Open Microscopy Environment Centre for Gene Regulation & Expression School of Life Sciences, University of Dundee Dundee, Scotland, UK OME and OMERO ImageJ.

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Presentation transcript:

Open Microscopy Environment Centre for Gene Regulation & Expression School of Life Sciences, University of Dundee Dundee, Scotland, UK OME and OMERO ImageJ conference, Madison 2015 Petr Walczysko University of Dundee The OME Consortium

Outline o Brief Overview o Scientific Data paradigm o What is OME o What is OMERO o ImageJ and OMERO o Questions 1

Brief Overview o Founded in 2000 o Funded by Wellcome Trust, BBSRC, EPSRC o International consortium of software development sites o Open Source (mainly GPL) 2

The Standard Paradigm 3

The “Scientific Data” Paradigm 4 Gray et al, 2005, Scientific Data Management in the Coming Decade, Microsoft Research

OME : What We Do 5 Open, exchangeable file formats Open Image Management Platform

The Extensible OMERO platform 6

ImageJ and OMERO 7

OMERO and ImageJ: next steps o Java gateway (available in v5.2) o Re-usable UI components o ImageJ2: Server side integration (started by C. Rueden)Server side integration 8

Thank you 9

OME Consortium o Dundee – Jason Swedlow, Colin Blackburn, Jean-Marie Burel, Mark Carroll, Gus Ferguson, Helen Flynn, Kenny Gillen, Roger Leigh, Simon Li, Dominik Lindner, Josh Moore, Will Moore, Balaji Ramalingam, Aleksandra Tarkowska, Petr Walczysko o University of Wisconsin, Madison (LOCI) - Kevin Eliceiri, Curtis Rueden, Mark Hiner o UT Southwestern – Gaudenz Danuser, Sebastian Besson o Oxford – Ilan Davis, Douglas Russell o CRS4 - Gianuigi Zanetti, Gianmauro Cucurru, Simone Leo, Luca Lianas o Edinburgh – Richard Baldock, Bill Hill, Jianguo Rao o Carnegie-Mellon – Robert Murphy, BK Cho, Ivan Cao-Berg o Imperial – Paul French, Chris Dunsby, Ian Munro, Yuriy Alexandrov o NIA, NIH – Ilya Goldberg, Chris Coletta o Pasteur – Spencer Shorte, Sebastien Simard, Anne Danckaert o EBI – Gerard Kleywegt, Ardan Patwardhan, Ingvar Lagerstedt o Glencoe Software – Chris Allan, Joshua Ballanco, Andreas Knab, Melissa Linkert, Chris MacLeod, Josh Moore, Emil Rozbicki, Liza Unson, Rebecca Walker, Wilma Woudenberg 10