Scientific Programme


Confirmed Keynote speakers

Anne Carpenter -  Broad Institute of MIT and Harvard, Boston - USA

Fred Hamprecht - University of Heidelberg, Germany

Christophe Zimmer - Institut Pasteur, Paris - France

Confirmed Invited speakers

Anatole Chessel - École Polytechnique, Palaiseau (Paris) - France

Lucy Collinson - The Francis Crick Institute, London - UK

Alexandre Dufour - Institut Pasteur, Paris - France

Martin Horn - Univeristy of Konstanz, Germany

Florian Jug - Max Plank Institute for Cell Biology & Genetics, Dresden - Germany

Michal Kozubek - Masaryk University, Brno - Czech Republic

Nadine Peyriéras - CNRS - Institut de Neurobiologie Alfred Fessard, Gif s/Y. - France

Stephan Preibisch - Berlin Institute of Medical Systems Biology, Germany

Anne-Lise Routier-Kierzkowka  MPI for Plant Breeding Research, Cologn - Germany

Curtis Rueden - LOCI, University of Wisconsin, Madison - USA

Daniel Sage - Ecole Polytechnique Fédérale de Lausanne (EPFL) - Switzerland

Jean-Baptiste Sibarita - Interdisciplinary Instittue for Neuroscience (IINS), Bordeaux - France

Pavel Tomancak - Max Plank Institute for Cell Biology & Genetics, Dresden - Germany



Provisional Schedule (Table)

(more information coming and changes still expected)


Wednesday 15th February
15h Registration Coffee, Set up Posters
16h Welcome Welcome
16h10 Keynote Anne Carpenter - Broad Institute, Boston [Invited] "Information in images: Targeting diseases & characterizing compounds via CellProfiler and Cell Painting"
17h Flash Talks (of posters) Perrine Paul-Gilloteaux eC-CLEM: Flexible multidimensional registration software for correlative microscopies with refined accuracy mapping
Jose Miguel Serra Lleti Developing a software tool for multiple targeting and automated acquisition in correlative light-electron microscopy.
Christian Tischer ImageJ Plugins for Efficient Streaming, Tracking and Adaptive Cropping of TeraByte-sized Data Sets
Marlies Verschuuren Deep coverage image analysis of morphofunctional connectivity in neuronal networks
Marta Alabrudzinska Intravital imaging and 4D quantification of tumor growth and the tumor vasculature
Lassi Paavolainen Image-based phenotypic profiling of patient-derived cancer cells
Winnok De Vos Cellular Redox Profiling Using Deep Coverage Microscopy
Hugo Botelho Modular high content image analysis workflows leveraging biology and biomedicine
Emilio Gualda Beyond 3D imaging: virtual reality & colour 3D printing of microscopy 3D
Chong Zhang/Carlos Yagüe The Rocket App: a " exible, modular, Cloud-based platform for the management of heterogeneous data/information from multiple acquisition/tools for biomedical and clinical research
17h30 - 19h30 - Open ended Hands On Demos / Workshops Companies to explain and demo their latest developments in Analysis and IT solutions, Talks and/or Booth format. Confirmed exhibitors: GE Healthcare, Arivis Confirmed exhibitors: GE Healthcare, Arivis, Carl Zeiss
19h15 -21h OSS Lounge: Open Source Software & -Tools Forum Experts and/or developers available to demo the latest updates and functionalities of a broad selection of Open Software tools. Booth/digital poster format Confirmed OSS/tools represented: IJ/IJ2/Fiji, CellProfiler, Icy, ilastik, KNIME, MorphoDynaMX, SR-Tesseler, CATMAID-ONTO, Cytomine, OpenImadis, Bioemergences web platform, SuRVos, and more...
21h Free Evening Free Evening
Thursday 16th February
9h00 Keynote Fred Hamprecht - University of Heidelberg [Invited] "Shallow and Deep Learning for Bioimage Analysis"
9h50 NEUBIAS State of Affairs of the Community Reports on the progress and Deliverables of NEUBIAS, e.g. Events, Webtools development, Career Path, Open Publications, Outreach, Strategy and Future
10h40 Coffee Coffee
11h10 Session 1
Session 1 Anne-Lise Routier-Kierzkowska [Invited] "MorphoDynamX: from 4D image analysis to computational modeling"
Daniel Sage [Invited] "Computational methods for high resolution 3D fluorescence microscopy"
Nadine Peyriéras [Invited] "From 3D+time imaging data to digital and virtual specimens"
Jean-Baptiste Sibarita [Invited] "Toward quantitative multicolor single-molecule localization microscopy"
12h30 Lunch ... and Posters Posters - Part I
or MC meeting On invitation (with lunch...)
14h15 NEUBIAS "Call For Help" / "Shout Your Problem" / "Analysis Clinics" Interactive Session: Life Scientists and Bioimage Analysts facing Image Analysis Roadblocks in their research projects can submit their problem and developers / Analysts will address them, build and benchmark Solutions
15h50 Session 2 Session 2
Michal Kozubek [Invited] "Virtual Cell Imaging: Synthetic Image Datasets for Benchmarking Bioimage Analysis Methods"
Pavel Tomancak [Invited] "CATMAID-ONTO: Ontology-based online analysis of large image datasets"
Manuel Schölling "How to make Image Segmentation with Deep Learning available for Everyone"
Nicolas Chiaruttini "Lipid membranes and surface reconstruction - a biologically inspired method for 3D segmentation"
17h Coffee
17h30 Session 3
Session 3 Florian Jug [invited] "Big Data and 3D Visualization"
John Bogovic "Much Better Stitching"
Hugo Pereira "OPenT - simplified acquisition and processing of optical tomography datasets"
18h20 Session 4 Open Software Showcase
Session 4 Curtis Rueden [Invited] "What's New in ImageJ2 ? "
Martin Horn [Invited] "Image Analysis with KNIME"
Alexandre Dufour [Invited] "Icy: the next-generation open bio-imaging platform"
Raphaël Marée "Collaborative analysis of multi-gigapixel imaging data using Cytomine"
19h40 Drinks ... and Posters Posters - Part II
20h45 Departure for Dinner included for all Outside Venue (TBA)
Friday 17th February
9h00 Keynote Christophe Zimmer - Institut Pasteur [Invited] "Expanding single molecule localization microscopy in 3D and time"
9h50 NEUBIAS STSM Reports 3x10' talks, experience and report of Short Term Scientific Missions funded by NEUBIAS. Confirmed speakers: Laure Plantard, STSM grantee (CFIM, Univ. Copenhagen); Martin Jones, Host Lab (Francis Crick Inst.)
10h20 Coffee
10h50 Session 5
Session 5 Lucy Collinson [Invited] "Challenges in Image Analysis for 3D Electron Microscopy and Correlative Imaging"
Stephan Preibisch [Invited] "Reconstruction of large tiled image acquisitions using ImgLib2 and BigDataViewer"
Michele C Darrow "Super-Region Volume Segmentation (SuRVoS) Workbench for Segmentation of Three-Dimensional Cellular Data"
Natasa Sladoje "Detection and enhancement of objects in low resolution transmission electron microscopy images for multi-scale imaging and structural analysis"
12h00 NEUBIAS Developers, Analysts, Life Scientists Panel discussion: How to improve Bioimage Analysis knowledge exchange within the Bioimaging Ecosystem
13h00 Lunch
13h45 Gold Sponsor Florian Bossard (GE Healthcare) Multiparameter phenotypic pro! ling for predictive toxicity using High Content Analysis
14h05 Session 6
Session 6 Anatole Chessel [Invited] "High content microscopy pipelines and algorithms for a systemic study of polarity"
Anne Beghin When High Content Screening meets super-resolution microscopy
Josh Moore The Image Data Resource: a platform for publishing, integrating and mining imaging-derived biological data at scale
Tania Perestrelo Quantification of Embryonic Stem cell Pluripotency through Image-based Analysis Software
Aliaksandr Halavatyi AutoMicTools package to manage Automated Feedback Microscopy data acquisition and analysis
Ricardo Henriques Democratising live-cell high-speed low-illumination super-resolution microscopy through Super-Resolution Radial Fluctuations
15h40 NEUBIAS Life of a BioImage Analyst: Handling multiple data sources & workflows Success Stories, guided panel discussions on the role and Career Path of Bioimage Analysts in Life Science
16h30 Closing Remarks - End of the Symposium

Topics for scientific Sessions

Feature Extraction Validation and Modelling

High-Throughput Analysis and Model systems

Storage and Biological Big Data projects

Device Integration, Intelligent Imaging and Imaging of Delicate or Rare Biological Events

Multidimensional datasets and visualization



Gala dinner - how to get to the gala dinner restaurant: