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Discovery of Image Analysts - Eubias & Biii ELMI 2015 Discovery of Image Analysts - EuBIAS & Biii - Kota Miura ([email protected]) EMBL Heidelberg National Institutes of Natural Sciences, Tokyo National Institute of Basic Biology, Okazaki ELMI 2015 Post-Imaging Bottleneck Imaging -> Experiments -> Microscopy -> Image Processing, Analysis -> Results ELMI 2015 Post-Imaging Bottleneck Imaging -> Experiments -> Microscopy -> Image Processing, Analysis -> Results Bottleneck! ELMI 2015 Publications with ImageJ TextText Fiji: 700 commands source: pubmed ELMI 2015 Survey Mar. 2015 Text 1800 people answered in three days ELMI 2015 Survey Mar. 2015 ... more will be published somewhere ELMI 2015 Authors / Paper Increasing source: PubMed ELMI 2015 BioImage Analysis - good old 90’s - Biological Problems Image Processing & Analysis Tools, Functions, e.g. NIH Image, Metamorph Libraries ELMI 2015 BioImage Analysis - good old 90’s - Biological Problems Image Processing & Analysis Tools, Functions, e.g. NIH Image, Metamorph Libraries ELMI 2015 BioImage Analysis 00’s -: Developer’s Eforts Biological Problems more complex image sets, more techniques Image Processing & Analysis Tools, Functions, Libraries more packages, algorithms, libraries ELMI 2015 BioImage Analysis Biological Problems Image Processing & Analysis Tools, Functions, Libraries Which one should be used? ELMI 2015 BioImage Analysis Biological Problems Image Processing & Analysis Tools, Functions, Libraries ELMI 2015 Biological Problems Image Processing & Analysis Tools, Functions, Libraries 2nd Round... Which combination should be used? ELMI 2015 Enlarging the Bottle Neck Biological Problems BioImage Analysts Developers Biologists Physicists Electric Engineers Image Processing and Mathematician Analysis Programmers ELMI 2015 So many diferent knives from blade smith ... Sushi master chooses the right knife at each step... ... Results in beautiful sushi. ELMI 2015 So many diferent knives from blade smith ... Sushi master chooses the right knife at each step... ... Results in beautiful sushi. ELMI 2015 So many diferent knives from blade smith ... Developers & Software Packages Sushi master chooses the right knife at each step... Image Analysts ... Results in beautiful sushi. Great Results! ELMI 2015 Euro-BioImage Analysis Symposium (EuBIAS) Barcelona, Oct 9 - 11, 2013 http://biii.info/eubias ELMI 2015 2014/2015 EuBIAS Showcase Taggathon Jan. 5-6, 2015 Dec. 8-9, 2014 Institut Curie, Paris, Sponsored by FBI ELMI 2015 1. Create Community 2. Showcase Meeting 3. Webtool / Taggathon 4. Courses and Open Textbooks http://biii.info ‘bioimage information index’ ELMI 2015 Image Data component: The implementation of image processing and workflow analysis algorithms. component Software/Library: A component package of various components. component Workflow: Image component analysis workflow (a sequence of components) for biological research. Numbers ELMI 2015 2014 2013 Taggathon: biii.info ELMI 2015 ELMI 2015 - example: detect FOCI in 3D data -> function hits! regardless of packages - We gather periodically do taggathon to do work (people are lazy) - Minimal descriptions, link and tag (people are lazy) ELMI 2015 biii.info Taggers Jason Swedlow, Univ. Dundee & EuroBioimaging WP11 Stuart Berg, Janelia Farm, HHMI (Ilastik) Kota Miura, EMBL Heidelberg Luis Pedro Coelho, EMBL Heidelberg (Mahotas) Julien Colombelli, IRB Barcelona Joe Barry, EMBL Heidelberg (EBImage) Sébastien Tosi, IRB Barcelona Peter Majer, Bitplane (Imaris) Perrine Paul-Gilloteaux, Curie, Paris Ronald Ligteringen, Delft Univ. of Technology (DIPimage) Christian Tischer, EMBL Heidelberg Fabrice Cordelières, Bordeaux Imaging Center Christoph, Moehl, DZNE Bonn Ofra Golani, Weizmann, Rehovot Thomas Pengo, CRG Barcelona Chong Zhang, CellNetworks, Univ. Heidelberg Simon F Nørrelykke, ETH Zurich Nikolay Kladt, CECAD, Koeln Carlos Ortiz de Solórzano Aurusa, CIMA, Pamplona Petr Walczysko, Univ. Dundee (OME) Ricard Delgado Gonzalo, BIG - EPFL Thomas Walter, Mines Paris Johannes Schindelin, LOCI, Univ. Madison (Fiji / ImageJ) Fabrice de Chaumont, Pasteur, Paris (ICY) Martin Horn, Univ. Konstanz (KNIME) Lee Kamentsky, Broad Institute, Boston (CellProfiler) Christoph Sommer, IMBA Vienna (CellCognition) Ullrich Kloethe, U. Heidelberg (VIGRA) Nicolas Rey-Villamizar, Houston (Farsight) Laszlo Marak, ESIEE (PINK) Graeme Ball, Univ. Dundee Peter Bankhead, QUB UK, Belfast Olivier Burri, EPFL, Lausanne Torsten Stöter, LIN Magdeburg Special Thanks to: Curtis Ruden, U of Wisconsin Madison Laurent Gelman, FMI Basel Marie-Laure Boizeau, ex-Itav, Toulouse Nicolas Signolle, Institut Curie, Paris Volker Bäcker, MRI, Montpellie.
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