20160712 GerBI

NEUBIAS, the network of bioimage analysts and its activities

Kota MiuraFreelance Image Analyst

Nikon Imaging Center, Uni-HeidelbergNational Institute of Basic Biology, Okazaki

Stem Tillia sp.

Arnold Dodel

20160712 GerBI

“ 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.”

Gonzalez & Woods, “Digital Image Processing”

Definition of Image Analysis

e.g. “Computer Vision”

20160712 GerBI

In biology, image analysis is a process of identifyingspatial and temporal distribution of biological components in images, and measure their characteristics to study their underlying mechanisms in an unbiased way.

Definition of Bioimage Analysis

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

-> Experiments -> Microscopy-> Image Processing & Analysis-> Results

Bottleneck!

Imaging

(50 million Euros in Germany)

20160712 GerBI

There will be An Ultimate Software Package that solves all image analysis problems in biology, in a matter of several clicks.

... most likely not.

A Failure of Optimism

20160712 GerBI

NEUBIAS: Web Platform components: The implementation of image processing and analysis algorithms.

Workflow: a sequence of components for biological research.

Software/Library: A package of various components.

Image Data

Numbers

component

component

component

component

workflow

20160712 GerBI

Image Processing & Analysis

Tools, Functions, Libraries

Biological Problems

2nd Round...

Which combination should be used?

Amazon Problem

20160712 GerBI

Pilots in the Amazon:Bioimage Analysts

BioImage AnalystsDevelopersBiologistsPhysicistsElectric EngineersMathematicianProgrammers

Biological Problems

Image Processing and Analysis

20160712 GerBI

So many different knives from blade smith ...

Sushi master chooses the right knife at each step...

... Results in beautiful sushi.

Image Analysts

Developers &Software Packages

Great Results!

20160712 GerBI

Barcelona, Oct 9 - 11, 2013

ParisDec. 8-9, 2014 Jan. 5-6, 2015

Textbook(Jan 2016)

EMBL Master Course (2013-) Euro-BioImage Analysis

Symposium (EuBIAS)

20160712 GerBI

Jason Swedlow, Univ. Dundee & EuroBioimaging WP11Kota Miura, EMBL HeidelbergJulien Colombelli, IRB BarcelonaSébastien Tosi, IRB BarcelonaPerrine Paul-Gilloteaux, Curie, ParisChristian Tischer, EMBL HeidelbergChristoph, Moehl, DZNE BonnThomas Pengo, CRG BarcelonaSimon F Nørrelykke, ETH ZurichCarlos Ortiz de Solórzano Aurusa, CIMA, PamplonaPetr Walczysko, Univ. Dundee (OME)Ricard Delgado Gonzalo, BIG - EPFLThomas Walter, Mines ParisJohannes 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. DundeePeter Bankhead, QUB UK, BelfastOlivier Burri, EPFL, LausanneTorsten Stöter, LIN MagdeburgLaurent Gelman, FMI BaselMarie-Laure Boizeau, ex-Itav, ToulouseNicolas Signolle, Institut Curie, ParisVolker Bäcker, MRI, Montpellie

Stuart Berg, Janelia Farm, HHMI (Ilastik)Luis Pedro Coelho, EMBL Heidelberg (Mahotas)Joe Barry, EMBL Heidelberg (EBImage)Peter Majer, Bitplane (Imaris)Ronald Ligteringen, Delft Univ. of Technology (DIPimage)Fabrice Cordelières, Bordeaux Imaging CenterOfra Golani, Weizmann, RehovotChong Zhang, CellNetworks, Univ. HeidelbergNikolay Kladt, CECAD, Koeln

biii.info

Special Thanks to: Curtis Ruden, U of Wisconsin Madison

20160712 GerBI

EuBIAS -> NEUBIAS COST Action (Oct. 2015-)

COST: Partner program of Horizon 2020. Focused on funding networking between researchers across Europe,and partner countries.

Network of EUropean BioImage AnalystS

20160712 GerBI

NEUBIAS: Proposed Activities

20160712 GerBI

NEUBIAS Participations

Mar. 2015: 50 proposers 15 EU Countries + EMBL + USA)

Nov. 2015 -> Apr 2016: 40 new members, 15 new countries.

Proposers

New!

coordinated country-wise

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

• Trainings

•A Web Platform for Bioimage Analysis

•Open Publications

NEUBIAS: What we do.

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)

Supports • Early Career Scientists• BioImage Analysts

Aim:• Collaboration to innovate image analysis• Direct access to data infrastructures and experts• Promote career paths and regional development

Proof-of-concept Call(Aug. 2016 - Dec. 2016)

More than 10 grants(and up to 20)

2017: up to 30x grants2018: up to 30x grants 2019: up to 40x grants

Missions duration: 1 to 12 weeks.

20160712 GerBI

NEUBIAS: Web Platform components: The implementation of image processing and analysis algorithms.

Workflow: a sequence of components for biological research.

Software/Library: A package of various components.

Image Data

Numbers

component

component

component

component

workflow

20160712 GerBI

NEUBIAS: Web Platform

WORKFLOWS

Biology papers Scripts, workflows, high level functions

The Webtool

Biologists / Analysts Searching in Biological terms: e.g. Golgi segmentation

Developers / Analysts Searching in Image Processing terms: e.g. 3D Watershed

COMPONENTS

tags

tagsImage Processing (Algorithm) papers, Documentation, APIs, Source codes

External Web resources

Workflow/Component Organization

biii.info

20160712 GerBI

NEUBIAS: Web Platform

WORKFLOWS

Biology papers Scripts, workflows, high level functions

The Webtool

Biologists / Analysts Searching in Biological terms: e.g. Golgi segmentation

Developers / Analysts Searching in Image Processing terms: e.g. 3D Watershed

COMPONENTS

tags

tags Image Processing (Algorithm) papers, Documentation, APIs, Source codes

External Web resources

Workflow/Component Organization

biii.info upgraded to “BISE ”

Sample Images

Bench- marks

20160712 GerBI

NEUBIAS: Web Platform

Evaluate workflowsSubmit user data & testUsers

BioImage Analysts

Developers/companies

Add contents, Design Schemes/Server Managements/ Validations

Add contents, especially their components (implementations)

what could you do?

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/eventsSebastian MunckArne Seitz

WG3 OutreachJean SalameroPaula Sampaio

WG7 Carrer Path STSMsJulia Frenandez-RodriguezClara Prats

WG6 Open PublicationsJuergen ReymannNatase Sladoje-Matic

WG2 TrainingGaby MartinsFabrice Cordelières

WG4 webtoolPerrine Paul-GilloteauxChong Zhang

WG5 Benchmarking & Sample datasets

Sébastien TosiGraeme Ball

Chair: Julien Colombelli

Vice ChairKota Miura

20160712 GerBI

Workshop: Course for facility Staff13-16 Sept, 2016, Barcelona

Conference 201712 – 17, 2017, Lisbon

more details: neubias.org

20160712 GerBI