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Stemmann and Villefranche Plankton image team CNRS-UPMC

WP3 and 4 : Monitoring plankton communities with billions of images: The next challenge for JERICO-NEXT. Stemmann and Villefranche Plankton image team CNRS-UPMC. Bio-optical sensors and data Wednesday 22 nd of March 2017.

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Stemmann and Villefranche Plankton image team CNRS-UPMC

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  1. WP3 and 4 : Monitoring plankton communities with billions of images: The next challenge for JERICO-NEXT Stemmann and Villefranche Plankton image team CNRS-UPMC Bio-optical sensors and data Wednesday 22nd of March 2017

  2. High throughput Imaging systems provide great perspectives in pelagic ecology and monitoring In situ image Particles are vectors of carbon and pollutant flux • Images of organisms • provide Indicators of ecosystem status (abundance, biomass, taxa, size spectra), particularly useful for marine resources management. • can be obtained for all trophic levels (from bacteria to fish larvae) using commercially available sensors. • can be obtained by lab scanners or by in situ sensors, they provide high frequency data suitable for spatial monitoring. • These indicators can be used to develop and constrain biogeochemical models, Lagrangian model of particles/plankton transport, population dynamics models and also end to end ecosystem models for fisheries management. Biodiversity and dynamics of plankton

  3. MSFD and Copernicus requirementsthe need for new development of sensors 7,5: On the shelf sensors, almost standard procedures 11: On the shelf sensors, no current procedures 8: Sensors available or under development, more tests needed 1,4,6,10: Sensors under development, e.g. “Octopus” in WP5 2,3: need for several sensors available or under development. More speculative Caméra on gliders, floats and moored systems

  4. The TARA pilot experiment to compare imaging and genomic high throuput systems for biological data 5 106 images, hard to sort, genomic came first 2015 5 publications mainly genomic 2 publications imaging 2016 • Need a software for : • Image archiving, • Image annotation (semi-automated ) • Image, metadata and data exchange • In a network approach for intensive work across the internet JERICO Second Plankton Workshop 107 plankton images

  5. Instruments used in JERICO and JERICONEXT • pilot sites : • JERICO: Point B (Med. Sea) • JERICONext: Baltic sea • Other collaborations : • Microscopy (TARA) • IFCB (Takuvik Canada, WHOI, Texas A&M) • UVP5 (GEOMAR, AWI, SCRIPPS, Univ. Alaska) • ISIIS (Univ. South Florida) • Zooscan (CSIRO, IFREMER, Univ. Cap Town, JiaZhou Marine Lab, Lousiana State University) • Zoocam (IFREMER) • FlowCam (Univ. of Maine) 107 plankton images JERICO Second Plankton Workshop

  6. WHAT IS ? • A COLLABORATIVE WEB BASED TOOL FOR IMAGE ANNOTATION • DEVELOPPED IN THE FRAME OF TARA AND OCEANOMICS PROJECTS • MAIN FEATURES : • CLASSIFICATION (annotation) of ORGANISMS usingindividual images • COLLABORATIVE annotation via WEB interface (all successive annotations are recorded) • OPTIMIZED for large datasets( > 40 000 000 images per instance) • USES classification tools to assisttaxonomistclassifying large datasets : • SVM • Random Forest • Deep Learning (SOON) • PROVIDES A REFERENCE TAXONOMY for SORTING 2014 2015 2016 2017 Contracting Development Production (20M images, 20 users Specifications v 1 Specifications v 2

  7. TODAY , two servors: 20 000 000 images Roscoff Villefranche Expected few millions more/year

  8. BRIEF VISIT @ ecotaxa.sb-roscoff.fr / ecotaxa.obs-vlfr.fr

  9. BRIEF VISIT @ ecotaxa.sb-roscoff.fr / ecotaxa.obs-vlfr.fr OPEN access to visit « Validated » data across all projects

  10. EXPLORE (free access) PROJECT / SAMPLE POSITION DATE / TIME DEPTH

  11. EXPLORE (free access) PROJECT / SAMPLE POSITION DATE / TIME DEPTH TAXONOMY filter

  12. EXPLORE (free access) PROJECT / SAMPLE POSITION DATE / TIME DEPTH OBJECT PAGE TAXONOMY filter

  13. BRIEF VISIT @ ecotaxa.sb-roscoff.fr / ecotaxa.obs-vlfr.fr RESTRICTEDaccess to view / annotate images per project

  14. CONTRIBUTE @ ecotaxa.sb-roscoff.fr / ecotaxa.obs-vlfr.fr SELECT A PROJECT (after requesting permission)

  15. CONTRIBUTE @ ANNOTATE Zooscan Tara OceansRegent 680 • ACTIONS : • IMPORT DATA • AUTOMATIC CLASSIFICATION (prediction) • EXPORT results • Other : settings, corrections, subsets…

  16. CONTRIBUTE @ ANNOTATE Zooscan Tara OceansRegent 680 • FILTERS : • PROJECT / SAMPLE • POSITION • DATE / TIME • DEPTH

  17. CONTRIBUTE @ ANNOTATE Zooscan Tara OceansRegent 680 TAXONOMY filter & PRESET

  18. CONTRIBUTE @ ANNOTATE Zooscan Tara OceansRegent 680 TAXO tree • MANUAL ANNOTATION : • DRAG & DROP • AUTOCOMPLETION

  19. CONTRIBUTE @ ANNOTATE Zooscan Tara OceansRegent 680 • SORTING & DISPLAY : • SORT using SCORE (of prediction) • Display variables • Zoom • Legend

  20. CONTRIBUTE @ ANNOTATE Zooscan Tara OceansRegent 680 • FILTERS : • PROJECT / SAMPLE • POSITION • DATE / TIME • DEPTH 40h : 80 000 objects / 24 categories • SORTING & DISPLAY : • SORT using SCORE (of prediction) • Display variables • Zoom • Legend • MANUAL ANNOTATION : • DRAG & DROP • AUTOCOMPLETION TAXONOMY filter & PRESET

  21. Importance of UniEuk initiative • ECOTAXA • relies on a updatedtaxonomy => UniEuk • Can providefield images to beassociatedwithsequences

  22. UniEuk • WHAT ECOTAXA needs : • VALIDATED Taxonomy (linked with Genetics) for Eukaryotes • => Application interface to link both systems • RESPONSIVE Taxonomy (EcoTaxa users require that « their » classical taxon are usable for sorting even if no sequence available yet) • POSSIBILITY for users to create themself a temporary taxon if missing in the implemented taxonomy • Application manager tools to create & validate the « true » taxon Ecotaxa architecture UniEuk architecture

  23. Importance of JERICOnext • JERICONext aims at identifying tools for phytoplankton monitoring • Images are one of the method (IFCB, Cytosens) selected by JERICONext • One can expect large numbers of images • -> provide numerous images for deep learning • -> develop common or define protocols for image analysis and computer assisted classification • -> set formats for image, data and metadata archiving and distribution • -> help to define ECOTAXA 2.0

  24. Development at LOV with ECOTAXA 2.0 (middle of 2017) • ECOTAXA (main) • - Display all metadata (map, tables) • Display images of selectedprojects (with conditions) • allow to contact specific data providers for furthersorting or data export • allow to sharelearning sets • maintain the taxonomicreferences (UniEuk) • ECOTAXA (local users) • - Images, data and metadata archiving • Display, annotate, classify images • - Export local datasets • ECOTAXA (local users) • - Images, data and metadata archiving • Display, annotate, classify images • - Export local datasets …..

  25. What about long term archiving and distribution • ECOTAXA (main) • - Display all metadata (map, tables) • Display images of selectedprojects (with conditions) • allow to contact specific data providers for furthersorting or data export • allow to sharelearning sets • maintain the taxonomicreferences (UniEuk) • ECOTAXA (local users) • - Images, data and metadata archiving • Display, annotate, classify images • - Export local datasets • ECOTAXA (local users) • - Images, data and metadata archiving • Display, annotate, classify images • - Export local datasets ?? ….. Long termarchiving distribution ???? : Portail (EMODNET??) tables (Pangeawithversioning, ???) Images (EBI ??) ?? ??

  26. Challenges for an European infrastructure to monitor plankton in coastal and open marine systems. • long term archiving of images, their annotation (including versionning) and metadata (methods and link with environments) • long term distribution of the datasets • network of taxonomic experts • network outreach: citizen science

  27. Valorisation through applied joint research: JRAP-1 on pelagic biodiversity Participate to cruises in Baltic Sea, Skagerrak-Kattegat, Ligurian Sea Discussion around future sensors now in development in the frame of FP8 BRIDGES. WP4: In situ imaging systems to observe plankton in coastal operational oceanography Jerico-Next – Kick-Off meeting - Mallorca

  28. THANK YOU !!! UniEuk

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