A National Research Infrastructure for Biological Imaging

EU-LIFE symposium on Big Microscopy Data Management

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Date and location
Date: 17 November 2017
Time: 9am-6pm
Location: Friedrich Miecher Institute, room 5.30
The symposium is free of chargeOrganisers
Christel Genoud and Laurent Gelman

Contact person

Preliminary Program

09:00 09:15 Welcome
09:15 09:35 Dean Flanders (Head of IT, FMI): Coping with Large Life Science Data Sets from Acquisition to Archive
09:35 09:55 Urs Ziegler (University of Zurich): VM infrastructure for image processing at the University of Zurich
09:55 10:15 Enrico Tagliavini (IT, FMI): High performance storage fundamentals

10:15 10:30 Coffee break

10:30 10:50 Henry Luetcke (ID SYS, ETHZ): Distributed workflows for scalable analysis of large imaging datasets.
10:50 11:10 Katrin Volkmann (FAIM, FMI): High-Contect Screening Workflows at the FMI
11:10 11:30 Urs Mayr (Group Liberali, FMI): TissueMap, an image-processing platform for high-performance computing infrastructures

11:30 13:00 Lunch

13:00 13:20 Andrzej Rzepiela (ETH, Zurich): Phaedra – handling, analyzing, and visualizing HCS data
13:20 13:40 Stephan Gerhard (Group Friedrich, FMI):, an image processing and analytics platform for large-scale EM connectomics
13:40 14:00 Michael Stadler (Head of Bioinformatics, FMI): Identification of cell types from single cell transriptomics data

14:00 14:15 Coffee break

14:15 14:35 Christian Tischer (AMLF, EMBL): Plugins to analyze and process big datasets in ImageJ
14:35 14:55 Thorsten Falk (IT, Uni Freiburg im Breisgau): Fully convolutional neural networks for 5-D microscopic image analysis
14:55 15:15 Raphaël Thierry (FAIM, FMI): Neural networks and Machine Learning for Image Classification

15:15 15:30 Coffee break

15:30 15:50 Andreas Schenk (FAIM/Group Thomä, FMI): Big data analysis in Structural EM
15:50 16:10 Fabian Svara and Jörgen Kornfeld (ariadne-service): Combining human and artificial intelligence for high-throughput image annotation
16:10 16:30 Dieter Goehlmann (Bitplane): Imaris 9 – New Billion Triangle Surface Model. Analysis of huge datasets using multi resolution surface segmentation
16:30 16:50 Maria Marosvölgyi (Arivis): Interactive Visualization and Analysis of Large Image Data via Desktop, Web and Virtual Reality

16:50 17:00 Closing remarks
17:00 – Apero in Basel (optional)


• September 25, 2017