Location & dates EMBL Heidelberg, Germany 6 - 8 Dec 2018
Deadlines Registration closed Abstract submission closed

Programme

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Day 1 - Thursday 6 December 2018
TimeSpeaker
11:00 - 12:45 Arrival and registration
12:45 - 13:00 Welcome and opening remarks
13:00 - 13:45

ImageJ
Curtis Rueden - Laboratory for Optical and Computational Instrumentation, USA
Tobias Pietzsch - Max Planck Institute of Molecular Cell Biology and Genetics, Germany
Christian Dietz - KNIME, Germany

13:45-15:00

Session 1 - Light microscopy 1
Chair:
Pavel Tomancak, Max Planck Institute of Molecular Cell Biology and Genetics, Germany

13:45-14:15 Using morphological profiling to extract the most from your images
Beth Cimini - Broad Institute, USA
14:15-14:45 Title TBC
Jeremy Freeman - Chan Zuckerberg Initiative, USA
14:45-15:00 Quantitative imaging of motile cilia to investigate fluid flows and chirality in the left-right organizer
Willy Supatto - Ecole polytechnique, CNRS , INSERM, France
15:00-15:30 Coffee break and Meet the Invited Speaker: Beth Cimini, Jeremy Freeman
15:30-18:00 Session 2 - Machine learning
Chair:
Anna Kreshuk EMBL Heidelberg, Germany
15:30-16:00 The road to deeper ilastik
Anna Kreshuk EMBL Heidelberg, Germany
16:00 - 16:15

KNIME Image Processing: Status Quo and Future Directions
Christian Dietz - KNIME, Germany

16:15 - 16:30 Introducing Yapic: A New Tool for Biologists to Perform Complex Image Segmentation with Deep Learning
Christoph Möhl - German Center for Neurodegenerative Disease (DZNE), Germany
16:30 - 17:00 Coffee break
17:00 - 17:30 Content-Aware Image Restoration for Light and Electron Microscopy Facilitates Quantitative Data Analysis
Florian Jug - Max Planck Institute of Molecular Cell Biology and Genetics, Germany
17:30 - 17:45 Automated Annotation of C. Elegans: How much Training Data is Needed?
Dagmar Kainmueller - Berlin Institute of Health, Max Delbrück Center for Molecular Medicine, Germany
17:45-18:00 Flash talks (1 slide/2mins each)
Albert #23 / Botelho #31/ Bujak #35 / Meyenhofer #79 / Schmidt #95
18:00-19:30

Poster Session 1 (odd numbers)

19:30

Free evening

Day 2 - Friday 7 December 2018
TimeSpeaker
09:00-10:15
Session 3 - Light microscopy 2
Chair:
Florian Jug - Max Planck Institute of Molecular Cell Biology and Genetics, Germany
09:00-09:30

Correlative Light-Electron Microscopy Based High Resolution Nuclear Model of C. elegans Dauer
Ella Bahry - Max Delbrück Center for Molecular Medicine, Germany

09:30-10:00 NanoJ-SQUIRREL: quantitative mapping and minimisation of super-resolution optical imaging artefacts
Siân Culley  - University College London, UK
10:00-10:15

BigStitcher: Reconstructing high-resolution image datasets of cleared and expanded samples
Stephan Preibisch - Max Delbrück Center for Molecular Medicine, Germany

10:15-10:45 Coffee break and Meet the Invited Speaker: Stephan Preibisch
10:45-12:00

Session 4 - Electron Microscopy analysis
Chair:
Christian Tischer - EMBL Heidelberg, Germany

10:45-11:15

Mapping and analyzing neuronal circuits with CATMAID software
Albert Cardona Janelia Research Campus, USA

11:15-11:45

N5, ImgLib2-Cache, BigDataViewer, and Spark: my favorite open-source eco-system for super-large image data
Stephan Saalfeld - Howard Hughes Medical Institute, USA

11:45-12:00

webKnossos: efficient online 3D data annotation
Norman Rzepka - scalable minds GmbH, Germany

12:00-13:30

Lunch

13:30-15:00

5 Parallel Workshops - Session 1

15:00-15:30

Coffee break and Meet the Invited Speakers: Albert Cardona, Stephan Saalfeld

15:30-16:55 5 Parallel Workshops - Session 2
17:00-17:15

NEUBIAS talk
Julien Colombelli, IRB Barcelona, Spain

17:15 - 17:30

A natural-language based syntax for animating 3D/4D imaging data
Benjamin Schmid - Friedrich-Alexander University of Erlangen-Nuremberg, Germany

17:30 - 17:45

Mastodon -- a large-scale track-editing framework for Fiji
Tobias Pietzsch - Max Planck Institute of Molecular Cell Biology and Genetics, Germany

17:45-18:00

Flash Talks (1 slide / 2mins each)
Arzt #25 / Cheeseman #41 / Günther #54 / Jain #63 / Mais #75

18:00-19:30

Poster Session 2 (even numbers)

19:30-21:30

Conference Dinner

21:30-00:00

Conference Party

Day 3 - Saturday 8 December 2018
TimeSpeaker
09:00-10:15 Sesion 5 - Atlas projects
Chair:
Christophe Zimmer - Institut Pasteur, France
09:00-09:30

Deep learning as a tool in microscopy data analysis and digital pathology
Carolina Wählby - Uppsala University, Sweden

09:30-10:00 Archives, Resources and Atlases: An OME Perspective on Structuring Data for the Long Haul
Josh Moore - University of Dundee, UK
10:00-10:15 The mitotic cell atlas
Jean-Karim Heriche - EMBL Heidelberg, Germany
10:15-10:45

Coffee break and Meet the Invited Speaker: Josh Moore, Virginie Uhlmann, Christoph Zimmer

10:45-12:00

Session 6 - Tools and Methods
Josh Moore - University of Dundee, UK

10:45-11:15

New computational lenses for single molecule super-resolution microscopy
Christophe Zimmer - Institut Pasteur, France

11:15-11:45

Title TBC
Virginie Uhlmann - EMBL-EBI, United Kingdom

11:45-12:00

Example of an end-to-end application of imaging and image analysis to solve a biological problem
Pavel Tomancak, Max Planck Institute of Molecular Cell Biology and Genetics, Germany

12:00-12:15

Closing remarks and Poster Prizes

12:15-12:45

Packed lunch and departure

12:45 Bus departures downtown and to Frankfurt Airport