NEUBIAS, the Network of Bioimage Analysts and Its Activities

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