20160712 GerBI NEUBIAS, the network of bioimage analysts and its activities Kota Miura Freelance Image Analyst Nikon Imaging Center, Uni-Heidelberg National Institute of Basic Biology, Okazaki Arnold Dodel Stem Tillia sp. 20160712 GerBI Definition of Image Analysis Gonzalez & Woods, “Digital Image Processing” “ Image analysis is a process of discovering, identifying, and understanding patterns that are relevant to the performance of an image-based task. One of the principal goals of image analysis by computer is to endow a machine with the capability to approximate, in some sense, a similar capability in human beings.” e.g. “Computer Vision” 20160712 GerBI Definition of Bioimage Analysis In biology, image analysis is a process of identifying spatial and temporal distribution of biological components in images, and measure their characteristics to study their underlying mechanisms in an unbiased way. We do not have to be bothered with similarity to the human recognition - we have more emphasis on the objectivity of quantitative measurement, rather than how that computer-based recognition becomes in agreement with human recognition. 20160712 GerBI Survey Mar. 2015 1800 people answered in three days 20160712 GerBI Imaging Bottleneck Imaging -> Experiments -> Microscopy (50 million Euros in Germany) -> Image Processing & Analysis -> Results Bottleneck! 20160712 GerBI A Failure of Optimism There will be An Ultimate Software Package that solves all image analysis problems in biology, in a matter of several clicks. ... most likely not. 20160712 GerBI NEUBIAS: Web Platform components: The Image Data implementation of image processing and analysis algorithms. workflow component Workflow: a sequence of components for component biological research. component Software/Library: A package of various component components. Numbers 20160712 GerBI Biological ProblemsAmazon Problem Image Processing & Analysis Tools, Functions, Libraries 2nd Round... Which combination should be used? 20160712 GerBI Pilots in the Amazon: Bioimage Analysts Biological Problems BioImage Analysts Developers Biologists Physicists Electric Engineers Image Processing and Mathematician Analysis Programmers 20160712 GerBI 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! 20160712 GerBI EMBL Master Course Euro-BioImage Analysis (2013-) Symposium (EuBIAS) Barcelona, Oct 9 - 11, 2013 Paris Dec. 8-9, 2014 Jan. 5-6, 2015 Textbook (Jan 2016) 20160712 GerBI biii.info 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 Koethe, 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 20160712 GerBI EuBIAS -> NEUBIAS COST Action (Oct. 2015-) Network of EUropean BioImage AnalystS COST: Partner program of Horizon 2020. Focused on funding networking between researchers across Europe,and partner countries. 20160712 GerBI NEUBIAS: Proposed Activities 20160712 GerBI NEUBIAS Participations coordinated country-wise Mar. 2015: 50 proposers 15 EU Countries + EMBL + USA) Nov. 2015 -> Apr 2016: 40 new members, 15 new countries. Proposers New! 20160712 GerBI NEUBIAS Germany Kota Miura (Freelance, Univ-Heidelberg) Vice Chair, Management Committee Juergen Reymann (Univ-Heidelberg, Univ-Freiburg) WG6, Management Committee Pavel Tomancak (MPI-CBG) Torsten Stoeter (Leibniz Institute for Neurobiology, Magdeburg) Christian Tischer (EMBL) Giovanni Cardone (MPI Biochemistry, Munich) 20160712 GerBI NEUBIAS Participations breakdown by expertise 20160712 GerBI NEUBIAS: What we do. • Trainings • A Web Platform for Bioimage Analysis • Open Publications 20160712 GerBI NEUBIAS: Trainings •400 trainees in 4 years •Courses for •Early Career Scientists •Facility Staffs •BioImage Analysts 13-16th Sep. 2016 @University Pompeu Fabra, Barcelona • Application Deadline: July 15th (this Friday) • more details: neubias.org 20160712 GerBI NEUBIAS: Trainings short-term scientific missions (STSM) Proof-of-concept Call Supports (Aug. 2016 - Dec. 2016) • Early Career Scientists BioImage Analysts More than 10 grants • (and up to 20) Missions duration: 2017: up to 30x grants 1 to 12 weeks. 2018: up to 30x grants 2019: up to 40x grants Aim: • Collaboration to innovate image analysis • Direct access to data infrastructures and experts • Promote career paths and regional development 20160712 GerBI NEUBIAS: Web Platform components: The Image Data implementation of image processing and analysis algorithms. workflow component Workflow: a sequence of components for component biological research. component Software/Library: A package of various component components. Numbers 20160712 GerBI NEUBIAS: Web Platform Workflow/Component Organization Biologists / Analysts Searching in Biological terms: External Web resources e.g. Golgi segmentation The Webtool Biology papers Scripts, workflows, WORKFLOWS high level functions tags tags Image Processing COMPONENTS (Algorithm) papers, Documentation, APIs, Source codes Developers / Analysts Searching in Image Processing terms: e.g. 3D Watershed biii.info 20160712 GerBI NEUBIAS: Web Platform Workflow/Component Organization Biologists / Analysts Searching in Biological terms: External Web resources e.g. Golgi segmentation The Webtool Biology papers Scripts, workflows, Sample WORKFLOWS Images high level functions tags tags Bench- Image Processing marks COMPONENTS (Algorithm) papers, Documentation, APIs, Source codes Developers / Analysts Searching in Image Processing terms: e.g. 3D Watershed biii.info upgraded to “BISE ” 20160712 GerBI NEUBIAS: Web Platform what could you do? Users Evaluate workflows Submit user data & test BioImage Add contents, Design Schemes/ Analysts Server Managements/ Validations Developers/ Add contents, especially their companies components (implementations) 20160712 GerBI NEUBIAS: Open Publications Textbooks (workflow-oriented) “Stable Release” (like conventional books) “Continuous release” updated continuously, access in Internet. Revision tracked. Journals (?) 20160712 GerBI NEUBIAS: Proposed Activities 20160712 GerBI WG1 Strategy/events Sebastian Munck Arne Seitz Chair: Julien Colombelli WG2 Training Gaby Martins Vice Chair Fabrice Cordelières Kota Miura WG3 Outreach WG6 Open Publications Jean Salamero Juergen Reymann Paula Sampaio Natase Sladoje-Matic WG4 webtool WG7 Carrer Path STSMs Perrine Paul-Gilloteaux Julia Frenandez- Rodriguez Chong Zhang Clara Prats WG5 Benchmarking & Sample datasets Sébastien Tosi Graeme Ball 20160712 GerBI Workshop: Course for facility Staff 13-16 Sept, 2016, Barcelona Conference 2017 12 – 17, 2017, Lisbon more details: neubias.org 20160712 GerBI.