Analysis

Session Chair: Keith A Lidke

Session: Applications in Cell Biology and Biophysics

Session Chair: Alessandra Cambi

Session: Software

Session Chair: Mark Bates

Coffee Break

Poster Session: Tracking

Poster Session: Applications in Cell Biology and Biophysics

Poster Session: Spatial Statistics

Poster Session: Single Molecule Counting and Cluster Analysis

Poster Session: Image Analysis Methods Development

Poster Session: Digital Pathology

Poster Session: Software

Poster Session: Structured Illumination

Sponsor Session: New R&D microscopy advances in France-BioImaging by Jean Salamero

GdR Imabio - Complex diffusion analysis challenge by Cyril Favard

Session: Image Analysis Methods Development

Session Chair: Keith A Lidke

Session: Tracking

Session Chair: Patrick Bouthemy

Session: Digital Pathology

Session Chair: Sripad Ram

Conference Closing

Poster Award Announcement - Sponsored by Institut de Recherches Servier

Closing Gala Dinner Reception

A dynamic reconstruction of the endocytic machinery in yeast from static superresolution images ( # 131 , Board: 41 )

Yu-Le Wu, Philipp Hoess, Markus Mund, Joran Deschamps, Jonas Ries
European Molecular Biology Laboratory, Heidelberg, DE

Adaptive Holographic Region of Interest Illumination with Oblique Angles for use in Single Molecule Localization Microscopy ( # 216 , Board: 47 )

Alexander Jügler, Jan Becker, Patrick Then, Ronny Förster, Rainer Heintzmann
Leibniz-Institute of Photonic Technology, Jena, DE

Biological Deep Thermal Imaging with Fluorescence Lifetime of Rare-Earth-Based Ceramics Particles that Emit Near-Infrared Light in the Second Biological Window ( # 223 , Board: 54 )

Takumi Chihara, Masakazu Umezawa, Keiji Miyata, Shota Sekiyama, Naoki Hosokawa, Kyohei Okubo, Masao Kamimura, Kohei Soga
Tokyo University of Science, Katsushika, JP

Correlative STED and SMLM, without demons ( # 232 , Board: 66 )

Kirti Prakash
University of Cambridge, Cambridge, GB

Design of an "orthogonality-breaking" polarimetric confocal microscope to study intracellular architecture dynamics ( # 128 , Board: 5 )

Stephanie Dutertre, Mehdi Alouini, Julien Fade, Emilie Gillier, Cyril Hamel, Sébastien Huet, Gilles Le Marchand, Rebecca Smith, Paulami Ray, Marc Tramier
Univ Rennes, RENNES, FR

Improved single molecule localization from dual-objective microscopes with ZOLA-3D ( # 206 , Board: 1 )

benoit lelandais, MICKAEL LELEK, christophe Zimmer
institut pasteur, paris, FR

Intracellular dry-mass density measurements of bacteria using quantitative phase microscopy ( # 76 , Board: 25 )

Enno Oldewurtel, Sven van Teeffelen
Institut Pasteur, Paris, FR

Label-free refractometry and pathogen detection by super-critical angle fluorescence ( # 196 , Board: 14 )

Boris Ferdman, Lucien Weiss, Onit Alalouf, Yonathan Haimovich, Yoav Shechtman
Technion – Israel Institute of Technology, Adi, IL

Mapping fluid and single-cell dynamics in a controlled thermal landscape ( # 87 , Board: 36 )

Jaime Ortega Arroyo, Matz Liebel, Bernard Ciraulo, Stefan Wieser, Niek van Hulst, Romain Quidant
ICFO - The Institute of Photonic Sciences, Casteldefels, ES

Nanostructured substrates for super-resolution imaging ( # 212 , Board: 58 )

Maia Brunstein, Anne Talneau, Minh-Chau Nguyen, Pacal Berto, Anne-Laure Fehrembach, Anne Sentenac, Martin Oheim
Université Paris Descartes, Paris, FR

PRACTICAL IMPLEMENTATION OF THE OFF-AXIS HOLOGRAPHIC MICROSCOPE ( # 235 , Board: 38 )

Radim Kolar, Vratislav Cmiel, Larisa Baiazitova, Ivo Provaznik
Brno university of technology, Brno, CZ

Probing cells dynamics with quantitative Dynamic Full-Field OCT ( # 19 , Board: 62 )

Kassandra Groux, Jules Scholler, Kate Grieve, Claude Boccara
ESPCI, Paris, FR

Quantitative phase imaging of adherent mammalian cells: a comparison of three different techniques ( # 63 , Board: 19 )

Cédric Allier, Julien Savatier, Serge Monneret, Yves Usson, Ondrej Mandula, Lionel Hervé, Pierre Blandin, Sophie Morales
CEA-LETI, Grenoble, FR

REFRACTIVE INDEX MATCHING FOR IN VIVO LIGHT-SHEET MICROSCOPY ( # 242 , Board: 72 )

Dimitri Kromm
EMBL, Heidelberg, DE

RSMLM: An R-package for pointillist based analysis of single molecule localization microscopy data ( # 209 , Board: 23 )

Jeremy Pike, Iain B Styles
University of Birmingham, , United Kingdom

Single molecule nucleocytoplasmic transport dynamics in live cells ( # 117 , Board: 9 )

Seoungjun Lee
King’s College London, London, GB

Structured illumination in laser scanning microscopy for super-resolved multiphoton imaging: theory and simulations of scanning SIM ( # 215 , Board: 28 )

Eli Slenders, Marcel Ameloot, M vandeVen
Hasselt University, Hasselt, BE

Temperature Sensing of Deep Abdominal Region in Mice by Using Over-1000 nm Near-Infrared Luminescence of Rare-Earth-Doped NaYF4 Nanothermometer ( # 224 , Board: 70 )

Shota Sekiyama, Masakazu Umezawa, Shuhei Kuraoka, Takuji Ube, Masao Kamimura, Kohei Soga
Tokyo University of Science, Katsushika, JP

The problem of orientation-induced mislocalizations of single emitters in cryo‐fluorescence microscopy ( # 160 , Board: 32 )

Oleksii Nevskyi, Jörg Enderlein, Ingo Gregor
Georg August University Goettingen, Goettingen, DE

Towards self-driving super-resolution microscopes for live-cell imaging ( # 240 , Board: 45 )

Dora Mahecic, Suliana Manley
EPFL, Lausanne, CH

Automated brain region recognition in fluorescent tissue slices using deep learning ( # 237 , Board: 68 )

Michaël Barbier, Hervé Maurin, Emiel Holvoet, Rony Nuydens, Peter Larsen, Peter Horvath, Winnok De Vos
University of Antwerp, Antwerpen, BE

CNN based semi-supervised FIB-SEM image segmentation via propagation of learned information from a small subset of a single image stack ( # 86 , Board: 30 )

Kevin G Loftis, Kevin Stoltz, Guillaume Thibault, Jessica L Riesterer, Young Hwan Chang, Joe Gray
Oregon Health & Science University, Portland, US

Calibrating a microscope by learning its diversity ( # 21 , Board: 64 )

Valentin Debarnot, Pierre Weiss, Thomas Mangeat, Paul Escande
ITAV, CNRS, Toulouse, FR

Deep learning for dense 3D single molecule localization microscopy ( # 203 , Board: 49 )

Elias E Nehme, Daniel Freedman, Tomer Michaeli, Yoav Shechtman
Technion - Israel Institute of Technology, Haifa, IL

Deep learning for quantitative bi-exponential fluorescence lifetime imaging ( # 12 , Board: 7 )

Jason T. Smith, Ruoyang Yao, Sez-Jade Chen, Nattawut Sinsuebphon, Alena Rudkouskaya, Margarida Barroso, Pingkun Yan, Xavier Intes
Rensselaer Polytechnic Institute, Troy, US

Establishing the theoretical density/SNR limits for SMLM analysis leads to the design of UNLOC a parameter-free and fast computing ImageJ plugin ( # 107 , Board: 12 )

Sébastien Mailfert, Nicolas Bertaux, Didier Marguet
Centre d'Immunologie de Marseille Luminy, Marseille cedex 09, FR

Experimentally-generated ground truth for tracking lymphocyte populations in image-based immunotherapy screens ( # 102 , Board: 34 )

Joseph Boyd, Zelia Gouveia, Franck Perez, Thomas Edgar Walter
MINES Paristech, Paris, FR

Image based modeling of leaf development ( # 37 , Board: 43 )

Mohamed Oughou, Patrick Laufs, Eric Cunha, Eric Biot, Nicolas Arnaud, Philippe Andrey, Jasmine Burguet
INRA, Nanterre, FR

Image profiling exposes a pharmacological window for modifiers of neuronal network connectivity ( # 230 , Board: 3 )

Marlies Verschuuren, Winnok De Vos
University of Antwerp, Antwerp, BE

Machine Learning Pipeline for Automated Classification and Novelty Detection in High Dimensional Images of Tumor Microenvironments ( # 241 , Board: 71 )

Andre Gosselink, Elvira Criado-Moronati, Stefan Borbe, Ali Kinkhabwala, Jutta Kollet
Miltenyi Biotec GmbH, Bergisch Gladbach, DE

PyMOL Molecular Graphics System for Immunoglobulin Cross-Reactivity Analysis ( # 233 , Board: 56 )

Nasreddine SAIDI
Institut Pasteur Tunis, Tunis, TN

Quantifying molecular confinement using sSTED-FCS: The case of lipid trapping during HIV-1 assembly in living T cells ( # 213 , Board: 26 )

Cyril Favard, Jakub Chojnacki, Christian Eggeling, Delphine Muriaux
CNRS, Montpellier, FR

Quantitative evaluation of a next generation scientific CMOS (sCMOS) camera for high fidelity imaging ( # 114 , Board: 21 )

Shigeo Watanabe, Takafumi Higuchi, Teruo Takahashi, Katsuhide Ito
Hamamatsu Photonics K.K., Hamamatsu-city, JP

Scalable analysis of ultra-terabyte brain images with deep learning ( # 73 , Board: 17 )

Giacomo Mazzamuto, Francesco Orsini, Matteo Roffilli, Paolo Frasconi, Francesco Pavone, Ludovico Silvestri
National Institute of Optics, National Research Council, Sesto Fiorentino, IT

Segmentation of adjacent cells in a C. elegans embryo using a multi-compartment active contour ( # 40 , Board: 60 )

Anaïs Badoual
Ecole Polytechnique Fédérale de Lausanne, Prilly, CH

Semi-quantitative analysis of the trace metallic elements with synchrotron radiation X-ray fluorescence analysis and the experimental concentration standard specimens ( # 22 , Board: 52 )

Motohiro Uo, Takahiro Wada
The University of Tokyo, Bunkyo-ku, JP

3D stochastic process simulation for better interpretation of molecular dynamics related to cell wall biogenesis observed with TIRF microscopy ( # 72 , Board: 6 )

Charles Kervrann, Alain Trubuil, Cyrille Billaudeau, Rut Carballido-Lopez, Yunjiao LU
INRA, Jouy-en-Josas, FR

3D tracking of endocytic events using lattice light sheet microscopy ( # 92 , Board: 8 )

Cesar Augusto VALADES CRUZ, Alison Forrester, Christian Wunder, Charles Kervrann, Jean SALAMERO, Ludger Johannes
Institut Curie, Paris, FR

A mechano-imaging method to quantify intracellular biophysics ( # 140 , Board: 48 )

Aleix Boquet-Pujadas, Elisabeth Labruyere, Jean-Christophe Olivo-Marin
Institut Pasteur, Paris, FR

A pyramidal PDE-constrained approach to quasi-static optical elastography ( # 141 , Board: 51 )

Aleix Boquet-Pujadas, Jean-Christophe Olivo-Marin
Institut Pasteur, PARIS, FR

Adaptive optics flood-illumination ophthalmoscope with structured illumination capabilities ( # 123 , Board: 16 )

Yann Lai-Tim, Laurent Mugnier, Elena Gofas-Salas, Pedro Mece, Cyril Petit, Francois Orieux, Michel Paques, Serge Meimon
ONERA, Chatillon Cedex, FR

Analysing and quantifying intracellular particles movements in 3D LLSM data ( # 109 , Board: 44 )

Antoine Salomon, Vincent Briane, Myriam Vimond, Cesar Augusto VALADES CRUZ, Charles Kervrann
Inria Rennes, Rennes, FR

Automated inhibitor screening of aurka kinase activity based on a FRET biosensor ( # 13 , Board: 13 )

Florian Sizaire, Gilles Le Marchand, Giulia Bertolin, Sandrine Ruchaud, Claude Prigent, Otmane Bouchareb, Olivier Chanteux, Marc Tramier
Institut de Génétique et de Développement de Rennes, Rennes, FR

Automatic detection of tumoral tissue in hepatocellular carcinoma digital slides using deep convolutional networks ( # 65 , Board: 53 )

Qinghe Zeng, Nicolas Lomenie, Julien Calderaro, Christophe Klein
INSERM U1138 - Centre de Recherche des Cordeliers, Nantes, FR

Biophysical characterization of the interactions between Influenza A virus matrix protein M1 and host plasma membrane ( # 112 , Board: 24 )

Salvatore Chiantia
University of Potsdam, Potsdam / Golm, DE

Brownian motion using a piezo actuated microscope stage ( # 26 , Board: 4 )

Nicholas Vickers, Sean Andersson
Boston University, Quincy, US

Challenges in structured illumination microscopy ( # 30 , Board: 69 )

Verena Richter, Mathis Piper, Michael Wagner, Herbert Schneckenburger
Aalen University, Aalen, DE

Complex diffusion analysis challenge ( # 208 , Board: 11 )

Maxime Woringer, Hugues Berry, Dominique Bourgeois, Cyril Favard, Ignacio Izeddin
Institut Pasteur, , France

Computational pipeline for registration of 3D images of fixed specimens to 4D time-lapse recordings of developing biological systems ( # 138 , Board: 61 )

Manan Lalit, Mette Handberg-Thorsager, Florian Jug, Pavel Tomancak
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, DE

Determining biophysical parameters in living cells with Icy ( # 198 , Board: 10 )

Maria Manich, Aleix Boquet-Pujadas, Nancy Guillén, Jean-Christophe Olivo-Marin
Institut Pasteur, Paris, FR

High-resolution 2d+t imaging of calcium signaling microdomains in cardiac myocytes ( # 132 , Board: 27 )

Mouna Abdesselem
KU Leuven, Leuven, BE

Icy: A powerful and user friendly platform for Bio image analysis. ( # 211 , Board: 63 )

Fabrice de Chaumont, Stephane Dallongeville, Jean-Christophe Olivo-Marin
Institut Pasteur, Paris, FR

Imaging release of siRNAs from vesicles damaged by membrane-disrupting drugs ( # 239 , Board: 33 )

Hampus Du Rietz, Hampus Hedlund, Anders Wittrup
Lund University, Lund, SE

Large scale feature extraction and image classification for high content screening microscopy ( # 113 , Board: 57 )

Laurent Thomas, Gunjan Pandey, Jens H.Westhoff, Franz Schaefer, Jochen Gehrig
Uniklinikum Heidelberg and Acquifer, Heidelberg, DE

Measuring ligand 2D/surface density on various substrates using fluorescence fluctuation microscopy ( # 49 , Board: 35 )

Dwiria Wahyuni, Irène Wang, Antoine Delon
Université Grenoble Alpes, , France

Mechanistic investigation of mEos4b blinking suggests a strategy to reduce track interruptions in sptPALM ( # 25 , Board: 2 )

Daniel Thédié, Dominique Bourgeois, Elke De Zitter, Peter Dedecker, Virgile Adam
IBS (Institut de Biologie Structurale), Grenoble, FR

Mesoscopic organisation of polarity proteins in epithelial cells ( # 210 , Board: 29 )

Edo Dzafic, Leila A Muresan
Cambridge University, Cambridge, GB

Near real time analysis of stress fiber formation in stem cells ( # 31 , Board: 55 )

Lara Hauke, Benjamin Eltzner, Carina Wollnik, Stephan Huckemann, Florian Rehfeldt
Georg August Universität Göttingen, Göttingen, DE

Protein copy number estimation in biological samples with high fluorescent background ( # 75 , Board: 40 )

Johan Hummert, Klaus Yserentant, Wioleta Chmielewicz, Dirk-Peter Herten
Heidelberg University, , Germany

Protein counting in T-cell receptor microclusters ( # 139 , Board: 42 )

Wioleta Chmielewicz, Dirk-Peter Herten, Oliver T. Fackler
Heidelberg University, Heidelberg, DE

Protein counting in localisation microscopy ( # 62 , Board: 37 )

Daniel Varga, Miklós Erdélyi
University of Szeged, Szeged, HU

Quantitative 3D geometry for large scale connectomics data ( # 126 , Board: 46 )

Minh-Son Phan, Katherine Matho, Lamiae Abdeladim, Jean Livet, Emmanuel Beaurepaire, Anatole Chessel
Ecole Polytechnique Paris-Saclay, Palaiseau, FR

SIMTOOLBOX 2.0: AN OPEN-SOURCE TOOLBOX FOR STRUCTURED ILLUMINATION MICROSCOPY ( # 220 , Board: 67 )

Jakub Pospíšil, Tomáš Lukeš, Pavel Křížek, Martin Ovesný, Vojtěch Terš, Karel Fliegel, Miloš Klíma, Guy M. Hagen
UNI-Bielefeld, Bielefeld, DE

Simulator of benchmarking image datasets for time-lapse lightsheet microscopy ( # 134 , Board: 59 )

Vladimír Ulman
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, DE

Software framework for Advanced Single Molecule Data Analysis ( # 218 , Board: 65 )

Anish V Abraham, Dukwhan David Kim, Jerry Chao, E. Sally Ward, Raimund J Ober
Texas A&M University, College Station, US

Spatial analysis of protein or lipid distributions on the surface of spherical beads ( # 135 , Board: 50 )

Anastasia Solomatina, Alice Cezanne, Marino Zerial, Ivo F. Sbalzarini
MPI-CBG, Dresden, Germany, Dresden, DE

Studying oscillatory behavior in asymmetric division of Caenorhabditis elegans embryo with fluorescence miscroscopy ( # 24 , Board: 15 )

Anca Caranfil, Charles Kervrann, Yann Le Cunff, Jacques Pécréaux
INRIA Rennes - Bretagne Atlantique, France, RENNES, FR

Time resolve intensity photo bleaching (TRIP) as a tool for quantify bound /unbound fraction of lamin A protein in vivo. ( # 229 , Board: 31 )

‪Eugene Brozgol‬‏, Irena Bronshtein, Iatamar Kantor, Yuval Garini
Bar Ilan University, גבעת שמואל, IL

Ultrastructure of endo-lysosomes during cholesterol efflux studied by combined fluorescence and cryo-soft X-ray tomography ( # 35 , Board: 18 )

Alice Dupont Juhl, Frederik W. Lund, Maria Louise Vestbjerg Jensen, Maria Szomek, Gitte Krogh Nielsen, Christian W. Heegaard, Peter Guttmann, Stephan Werner, James McNally, Gerd Schneider, Sergey Kapishnikov, Daniel Wüstner
The University of Southern Denmark, Årslev, DK

Use of X-ray micro computed tomography imaging to analyze the morphology of wheat grain through its development ( # 60 , Board: 22 )

Thang Duong Quoc Le, Christine Girousse, David Legland, Anne-Laure Chateigner Boutin
INRA Angers-Nantes, Nantes, FR

Using time-lapse microscopy to unravel the stochastic nature of Listeria monocytogenes infection ( # 44 , Board: 20 )

Josephine C Moran, Andrew Berry, James Bagnall, Pawel Paszek, Ian Roberts
University of Manchester, Manchester, GB