QBI 2020 Conference Posters

6 Jan - 9 Jan

# 270

Glycine receptor copy numbers and packing density at spinal cord synapses revealed by quantitative dual-colour super-CLEM

Stephanie Maynard, Olivier Gemin, Philippe Rostaing, Antoine Triller, Christian G Specht

# 280

Filament Sensor – A tool for 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

# 285

Untying the Gordian Knot: Spatiotemporal Single Particle Tracking using Point Cloud Reduction

Jorge Zepeda O, Logan D Bishop, Chayan Dutta, Suparna Sarkar-Banerjee, Christy Landes
Rice University,

# 294

Multivariate spectral analysis for identification of spectral features of peripheral nerves using Raman microspectroscopy

Takeo Minamikawa, Yoshiki Terao, Ryosuke Shiomi, Takeshi Yasui
Tokushima University,

# 295

Joint denoising deconvolution

Jerome Boulanger, Nick Barry, Suman Kumar Maji
MRC-LMB, Cambridge, US

# 301

Simple, compact and robust phase and fluorescence microscope for statistical analysis of cell cycle

Ondrej Mandula, Jean-Philippe Kleman, Francoise Lacroix, Cédric Allier, Daniel Fiole, Sophie Morales
CEA-Leti, Grenoble Cedex 9, FR

# 302

Phase Retrieval and Point Spread Function Design for Single Molecules Based on the Vectorial Diffraction Model

Boris Ferdman, Lucien Weiss, Elias Nehme, Yoav Shechtman
Technion – Israel Institute of Technology, Adi, IL

# 303


Sylvain Prigent, Charles Kervrann, Jean SALAMERO
Inria, Rennes, FR

# 306

3D tracking of endocytic and exocytic events using lattice light sheet microscopy

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

# 324

An image-based machine learning approach as screening tool of pathological calcium oxalate crystallization inhibitors

Anna Kletzmayr, Jean-Christophe Leroux, Mattias E. Ivarsson
ETH Zurich,

# 326

Simulation and implementation of digital micromirror devices (DMDs) for cost-effective structured illumination microscopy

Alice Sandmeyer, Mario Lachetta, Hauke Sandmeyer, Wolfgang Hübner, Thomas Huser, Marcel Müller
Bielefeld University, Leuven, BE

# 330

Conquering the tumour microenvironment: Using image analysis and spatial statistics to map the phenotypic heterogeneity of human cancers

Jack Robertson, Guillaume Potdevin, Brenda Beatriz Garcia Iglesias, Fargol Mazaheri, Maria Udriste, Stephanie Ling, Edmond Wong, Richard Goodwin, Hadassah Sade, Jaime Rodriguez Canales, Guenter Schmidt, Andrew Pierce
Astra Zeneca,

# 331

Organization and dynamics of Escherichia coli outer membrane proteins

Patrick George Inns, Nicholas Housden, Joanna Szczepaniak, Renata Kaminska, Colin Kleanthous
University of Oxford,

# 337

Automated lens-free, fluorescent microscopy to study cell populations

Dorothee Kraemer, Cédric Allier, Lionel Hervé, Kiran Padmanabhan, Adlen Foudi, Sophie Morales

# 342

Multi-parameter Single Molecule Spectroscopy Imaging Reveals Intra- and Inter- Molecular Conformations of HIV-1 Envelope on Native Viruses

Irene Carlon-Andres, Sergi Padilla-Parra
University of Oxford,

# 343

Towards multi-dimensional FLImP

Michail Vrettas, Daniel James Rolfe, Ben Davis

# 345

User-friendly Building of Reconstruction Algorithms with GlobalBioIm

Laurène Donati, Emmanuel Soubies, Michael Unser

# 347

SpineJ: A software tool for quantitative analysis of nanoscale spine morphology

Florian Levet, Jan Tonnesen, Valentin Nägerl, Jean-Baptiste Sibarita
Interdisciplinary Institute for NeuroScience, Bordeaux, FR

# 355

High density 3D localization of fluorescent molecules

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

# 360

DeepSTORM3D: Deep learning for dense 3D single molecule localization microscopy

Elias E Nehme, Daniel Freedman, Racheli Gordon, Boris Ferdman, Lucien Weiss, Onit Alalouf, Reut Orange, Tomer Michaeli, Yoav Shechtman
Technion - Israel Institute of Technology, Haifa, IL

# 362

Creating interactive, explorable simulations of cell migration at tissue scale using CPMjs

Inge M N Wortel, Johannes Textor
Radboud Institute for Molecular Life Sciences,

# 363

High-Throughput Structured Illumination Microscopy (HiT-SIM)

Robin Van den Eynde
KU Leuven,

# 364

Quantitative comparison of camera technologies for cost-effective super-resolution optical fluctuation imaging (SOFI)

Robin Van den Eynde
KU Leuven,

# 365

Quantitative image-analysis of organoids with high-throughput digital holography microscopy

Thanh-an Pham, Nathalie Brandenberg, Sylke Hoehnel, Benjamin Rappaz, Michael Unser, Matthias Lütolf, Daniel Sage
EPFL, St-Sulpice, CH

# 370

Localization microscopy shows the 3D organization of LPS in the Escherichia coli outer-membrane

Sandip Kumar
University of Oxford,

# 372

An LPV approach to the estimation of time-varying Single Particle Tracking models

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

# 374

The dual approach to non-negative super-resolution

Bogdan Toader
University of Cambridge,

# 375

Model-based Imaging Biomarkers for Non-rectangular Regions of Interest

ShengLi Tzeng
National Sun Yat-sen University,

# 377

Feature representations for the identification of mRNA localization patterns from smFISH data

Arthur Imbert, Edouard Bertrand, Florian Mueller, Thomas Edgar Walter
Mines ParisTech,

# 378

Axial stimulated emission depletion spectroscopy to study lipid dynamics

Aurélien Barbotin, Iztok Urbancic, Martin Booth, Christian Eggeling, Erdinc Sezgin
University of Oxford, Oxford, GB

# 382

Method of Synthetic Motion for Testing Single Particle Tracking Microscopes

Nicholas Vickers, Sean Andersson
Boston University, Quincy, US

# 383

Quantitative analysis of the structural organization and diffusion properties of a bacterial biofilm matrix

Valentin Dunsing, Tobias Irmscher, Stefanie Barbirz, Salvatore Chiantia
University of Potsdam, Berlin, DE

# 385

Single-Cell / Single-Molecule microscopy on endogenous pulsed-labeled p53 dissects the regulation layers involved in its activation

Eugenia Cammarota, Alessia Loffreda, Matteo Mazzocca, Valeria Caiolfa, Moreno Zamai, Carlo Tacchetti, Davide Mazza
Ospedale San Raffaele,

# 389

A comprehensive system calibration protocol for widefield fluorescence microscopy

Sreevidhya Ramakrishnan, Jerry Chao, Anish V Abraham, Sungyong You
Texas A&M University, , United States

# 395

Analysis of Nieman Pick C2 Protein in Regulation of Intracellular Membrane Transport by Combined and Correlative Fluorescent and Soft X-ray Microscopy

Alice Dupont Juhl, Daniel Wüstner
The University of Southern Denmark, Årslev, DK

# 400

Edge correction in density estimation from repeated point patterns in biological imaging

Jasmine Burguet, Philippe Andrey
INRA, Versailles, FR

# 404

Quantitative Analysis of Spatial-Temporal Imaging of Auxin to Cytokinin Ratio During Nodule Development in Soybean (Glycine max) by Two-Photon Induced Fluorescence

Ni Putu Dewi Nurmalasari, Paul Gaillard, Senthil Subramanian, Steve Smith
South Dakota School of Mines and Technology,

# 405

Investigating spatial relationships of host-associated microbes using correlative light and electron microscopy

Martin Thomas Jahn
GEOMAR Helmholtz Centre for Ocean Research,

# 410

3D TIRF nanoscopy with sub-10 nm resolution

Sabrina Simoncelli, Alan Szalai, Brueno Siarray, Jeronimo Lukin, David Williamson, Nicolas Unsain, Damian Refojo, Alfredo Caceres, Mauricio Pilo-Pais, Guillermo Acuna, Dylan Owen, Fernando Stefani
King's College London,

# 415

4Pi aberration correction in single molecule switching microscopy

Jingyu Wang, Martin Booth, Ian M Dobbie, Jacopo Antonello, Mick A Phillips, Richard M Parton, Chao He
University of Oxford,

# 416

A universal framework for sensorless adaptive optics

Qi Hu, Jingyu Wang, Matthew Wincott, Jacopo Antonello, Martin Booth
University of Oxford,

# 417

Implementation of Confocal Adaptive Optical Microscopy for Clinical Tissue Analysis

Jiahe Cui, Raphael Turcotte, Karen M Hampson, Martin Booth
University of Oxford,

# 424

Deciphering genuine transient pauses in super-localized trajectories of single-molecule tracers

Jaladhar Mahato, Arindam Chowdhury
Indian Institute of Technology Bombay,

# 427

Calibration of a Remote Focusing Microscope Using Deflectometry

Syed Asad Hussain, Karen M Hampson, Matthew Wincott, Jacopo Antonello, Martin Booth
University of Oxford,

# 430

Quantification of DNA by Mass Photometry

Yiwen Li, Katharina Haeussermann, Weston Struwe, Philipp Kukura
University of Oxford,

# 431

Site-selective visualization and tracking of DNA methylation in fixed cells

Krystian Ubych, Paco Fernandez-Trillo, Clare Davies, Robert Neely
University of Birmingham,

# 433

Ultrashort dual colour laser at 1.55 and 1.88 μm for the detection of tumour through Raman imaging

Syed Asad Hussain
University of Oxford,

# 435

ConCoR: A software pipeline for high-throughput image analysis of time-dependent colocalization data

Greg Bass, Isabelle Glauser, Jenny Chia, Anne Verhagen, Steve Dower, Milica Ng
CSL Innovation,

# 438

FCS and anomalous diffusion model as tools to monitor molecular interactions in living cells

Alessandro Furlan, Aymeric Leray, Melanie Henry, Mariano Gonzalez Pisfil, Dorian champelovier, Thorsten Wohland, Corentin Le Nezet, Olivier Benbsude, Bernard Vandenbunder, Gabriel Bidaux, Laurent HELIOT

# 442

Dynamic contrast for micro- and macro-scale multiplexed fluorescence imaging against autofluorescence and ambient light

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

# 443

Statins – not just about cholesterol reduction

Dilip Shrestha
University of Oxford,

# 448

Epidermal growth factor receptor localization and dynamics inside nanodomains across different cell types

Thuy Thi HOANG, Nicolas Olivier, Hélène Lazareth, Pierre-Louis Tharaux, Cedric Bouzigues, Antigoni Alexandrou
école polytechnique,

# 452

ALFRED: user-friendly approach to obtain length and curvature and its application to microtubule networks in nerve cells

Beatriz Costa-Gomes, Nuno Nobre, André Voelzmann, Matthias Heil, Andreas Prokop
University of Manchester,

# 455

3D Model Building Pipeline for Light-Sheet Imaging of Hippocampal Neurons for Simulation and Analysis of Calcium Dynamics

James Barnard Wilsenach, Charlotte M. Deane, Gesine Reinert
University of Oxford,

# 457

Extending molecular counting by photon statistics

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

# 458

Cell segmentation and tracking for mathematical modelling of cell motility

Rituparna Sarkar, Pascal Bochet, Maria Manich, Aleix Boquet-Pujadas, Nancy Gullien, Elisabeth Labruyere, Jean-Christophe Olivo-Marin
Institute Pasteur,

# 462

Investigating membrane proteins interactions and membrane mimetic systems using mass photometry

Anna Olerinyova, Philipp Kukura, Weston Struwe, Adar Sonn Segev
University of Oxford,

# 465

Adaptive optics in bioimaging for improved quantitative exploitation of microscopy images

Audrius Jasaitis, Cynthia Veilly, Fabrice Harms, Xavier Levecq
Imagine Optic,

# 467

Characterization of Flat-Fielding Systems for Super-Resolution Microscopy

Khalid Ibrahim, Dora Mahecic, Suliana Manley

# 468

Quantitative imaging of sparse targets with DNA-PAINT

Alexander H Clowsley, Christian Soeller
The University of Exeter,

# 471

Towards a molecular mechanism of dynamin polymerization with mass photometry

Manish Singh Kushwah, Philipp Kukura
University of Oxford,

# 479

Biolapse Toolbox

Léo Lebrat, Valentin Debarnot, Thomas Mangeat
CSIRO Health and Biosecurity Flagship: The Australian e-Health Research Centre Brisbane, QLD, Australia,

# 480

Single-molecule and super-resolution investigation of chemokine receptor behaviour within the T cell immunological synapse

James Felce, Michael Loran Dustin
University of Oxford,

# 483

ICYTOMINE: A User-Friendly Tool for Reproducible Analysis of Gigapixel Images

Daniel Felipe González Obando, Diana Mandache, Jean-Christophe Olivo-Marin, Vannary Meas-Yedid
Institut Pasteur,

# 488

Full field interferometry for characterizing and counting biotic nanoparticles

Samer Alhaddad, Yasmina Fedala, Ignacio Izeddin, Claude Boccara, Martine Boccara
ESPCI, PSL University, CNRS,

# 490

Quantitative mapping of fluorescently tagged ribosomes throughout the cell cycle of S. cerevisiae using FCS-calibrated imaging

Madlen Luckner, Gabriele Schreiber, Edda Klipp, Salvatore Chiantia
University of Potsdam,

# 491

Versatile uniform illumination method toward quantitative single molecule localization microscopy

Adrien - Mau, Nicolas Bourg, Sandrine Leveque-Fort
Ismo / Abbelight,

# 499

Computational analysis of filament polymerization dynamics in cytoskeletal networks

Paulo Caldas, Christoph Sommer, Philipp Radler, Martin Loose
Institute of Science and Technology Austria,

# 505

Measuring differential diffusion rates of distinct protein states by sptPALM imaging in live microbial cells

Bartosz Turkowyd
Max Planck Institute for terrestrial Microbiology,

# 507

Metadata and Performance Tracking for Fluorescent Microscopes III - MetaMax

Maximiliaan Huisman, Carlas Sierd Smith, Mathias Hammer, Russell Ulbrich, David Grunwald
UMass Medical School, WORCESTER, US

# 508

Metadata and Performance Tracking for Fluorescent Microscopes I - Metadata

David Grunwald, Mathias Hammer, Alex Rigano, Maximiliaan Huisman, Farzin Farzam
Umass Medical School, Worceser, US

# 509

Metadata and Performance Tracking for Fluorescent Microscopes II - Optics

David Grunwald, Mathias Hammer, Maximiliaan Huisman, Farzin Farzam
Umass Medical School, Worceser, US

# 512

Towards Quantitative 3D Super-Resolution Correlative Light-Electron Microscopy

Jonas Euchner, Klaus Yserentant, Dirk-Peter Herten
Heidelberg University,

# 515

Pixelwise H-score: a novel digital image analysis-based metric to quantify membrane biomarker expression from IHC images

Sripad Ram
Pfizer, Inc., , United States

# 531

Label-free intracellular dynamics studies using quantitative phase imaging with a high definition wavefront sensor

Roman Zinchuk, Benoit Wattellier, Antoine Federici, Julien Savatier, Serge Monneret
Aix-Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel,

# 533

Predicting Patient Outcome from Immunohistochemistry Images by Quantifying Spatial Distribution of Immune Cells

Morgan Oneka, Jenny Lazarus, Souptik Barua, Arvind Rao, Timothy Frankel
University of Michigan,