Discovery of Image Analysts · Results in beautiful sushi. Image Analysts Developers & Software...
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ELMI 2015 Discovery of Image Analysts Kota Miura ([email protected] ) - EuBIAS & Biii - EMBL Heidelberg National Institutes of Natural Sciences, Tokyo National Institute of Basic Biology, Okazaki
Transcript of Discovery of Image Analysts · Results in beautiful sushi. Image Analysts Developers & Software...
ELMI 2015
Discovery of Image Analysts
Kota Miura ([email protected])
- EuBIAS & Biii -
EMBL HeidelbergNational Institutes of Natural Sciences, TokyoNational Institute of Basic Biology, Okazaki
ELMI 2015
Post-Imaging Bottleneck
-> Experiments -> Microscopy -> Image Processing, Analysis-> Results
Imaging
ELMI 2015
Post-Imaging Bottleneck
-> Experiments -> Microscopy -> Image Processing, Analysis-> Results
Bottleneck!
Imaging
ELMI 2015
Text
Publications with ImageJ
source: pubmed
Text Fiji: 700 commands
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 -
e.g. NIH Image, Metamorph
Image Processing & Analysis
Tools, Functions, Libraries
Biological Problems
ELMI 2015
BioImage Analysis- good old 90’s -
e.g. NIH Image, Metamorph
Image Processing & Analysis
Tools, Functions, Libraries
Biological Problems
ELMI 2015
more complex image sets, more techniques
Image Processing & Analysis
Tools, Functions, Libraries
Biological Problems
more packages, algorithms, libraries
00’s -: Developer’s Efforts
BioImage Analysis
ELMI 2015
Image Processing & Analysis
Tools, Functions, Libraries
Biological Problems
Which one should be used?
BioImage Analysis
ELMI 2015
Image Processing & Analysis
Tools, Functions, Libraries
Biological Problems
BioImage Analysis
ELMI 2015
Image Processing & Analysis
Tools, Functions, Libraries
Biological Problems
2nd Round...
Which combination should be used?
ELMI 2015
Enlarging the Bottle Neck
BioImage AnalystsDevelopersBiologistsPhysicistsElectric EngineersMathematicianProgrammers
Biological Problems
Image Processing and Analysis
ELMI 2015
So many different knives from blade smith ...
Sushi master chooses the right knife at each step...
... Results in beautiful sushi.
ELMI 2015
So many different knives from blade smith ...
Sushi master chooses the right knife at each step...
... Results in beautiful sushi.
ELMI 2015
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!
ELMI 2015
Barcelona, Oct 9 - 11, 2013
Euro-BioImage Analysis Symposium (EuBIAS)
http://biii.info/eubias
ELMI 2015
2014/2015 EuBIAS
Institut Curie, Paris, Sponsored by FBI
TaggathonDec. 8-9, 2014Jan. 5-6, 2015
Showcase
ELMI 2015
1. Create Community2. Showcase Meeting3. Webtool / Taggathon4. Courses and Open Textbooks
http://biii.info‘bioimage information index’
ELMI 2015
Image Data
Numbers
component
component
component
component
workflow
component: The implementation of image processing and analysis algorithms.
Software/Library: A package of various components.
Workflow: Image analysis workflow (a sequence of components) for biological research.
ELMI 2015
2013
2014
ELMI 2015Taggathon: biii.info
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
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 Kloethe, 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 Taggers
Special Thanks to: Curtis Ruden, U of Wisconsin Madison
