QBI 2019 Conference Sessions

9 Jan - 11 Jan

Start End Location

Registration: Workshops (max capacity 150 per workshop)

08:00 16:00 Foyer (Hall 1)

Workshop: Adaptive Optics

Practical Aspects of Adaptive Optics for Microscopes

Martin Booth, Aurélien Barbotin, Mantas Žurauskas
University of Oxford, Oxford, GB

08:30 10:45 Lecture Room 2 (Dortoir)

Coffee Break

10:45 11:00 Lecture Room 1 (NEF)

Workshop: Machine Learning

11:00 12:30 Lecture Room 2 (Dortoir)

Lunch Break

12:30 13:45 (on own)

Workshop: Machine Learning

13:45 16:45 Lecture Room 2 (Dortoir)

Coffee Break

16:45 17:15 Lecture Room 1 (NEF)

Workshop: 3D Super resolution Microscopy

17:15 19:15 Lecture Room 2 (Dortoir)

Registration Desk Opens: Main Conference

17:15 21:15 Foyer (Hall 1): Registration Area

Opening Reception

18:15 20:30 Foyer (Hall 1)
Start End Location

Registration Desk Opens

08:00 20:30 Foyer (Hall 1): Registration Area

Opening Remarks

08:15 08:30 Lecture Room 1 (NEF)

Lecture (Machine Learning theme)

Sparse modeling of data and deep learning

Michael Elad
Technion - Israel Institute of Technology, Haifa, IL

08:30 09:10 Lecture Room 1 (NEF)

Lecture (Machine Learning theme)

Content-aware image restoration for light and electron microscopy

Florian Jug
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, DE

09:10 09:40 Lecture Room 1 (NEF)

Lecture (Single Molecule Microscopy theme)

An analysis of protein movement in the synapse

Silvio Rizzoli
University Medical Centre Goettingen, , Germany

09:40 10:10 Lecture Room 1 (NEF)

Coffee Break

10:10 10:40 Foyer (Hall 1)

Minisymposium: Machine learning in bioimage analysis and microscopy

From image to information: using advanced gene editing, microscopy, and modeling to advance cell biology

Mary (Molly) M Maleckar
Allen Institute for Cell Science, Seattle, US

Unraveling the Rules of Life a few photons at a time

Steve Pressé
Arizona State University, Tempe, US

Computational boosts to single molecule localization microscopy

Christophe Zimmer
Institut Pasteur, Paris, FR

10:40 11:40 Lecture Room 1 (NEF)

Session: Single Molecule Microscopy

Data fusion for localization microscopy

Bernd Rieger
TU Delft, Delft, NL

Nuclear pores as universal reference standards for quantitative microscopy

Jonas Ries
EMBL, Heidelberg, DE

Artefact free high density localisation microscopy analysis

Richard John Marsh
King's College London, London, GB

11:40 12:25 Lecture Room 1 (NEF)

Session: Optical Methods Developments

Super-resolution imaging of unlabeled living cells using superoscillatory polarization contrast

Edward T F Rogers, Shmma Quraishe, Katrine Rogers, Tracey Newman, Peter Smith, Nikolay Zheludev
University Of Southampton, Southampton, GB

Single-shot fluorescence holography for 3D tracking in live cells

Matz Liebel, Jaime Ortega Arroyo, Vanesa Sanz, Johann Osmond, Romain Quidant, Niek van Hulst
ICFO -The Institute of Photonic Sciences, Castelldefels, ES

Simple and compact microscope for time-lapse phase and fluorescence imaging based on chromatic aberration

Ondrej Mandula, Cédric Allier, Sophie Morales, Jean-Philippe Kleman, Francoise Lacroix, Lionel Hervé
CEA-Leti, , France

Speed OPIOM (Out-of-Phase Imaging after Optical Modulation) for quantitative multiplexed fluorescence imaging against autofluorescence under ambient light

Ruikang Zhang, Raja Chouket, Marie Aude Plamont, Zsolt Kelemen, Agathe Espagne, Alison Tebo, Arnaud Gautier, Lionel Gissot, Jean-Denis Faure, Ludovic Jullien, Vincent Croquette, Thomas le Saux
Ecole Normale Superieure, Paris, FR

Methods and applications of quantitative dynamic full-field coherence tomography

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

10:40 11:55 Lecture Room 2 (Dortoir)

Session: Biological Applications of Optical Developments

LIESS-FCS: spatially resolved diffusion modes measured by STED nanoscopy

Falk Schneider, Dominic Waithe, Erdinc Sezgin, Christian Eggeling
University of Oxford, Oxford, GB

Adaptive optics allows 3D STED-FCS measurements in the cytoplasm of living cells

Aurélien Barbotin, Silvia Galiani, Iztok Urbančič, Christian Eggeling, Martin Booth
University of Oxford, Oxford, GB

11:55 12:25 Lecture Room 2 (Dortoir)

Lunch (provided)

12:25 13:45 Foyer (Hall 1): Food Area

Pair Talk

Structure and dynamics of endosomes analyzed by imaging-based methods

Marino Zerial
MPI-CBG, , Germany

Structure and dynamics of endosomes analyzed by imaging-based methods

Yannis Kalaidzidis
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, DE

13:45 14:25 Lecture Room 1 (NEF)

Lecture (Software development theme)

The ImageJ ecosystem: An open platform for biomedical image analysis.

Kevin W Eliceiri
University of Wisconsin at Madison, Madison, US

14:25 14:55 Lecture Room 1 (NEF)

Lecture (Past chair lecture)

About the optimal optical transfer function of a microscope

Jörg Enderlein
Georg August University, Göttingen, DE

14:55 15:15 Lecture Room 1 (NEF)

Coffee Break

15:15 16:45 Foyer (Hall 1)

Poster Session

15:00 16:30 Foyer (Hall 1): Poster Area

Marketing Session: Oxford NanoImaging

16:25 16:40 Lecture Room 1 (NEF)

Minisymposium: Software design for microscopy hardware control

Why and how to automate your microscope

Winfried Wiegraebe
Allen Institute for Cell Science, Seattle, US

16:45 18:45 Lecture Room 1 (NEF)

Session: Applications of Single Molecule Microscopy

Unraveling molecular arrangement of synaptic proteins with multiple color super resolution microscopy ans statistical object distance analyse with icy soda

Thibault Lagache, Philippe Bun, Stephane Dallongeville, Alexandre Dufour, Jean-Christophe Olivo-Marin, Thierry Galli, Lydia A Danglot
Institute of Psychiatry & Neurosciences of Paris, PARIS, FR

Multiscale computational modelling of chromatin three-dimensional structure using iPALM microscopic high-resolution images

Zofia Anna Parteka, Dariusz Plewczyński
Centre of New Technologies, University of Warsaw, Warsaw, PL

A quantitative look at cellular oligonucleotide delivery

Leontien van der Bent, Natalia Feiner, R. Alis Olea, Johanna Berndt, Derick Wansink, Lorenzo Albertazzi, Roland Brock
Radboud University Medical Center, Nijmegen, NL

16:45 17:30 Lecture Room 2 (Dortoir)

Session: Single Molecule Microscopy Experimental Approaches

Imaging complex protein machines by high-throughput localization microscopy

Joran Deschamps, Markus Mund, Jonas Ries
EMBL, Heidelberg, DE

Multi-color cryo-fluorescence microscopy

Maximiliaan Huisman, Farzin Farzam, David Grunwald
UMass Medical School, WORCESTER, US

Wide depth reproducible multicolor bioimaging through a combination of 3D single molecule localization strategies

Clement Cabriel, Nicolas Bourg, Pierre Jouchet, Guillaume Dupuis, Christophe Leterrier, Aurélie Baron, Boris Vauzeilles, Emmanuel Fort, Sandrine Leveque-Fort
ISMO-CNRS, ORSAY, FR

A tilted light sheet for single-molecule super-resolution imaging in thick cells

Petar N Petrov, Anna-Karin Gustavsson, Yoav Shechtman, Maurice Lee, W. E. Moerner
Stanford University, Stanford, US

17:30 18:30 Lecture Room 2 (Dortoir)

Opening Reception and Poster Viewing

18:45 22:15 Foyer (Hall 1)

Plenary Discussion

19:45 20:45 Lecture Room 1 (NEF)
Start End Location

Registration Desk Opens

08:00 18:30 Foyer (Hall 1): Registration Area

Lecture (Quantitative tools for subcellular trafficking)

Using microscopy to dissect endolysosomal trafficking and function

Frederick Maxfield
Weill Cornell Medical College, New York, US

08:30 09:20 Lecture Room 1 (NEF)

Tutorial (Correlative imaging)

Correlative light - electron microscopy: approaches, applications and outlook

Judith Klumperman
University Medical Center Utrecht, , The Netherlands

09:20 09:50 Lecture Room 1 (NEF)

Lecture (Imaging for BioPharma applications theme)

Analyzing three-dimensional biological specimens observed with light sheet microscopy under near-natural conditions

Ernst HK Stelzer
Goethe-Universität Frankfurt am Main, Frankfurt am Main, DE

09:50 10:30 Lecture Room 1 (NEF)

Poster Award Lecture

Measuring the absolute degree of labeling for self-labeling protein tags

Klaus Yserentant, Felix Braun, Siegfried Hänselmann, Wioleta Chmielewicz, Johan Hummert, Florian Salopiata, Dirk-Peter Herten
Heidelberg University, Heidelberg, DE

10:30 10:40 Lecture Room 1 (NEF)

Coffee Break

10:40 11:10 Foyer (Hall 1)

Minisymposium: Quantitative tools to define subcellular trafficking processes

Lectin-driven and glycosphingolipid-dependent construction of endocytic pits

Ludger Johannes
Institut Curie, Paris Cedex 05, FR

Fluorescence studies of sterol transport between cellular membranes

Daniel Wüstner
The University of Southern Denmark, Odense, DK

Quantitative visualization of SNARE complex formation in living cells

Geert van den Bogaart
Radboud University Medical Center, , The Netherlands

11:10 12:10 Lecture Room 1 (NEF)

Session: Machine Learning in Single Molecule Microscopy and Deconvolution

Deep learning for dense and multicolor localization microscopy

Elias Nehme, Eran Hershko, Lucien Weiss, Tomer Michaeli, Yoav Shechtman
Technion, Israel Institute of Technology, Haifa, IL

3D ConvNets improve macromolecule localization in 3D cellular cryo-electron tomograms

Emmanuel Moebel, Charles Kervrann
Inria, Rennes, FR

Single molecule at the age of big data: probabilistic pipeline and unsupervised learning

Francois Laurent, Alexander Serov, Christian Vestergaard, Jean-Baptiste Masson
Institut Pasteur, Paris, FR

Semi-blind spatially-variant deconvolution and focus estimation in optical microscopy by use of convolutional neural networks

Adrian Shajkofci, Michael Liebling
Idiap Research Institute, Martigny, CH

11:10 12:10 Lecture Room 2 (Dortoir)

Lunch (provided)

12:10 13:30 Foyer (Hall 1): Food Area

Pair Talk

Uncovering transients in single molecule motion: Application to cell surface proteins

Anthony Vega, Spencer Freeman, Sergio Grinstein, Khuloud Jaqaman
UT Southwestern Medical Center, Dallas, US

Title To Be Announced

Spencer Freeman
Hospital for Sick Children, Toronto, CA

13:30 14:10 Lecture Room 1 (NEF)

Session: Application of Image Analysis Approaches

High content cell classification and tracking improvement by morphology and quantitative phase feature combination

Benoit Wattellier, Sherazade Aknoun, Manuel Yonnet, Fabrice Valentino, Djamel Brahmi, Michel Barlaud, Philippe Pognonec, Thierry Pourcher
PHASICS, SAINT AUBIN, FR

Two dynamic behaviors of the microtubules at the cell cortex reveal the pulling and pushing forces that position the mitotic spindle in C. elegans embryos

Hélène Bouvrais, Danielle Fairbrass, Laurent Chesneau, Nina Soler, Yann Le Cunff, Thierry Pécot, Charles Kervrann, Jacques Pécréaux
Institut de Génétique et Développement de Rennes (IGDR) - UMR 6290, Rennes, FR

Investigating the spatio-temporal patterning of neural stem cell activation events

Sebastien Herbert, Nicolas Dray, Laure Mancini, Willy Supatto, Jean-Yves Tinevez, Jean-Baptiste Masson, Laure Bally-Cuif
Institut Pasteur Paris, Paris, FR

Quantitative analysis of collagen microstructure in vitro and in vivo by means of multi-phasor analysis of second harmonic generation microscopy.

Giuseppe Chirico, MAddalena Collini, laura Sironi, Margaux Bouzin, laura D'Alfonso
Universita' di Milano-Bicocca, Milano, IT

Spatiotemporal quantification of 3D cellular parameters during leaf morphogenesis

Faïçal Selka, Thomas Blein, Jasmine Burguet, Eric Biot, Patrick Laufs, Philippe Andrey
INRA, Versailles, FR

Segmentation of 3D images of plant tissues at multiple scales using the level set method

Annamaria Kiss, Typhaine Moreau, Vincent Mirabet, Cerasela Iliana Calugaru, Arezki Boudaoud, Pradeep Das
ENS de Lyon, Lyon, FR

13:30 15:00 Lecture Room 2 (Dortoir)

Session: Sample Methods Development

DNA origami as a nanoscale platform for T-cell activation

Joschka Peter Hellmeier, Eva Sevcsik
TU Vienna, Vienna, AT

Characterisation of GFP and derivatives for super-resolution cryogenic single molecule localisation microscopy

Amy N Moores, Lin Wang, Laura Zanetti-Domingues, Benji Bateman, Marisa Martin-Fernandez
STFC, Didcot, GB

Novel tetrazine probes for fluorogenic protein labeling

Felix Braun, Philipp Werther, Klaus Yserentant, Achim Wieczorek, Richard Wombacher, Dirk-Peter Herten
Heidelberg University, Heidelberg, DE

14:10 15:05 Lecture Room 1 (NEF)

Coffee Break

14:50 16:20 Foyer (Hall 1)

Poster Session

14:50 16:20 Foyer (Hall 1): Poster Area

Marketing Session: QuantaCell

16:10 16:15 Lecture Room 1 (NEF)

Minisymposium: Microscopy in BioPharma

Volumetric imaging of whole-tumors reveal cancer malignancy

Per Uhlen
Karolinska Institutet, Stockholm, SE

Combining optical imaging of cleared tissue with mathematical modelling and in vivo imaging to predict drug delivery and therapeutic response

Simon Walker-Samuel, Paul Sweeney, Angela d'Esposito, Rebecca Shipley
University College London, London, GB

Analyzing development, function and pathofunction of the vascular systems using light sheet microscopy

Friedemann Kiefer
European Institute for Mol. Imaging (EIMI), Münster, DE

Fast nearly isotropic imaging of large samples like human tumors with ultramicroscopy

Hans-Ulrich Dodt, Saiedeh Saghafi, Klaus Becker, Christian Hahn, Marko Pende, Inna Sabdyusheva, Massih Foroughpour
TU Vienna, Vienna, AT

Microscopy as a tool in the development of antibody-based therapeutics

E. Sally Ward
University of Southampton / Texas A&M Health Science Center, , USA

16:20 18:00 Lecture Room 1 (NEF)

Session: Data Analysis Methods Development for Single Molecule Microscopy

1 nanometer precision by bayesian grouping of localizations

Mohamadreza Fazel, Bernd Rieger, Ralf Jungmann, Keith A Lidke
University of New Mexico, Albuquerque, US

4Pi single molecule localization with an experimental PSF model that achieves theoretical minimal uncertainty

Yiming Li, Jonas Ries
European Molecular Biology Laboratory, Heidelberg, DE

Simultaneous detection of 3D orientation and 3D spatial localization of single emitters for super resolution structural imaging

Miguel A Alonso
Institut Fresnel, Marseille, FR

Photon count estimation in single-molecule imaging

Rasmus Østergaard Thorsen, Bernd Rieger, Sjoerd Stallinga, Christiaan Hulleman
TUDelft, Rotterdam, NL

Polygon-based colocalization analysis for multicolor single-molecule localization microscopy data

Florian Levet, Jean-Baptiste Sibarita
Interdisciplinary Institute for NeuroScience, Bordeaux, FR

Preprocessing structured background signals to improve super-resolution fluorescence images

Siewert Hugelier, Tomas Lukes, Peter Dedecker, Paul Eilers, Cyril Ruckebusch
KU Leuven, Heverlee, BE

An automated bayesian pipeline for rapid analysis of single-molecule binding data

Carlas Sierd Smith, Karina Jouravleva, Maximiliaan Huisman, Samson M. Jolly, Phillip D. Zamore, David Grunwald
University of Massachusetts Medical School, Worcester, US

16:20 18:05 Lecture Room 2 (Dortoir)

Dinner Break

18:30 22:00 (on own)

QBI Society Meeting

20:30 22:00 Small Assembly Room
Start End Location

Registration Desk Opens

08:00 18:00 Foyer (Hall 1): Registration Area

Lecture (Structured Illumination theme)

Title To Be Announced

Rainer Heintzmann
Institute of Physical Chemistry, , Germany

08:30 09:20 Lecture Room 1 (NEF)

Lecture (Optics theme)

Measuring the phase and intensity of the light: from quantitative label-free imaging to fluorescence 3D super-resolution deep in tissues

Pierre Bon
CNRS - Univ. Bordeaux - IOGS, Bordeaux (Talence), FR

09:20 09:40 Lecture Room 1 (NEF)

Tutorial (Spatial Statistics)

A tutorial in spatial statistics for microscopy data analysis.

Edward Cohen
Imperial College London, London, GB

09:40 10:10 Lecture Room 1 (NEF)

Coffee Break

10:10 10:40 Foyer (Hall 1)

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

A signal processing view of Structured Illumination Microscopy

Jean-Christophe Olivo-Marin
Institut Pasteur - CNRS 3691, Paris, FR

Noise controlled image reconstruction for structured illumination microscopy

Sjoerd Stallinga
Delft University of Technology, Delft, NL

Robust adaptive optics for structured illumination microscopy fluorescence imaging

Mantas Žurauskas, Martin Booth
University of Oxford, Oxford, GB

High-speed, real-time reconstructed structured illumination microscopy of living cells

Thomas Huser
University of Bielefeld, , Germany

Random Illumination Microscopy: using uncontrolled speckles to improve the resolution of fluorescence microscopy

Anne Sentenac
CNRS Institut Fresnel, , France

10:40 12:10 Lecture Room 1 (NEF)

Session: Applications in Cell Biology and Biophysics II

A detailed analysis of the mobility of synaptic proteins reveals principles of protein segregation in the synapse and in the axon

Sofiia Reshetniak, Sven Truckenbrodt, Silvio Rizzoli
University Medical Center Goettingen, Goettingen, DE

Investigation of the cross-talk between desmosomes and tetraspanin-enriched microdomains

Maryam Arab, Iqra Arif, Jeremy Pike, Natalie Poulter, Martyn Chidgey, Elena Odintsova
University of Birmingham, Edgbaston, Birmingham, GB

The TCR is randomly distributed in the plasma membrane of resting T cells

Andreas M Arnold, Benedikt Rossboth, Gerhard J Schütz
TU Wien, WIEN, AT

Multimodal microscopy reveals stiffness-dependent nanoscale remodeling of different actin modules during cell protrusion

Alessandra Cambi
Radboud UMC, RIMLS, Nijmegen, NL

Functional insights into the intrinsically disordered protein α-synuclein

Amin Fakhree, Christian Blum, Mireille Claessens
University of Twente, Enschede, NL

Three-dimensional single molecule imaging, with cellular context, of an engineered FcRn antagonist using remote focusing multifocal plane microscopy

Sreevidhya Ramakrishnan, Sungyong You, Jerry Chao, Anish V Abraham, E. Sally Ward, Raimund J Ober
Texas A&M University, , USA

10:40 12:10 Lecture Room 2 (Dortoir)

Lunch (provided)

12:10 13:30 Foyer (Hall 1): Food Area

Session: Structured Illumination

Structured illumination for single molecule localization microscopy at depth

Pierre Jouchet, Clement Cabriel, Nicolas Bourg, Marion Bardou, Guillaume Dupuis, Christian Poüs, Emmanuel Fort, Sandrine Leveque-Fort
CNRS, Orsay Cedex, FR

Super-resolved live imaging for a wide range of biological applications using Random Illumination Microscopy (RIM)

Simon Labouesse, Emmanuel Martin, Renaud Poincloux, Sylvain Cantaloube, Tong Li, Christian Rouvière, Magali Suzanne, Nathalie Campo, Sophie Allard, Mathieu Pinot, Marc Allain, Jérome Idier, Anne Sentenac, Thomas Mangeat
CBI, Toulouse, FR

Novel method for structured illumination retinal imaging

Yann Lai-Tim, Laurent Mugnier
ONERA, , FR

Structured illumination - localization microscopy

Stefan Wieser
ICFO - The Institute of Photonic Sciences, Castelldefels, ES

13:30 14:30 Lecture Room 1 (NEF)

Session: Machine Learning in High Throughput Imaging

Use of deep learning in high-throughput flow imaging microscopy applications

Christopher P Calderon
University of Colorado, Denver, US

Advanced imaging flow cytometry

Andreas Kleiber, Thomas Henkel
Leibniz Institute of Photonic Technology, Jena, DE

High and deep imaging flow cytometry: a potential diagnostic tool for hematological disorders

Anne E Carpenter, Minh Doan
Broad Institute of MIT and Harvard, Cambridge, US

14:30 15:15 Lecture Room 1 (NEF)

Session: Spatial Statistics

Modelling the spatial distribution of the type 6 secretion system in Pseudonomas aeruginosa

Scott Ward, Edward Cohen, Niall Adams
Imperial College, , United Kingdom

Mapping and comparing spatial distributions in biological imaging

Jasmine Burguet, Philippe Andrey
INRA, Versailles, FR

Cluster analysis of the cell membrane

Jerome Boulanger, Leila A Muresan
MRC-LMB, Cambridge, US

13:30 14:15 Lecture Room 2 (Dortoir)

Session: Single Molecule Counting and Cluster Analysis

In vitro verification of a molecular counting technique based on fluorophore blinking statistics using DNA Origami

Daniel Felipe Nino, Daniel Djayakarsana, Nafiseh Rafiei, Anton Zilman, Josh Milstein
University of Toronto, Mississauga, CA

Measuring ligand surface density on various substrates using fluorescence fluctuation microscopy

Dwiria Wahyuni, Martial Balland, Olivier Destaing, Irène Wang, Antoine Delon
Université Grenoble Alpes, Grenoble, FR

Overcoming blinking artifacts in nanocluster detection with two-color storm

Magdalena Schneider, Andreas Arnold, Florian Baumgart, Gerhard J Schütz
Vienna University of Technology, Vienna, AT

Quantifying protein oligomerization in living cells: a systematic comparison of fluorescent proteins and application to developmental cell-cell fusion

Valentin Dunsing, Madlen Luckner, Boris Zühlke, Roberto Petazzi, Andreas Herrmann, Salvatore Chiantia
University of Potsdam, Berlin, DE

14:15 15:15 Lecture Room 2 (Dortoir)

Session: Applications in Cell Biology and Biophysics

Micro-fluctuations of the length of the mitotic spindle reveal its mechanics and its dynamics during cell division

Benjamin Mercat, Xavier Pinson, Yann Le Cunff, Jonathan Fouchard, Hadrien Mary, Sylvain Pastezeur, Yannick Gachet, Sylvie Tournier, Hélène Bouvrais, Jacques Pécréaux
IGDR, Rennes, FR

3D-EM-ISH – a novel tool to visualize specific chromatin regions

Blazej H Ruszczycki
Polish Academy of Sciences, Warszawa, PL

Combining 3D image analysis and computer modeling to understand cell division patterns in plant early embryogenesis

Julien Moukhtar, Elise Laruelle, Alain Trubuil, Katia Blecram, David Legland, Zhor Khadir, Jean-Christophe Palauqui, Philippe Andrey
INRA, Versailles, FR

13:30 14:15 Lecture Room 3

Session: Software

Combining annotation of movies and learning for fate prediction from early embryo development observation

Alain Trubuil, Alline Reis, Véronique Duranthon, Brigitte Le Guienne, Nathalie Le Brusq, Soundouss Messoudi, Guillaume Brocart
INRA, Jouy en Josas, FR

u-track 3D: A tracking framework to quantify, observe and contextualize intracellular dynamics in three dimensions.

Philippe Roudot, Wesley R. Legant, Kevin Dean, Ana David, Daniel Gerlich, Reto Fiolka, Eric Betzig, Gaudenz Danuser
UT Southwestern Medical Center, , USA

PartSeg - GUI for image processing algorithm in Python

Grzegorz Bokota, Nirmal Das, Subhadip Basu, Dariusz Plewczynski
University of Warsaw, Warszawa, PL

A human-in-the-loop approach to image analysis

Mohamed El Beheiry, Sebastien Doutreligne, Fabien Reyal, Jean-Baptiste Masson
Institut Curie, , france

14:15 15:15 Lecture Room 3

Coffee Break

15:15 16:45 Foyer (Hall 1)

Poster Session

15:15 16:45 Foyer (Hall 1): Poster Area

Session: Image Analysis Methods Development

Object detection networks for localization and classification of cells in fluorescence microscopy acquisition and analysis.

Dominic Waithe
University of Oxford, Oxford, GB

How accurately two or more fluorophores can be spectrally resolved in a fluorescence microscope?

Sripad Ram
Pfizer, Inc., , United States

Automatic registration for multidimensional correlative microscopies with error assessment and detections of deformations

Perrine Paul-Gilloteaux
CNRS, Nantes, FR

Membrane curvature estimation method for cryo-electron tomography

Maria Kalemanov, Javier F. Collado, Wolfgang Baumeister, Rubén Fernández-Busnadiego, Antonio Martínez-Sánchez
Max Planck Institute of Biochemistry, Martinsried, DE

Accordion-like collagen fibrils suggested by P-SHG image modeling : implication in liver fibrosis

Denis Rouede, Emmanuel Schaub, Jean-Jacques Bellanger, Frederic Ezan, François Tiaho
University of Rennes 1, Rennes - France, FR

16:45 18:00 Lecture Room 1 (NEF)

Session: Tracking

Local Maximum Likelihood estimation for time-varying Single Particle Tracking models

Boris I Godoy, Nicholas Vickers, Sean Andersson
Boston University, Boston, US

3D motion estimation in 3D light microscopy image sequences: application to cell migration

Sandeep Manandhar, Patrick Bouthemy, Philippe Roudot, Charles Kervrann
Inria, Rennes, FR

Non-equilibrium forces govern anomalous dynamics of subcellular domains in mammalian cells

Lorenz Stadler, Konstantin Speckner, Matthias Weiss
University of Bayreuth, Bayreuth, DE

The topography of biological membranes artefactually creates the appearance of anomalous diffusion: a remedy

Jeremy Adler, Ingela Parmryd, Robin Strand, Ida Sintorn
Uppsala University, Uppsala, SE

Fisher information matrix for molecules with stochastic trajectories

Milad Rafiee Vahid, Bernard Hanzon, Raimund J Ober
Texas A&M University, College Station, US

16:45 18:00 Lecture Room 2 (Dortoir)

Session: Digital Pathology

3D fluorescence whole slide imaging using confocal multi-line scanning

Leon van der Graaff, Sjoerd Stallinga
Delft University of Technology, Delft, NL

Medical image analysis: Brain tumor grade classification

Kawtar EL Karfi, Azeddine AIbrahimi
Medical and Pharmacy School, Mohammed V University, Rabat, Morocco, Temara, MA

Robust discrimination of antigen stain in histopathology

Laura Nicolas-Saenz, Paula Martin-Gonzalez, Patricia Garoz, Felipe Calvo, Sara Guerrero-Apizua, Arrate Muñoz-Barrutia
universidad carlos iii, madrid, ES

QuPath – a tool for quality assurance, enhanced user training, and improved reproducibility of image analysis in histopathology research

Zbigniew Mikulski, Katarzyna Dobaczewska, Angela Denn, Sara A McArdle
La Jolla Institute for Allergy and Immunology, La Jolla, US

Segmenting 3D vascular networks with deep learning

Natalie Holroyd, Claire Walsh, Monica Sidarous, Eoin Finnerty, Rebecca Shipley, Simon Walker-Samuel
University College London, London, GB

16:45 18:00 Lecture Room 3

Conference Closing

18:10 18:30 Lecture Room 1 (NEF)

Poster Award Announcement

18:30 18:45 Lecture Room 1 (NEF)

Closing Gala Dinner Reception

19:00 23:00 Le Mabilay (Neway Mabilais, 2 rue de la Mabilais)

9 Jan (Wed)

A dynamic reconstruction of the endocytic machinery in yeast from static superresolution images

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

Design of an "orthogonality-breaking" polarimetric confocal microscope to study intracellular architecture dynamics

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

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

Intracellular dry-mass density measurements of bacteria using quantitative phase microscopy

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

Label-free refractometry and pathogen detection by super-critical angle fluorescence

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

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

Probing cells dynamics with quantitative Dynamic Full-Field OCT

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

Quantitative phase imaging of adherent mammalian cells: a comparison of three different techniques

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

RSMLM: An R-package for pointillist based analysis of single molecule localization microscopy data

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

Single molecule nucleocytoplasmic transport dynamics in live cells

Seoungjun Lee
King’s College London, London, GB

The problem of orientation-induced mislocalizations of single emitters in cryo‐fluorescence microscopy

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

10 Jan (Thu)

CNN based semi-supervised FIB-SEM image segmentation via propagation of learned information from a small subset of a single image stack

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

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

Combining deep learning and active contours opens the way to robust, automated analysis of brain cytoarchitectonics

Nico Scherf, Konstantin Thierbach, Pierre-Louis Bazin, Walter de Back, Filippos Gavriilidis, Evgeniya Kirilina, Carsten Jaeger, Markus Morawski, Stefan Geyer, Nikolaus Weiskopf
Max Planck Institute for Human Cognitive and Brain Sciences, , Germany

Deep learning based detection of cells in 3D Light sheet fluorescence microscopy

Ali Ahmad, Pejman Rasti, Carole Frindel, David Sarrut, David Rousseau
Laboratoire LARIS, Université d'Angers, ANGERS, FR

Deep learning for dense 3D single molecule localization microscopy

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

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

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

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

Image based modeling of leaf development

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

Quantitative evaluation of a next generation scientific CMOS (sCMOS) camera for high fidelity imaging

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

Giacomo Mazzamuto, Francesco Orsini, Matteo Roffilli, Paolo Frasconi, Francesco Pavone, Ludovico Silvestri
European Laboratory for Non-linear Spectroscopy, Sesto Fiorentino, IT

Segmentation of adjacent cells in a C. elegans embryo using a multi-compartment active contour

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

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

11 Jan (Fri)

3D stochastic process simulation for better interpretation of molecular dynamics related to cell wall biogenesis observed with TIRF microscopy

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

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

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

A pyramidal PDE-constrained approach to quasi-static optical elastography

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

Adaptive optics flood-illumination ophthalmoscope with structured illumination capabilities

Yann Lai-Tim
ONERA, Chatillon Cedex, FR

Analysing and quantifying intracellular particles movements in 3D LLSM data

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

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

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

Salvatore Chiantia
University of Potsdam, Potsdam / Golm, DE

Brownian motion using a piezo actuated microscope stage

Nicholas Vickers, Sean Andersson
Boston University, Quincy, US

Challenges in structured illumination microscopy

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

Complex diffusion analysis challenge

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

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

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

Mouna Abdesselem
KU Leuven, Leuven, BE

Large scale feature extraction and image classification for high content screening microscopy

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

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

Mechanistic investigation of mEos4b blinking suggests a strategy to reduce track interruptions in sptPALM

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

Near real time analysis of stress fiber formation in stem cells

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

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

Protein counting in T-cell receptor microclusters

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

Protein counting in localisation microscopy

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

Quantitative 3D geometry for large scale connectomics data

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

Simulator of benchmarking image datasets for time-lapse lightsheet microscopy

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

Spatial analysis of protein or lipid distributions on the surface of spherical beads

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

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

Ultrastructure of endo-lysosomes during cholesterol efflux studied by combined fluorescence and cryo-soft X-ray tomography

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

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

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