The Book of Abstract (including Meet the developpers session Map) is available here.

Day 1: Monday 5th of January 2015

Arrival of Delegates

10h – 10h15

Coffee

10h15- 11h00

Session 1: BioImage Data Analysis Community: Status Quo

• 10h15-10h30: Julien Colombelli, Sébastien Tosi, Perrine Paul-Gilloteaux: Welcome and EUBIAS activity short report
• 10h30- 10h45: Jason Swedlow: Euro-BioImaging Update
• 10h45- 11h00: Jean Salamero: France BioImaging and IPDM node

11h00 -11h30

Keynote 1: Stephan Saalfeld, Janelia Farm. Improving Volume Reconstruction from Large Electron Microscopy Data

11h30- 12h50

Session 2.1: Open Software Showcase

• 11h30- 11h50 Introducing the ImageJ OPS framework ( Johannes Schindelin) Presentation
• 11h50- 12h10 ICY (Fabrice de Chaumont)
• 12h10- 12h30 CellCognition (Christoph Sommer)
• 12h30- 12h50 Knime for image Processing(Christian Dietz)

12h50 – 14h00

Lunch and coffee at Green café

14h00 -15h20

Session 2.2: Open Software Showcase

• 14h00- 14h20 Cell Profiler (Carolina Wählby) Presentation
• 14h20- 14h40 Ilastik (Chong Zhang)
• 14h40- 15h00 ITK/VTK (Jérôme Velut)
• 15h00- 15h20 Tango (Julien Cochennec) Presentation

15h20 – 15h40

Coffee break

15h40 -16h40

Session 3: Sponsor and commercial software bridging open source software session

• 15h40-15h55 AMIRA (FEI): Customizable 3D Processing Tool – Application to Correlative Imaging
• 15h55-16h10 Arivis: fast and unlimited: Visualize, analyze and share microscopic image data without limitations
• 16h10- 16h25 Nikon Lim: Integrating Flexible and Efficient Image Acquisition with Open software Presentation
• 16h25- 16h40 Zeiss ZEN: Open Application Development Tools for Smart Microscopy Presentation

16h40- 17h40

Meet the developers’ session 1
Speakers interact with participants at computer/poster: questions, demos etc… Room plan will be available in the program

17h40- 18h10

Keynote 2: Berndt Rieger, TU Delft. Image processing for super-resolution microscopy Presentation

18h10-19h30

Session 4: Applications/ New Developments from Scientific Computing

• 18h10-18h30 Marc Beal (BioSearch Technologies Inc) : StellarVision Commercial – Breaking the Optical Resolution Barrier Novel Next Generation Synthetic Aperture Optic (SAO) based Fluorescent Microscopy
• 18h30-18h50 Y. Natai (Keio university, Japan) Development of high-speed 3D imaging system with electrically tunable lens
• 18h50-19h10 Jerry Chao (Texas A&M University) FandPLimitTool: An application for calculating limits of accuracy for parameter estimation in single molecule microscopy
• 19h10- 19h30 Jan Brocher (BioVoxxel Inc) The BioVoxxel Image Processing and Analysis Toolbox

19h30-21h

Dinner at Green café

Day 2: Tuesday 6th of January 2015

9h30-10h00

Keynote 3 Ivo Sbalzarini, MPI-CBG, CSBD. Bioimaging requires novel computer vision approaches and open software

10h-11h20

Session 5-1: Cells and particles dynamics analysis

• 10h00-10h20 David Holcman (ENS Paris). BioNewMetrics and stochastics analysis of super resolution single particles trajectories Presentation
• 10h20-10h40 Thierry Pecot, (Inria Rennes). Space Time Representation Imaging and cellular dynamics of molecular complexes Presentation
• 10h40-11h00 Fabrice Cordelière (CNRS Bordeaux). Automated cell tracking and analysis in phase contrast videos (iTrack4U): Development of Java software based on combined mean shift processes
• 11h00- 11h20 David Kim, (College Station, Texas, USA). A Java implementation of MIATool for multidimensional image data analysis

11h20 – 11h50

Coffee break

11h50 – 12h50

Session 5-2: Cells and particles dynamics analysis

• 11h50-12h10 Jean-Yves Tinevez (Institiut Pasteur Paris). MaMuT: a software tool for visualization, tracking and lineaging in large multi-view SPIM images Presentation
• 12h10-12h30 Bo Shuang (Rice University, Houston USA). Fast Step Transition and state indentification (STASI) for discrete single molecule data analysis   Presentation
• 12h30-12h50 Zoltan Cseresnyes (DRFZ Berlin). Fourier transform-based fast characterization of cell shapes as a tool for intelligent classification of cells in intravital microscopy

12h50-14h00

Lunch

14h00-15h40

Session 6: Image Data management and visualization

• 14h00-14h20 Jason Swedlow (Univ Dundee). The Open Microscopy Environment: Open Image Informatics for the Life and Biomedical Sciences
• 14h20-14h40 Raphaël Marée (Univ Liege). Cytomine for data scientists and image analysis software developers
• 14h40-15h00 Aaron Ponti (ETH Zurich). openBIS Importer Toolset (oBIT)    Presentation
• 15h00-15h20 Stephen Taylor (Weatherall Institute of Molecular Medicine, Oxford). Zegami: A Platform for Image Centric Data Exploration
• 15h20-15h40 Elton Rehepaj (Institut Curie Paris) Integration of heterogeneous data sources for high content screening data exploitation and exchange   Presentation

15h40-16h10

Coffee break

16h10 – 17h10

Meet the developers’ session 2

17h10- 17h50

Session 7.1 : Open Community Panel Discussion: Meaning of Open source licensing 
Patrick Moreau (Head of Inria assets) , Jason Swedlow (Univ Dundee and Glencoe Software) , Jérôme Velut (ITK/VTK and Kitware company) , Johannes Schindelin (Fiji) , Fabrice de Chaumont (Icy) , Christian Götze ‎(founder of Arivis company).

Why licensing? The meaning of open source licenses (how to cite, re-use, inherit). How to license in a simple way? How to integrate open source software in a valuation strategy? Why Creative commons could not do the job for software? How to contribute to open source code? Why not always going open source? …

17h50- 18h30

Session 7.2: Open Community Panel Discussion : Reinforcing the BioImage community
Facility representative, image analyst, user (biologist focused on one topic), teachers…
A community of users, analysts and developers: The expectations of each of us and how to work together in the most efficient way to conduct and disseminate cutting edge BioImage analysis.

18h30 – 18h45

Concluding remarks, summary of discussions and perspectives, organization of the next event.