neubias, the network of bioimage analysts and its activities€¦ · 20160712 gerbi neubias:...
Post on 07-Oct-2020
2 Views
Preview:
TRANSCRIPT
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
top related