World Wide Whole Plankton inferred using

a series of imaging instruments

Lars Stemmann,

The Plankton Image Group of Villefranche

ICES 2016,

Global Zooplankton Symposium Bergen

Sorbonne Universites, UPMC Univ Paris 06,

Laboratoire d’Océanographie de Villefranche , FRANCE

http://rade.obs-vlfr.fr/RadeZoo

The Invisible Multitude

THE PLANKTON

becomes visible

WWW Plankton: high throughput data acquisition

Tara Ocean

special issue May 2015

UVP5

Zooprocess

& PkID

WWW Plankton: image analysis

Flow cytometry

and cytobotMicroscopy Flowcam Zooscan

Gorsky et al., 2010

UVP

How to share easely images? -> Now ECOTAXA (web application)

World Wide whole Plankton: Images acquisition (2008-

2016)

Biodiversity, Function, Resources

Gorsky et al., 2010, JPRPicheral et al., 2010, L&OStemmann and Boss 2014, Ann. Rev. Mar. Sci.

104 samples, 107 images

spatial survey of a single group

time series of WWW plankton

TARA route

WWW Plankton: a new player (>600µm) ??

Biodiversity, Function, Resources

Stemmann et al., 2008, 300 stations

Biard et al., 2016, Nature, 2000 stations

Rhizaria (this study)

Mesozooplankton

Moriarty&O’Brien (2013)

2.106 images, 105 pankton, 36000 Rhizarians

Biodiversity, Function, Resources

Biard et al., 2016, Nature

WWW Plankton: a new player (>600µm) ??

Biodiversity, Function, Resources

Biard et al., 2016, Nature

WWW Plankton: a new player (>600µm) ??

WWW Plankton: Weekly time series (2011)

Simultaneous quantitative sampling of each size fraction weekly

during one year

(flowcytometer, microscopy, FLOWCAM, ZOOSCAN)

0 m

75 m

Wa

ter c

olu

mn

inte

gra

ted

Sampling tools

Sampled

volume

Biological

target

Size class

Net Net Net

Romagnan et al., 2015, PLOS

x18

Romagnan et al., 2015, PLOS

Temp.

Sal.

Dens.

Nitrate

Chla

WWW Plankton: Weekly time series (2011)

x18

Romagnan et al., 2015, PLOS

WWW Plankton: Weekly time series (2011)

x18

Romagnan et al., 2015, PLOS

WWW Plankton: Weekly time series (2011)

WWW Plankton: Time series of full size spectrum

Romagnan et al., in prep

Zooscan

Flowcam

Microscopy

WWW Plankton: full size spectrum TARA ocean

Biodiversity, Function, Resources

One station among 171

Work in progress:

• need expert recognition of zooplankton samples in areas outside our

expertise (mostly european waters)

• need a software to handle all kind of images

Flowcam

Zooscan

Call for Postdocs working (capacity building program for specific countries South America, Africa):

http://www.embl.de/jobs/partners/index.html#anchor_postdoc

UVP

WWW Plankton: ECOTAXA (6 106 images)

Biodiversity, Function, Resources

Web based application to semi-automatically sort plankton images in a network (intranet/internet), share image metadata/data in a secured mode and directly connect images to genomic taxonomy (uniEuk).

WWW Plankton: linking

images with samples

Files

Metadata

Data

Raw image

Sorted vignettes

Analysis (ECOTAXA)

Digitalization (Zooscan)

MetadataFormolethanol

Pt B (150 nets/y since 1966)

TARA cruise (650 nets)

other cruises (100 nets/y)

See http://rade.obs-vlfr.fr/RadeZoo

Collection room(15000 samples)

Web applications

WWW Plankton: take home message

o Images can be obtained with high throughput imaging

systems for the whole plankton community

o Large image datasets can be easely analysed by a

community of scientists and data can be easely shared

for regional and global studies

o Images provide new information revealing poorly

known fragile groups

o Plankton size distribution per taxa is more informative

than only total plankton size distribution .

WWW Plankton: global and regional monitoring

Global network of observations- ARGO-> BIOARGO+vision- fixed stations + vision- cruises of opportunity

Oceanographic data center for QC and large diffusion

Particulate Organic Carbon

macro and mesoplankton (Taxa

size spectra)

-Ecosystem monitoring

- Data assimilation in models for Carbone fluxes and marine ressources.

Pico and microplankton(taxa, size spectra)

CTD and geochemical dataN

P

Zn

DPSD

BIOSOPE

Carmen Garia Comas, Pieter Vandromme,, F. Roullier, Anthony Ouba, Nicolas Mayot, Rizlaine IdAoud, JB Romagnan N Llopis- Montferrer, Marion Olivier

all cruise leaders:

M. Babin

E. Karsenti

V. Smetacek

S. Blain

T. Moutin

Z. Kolbert

M. Ohman

D. Checkley

P. Brandt

X. Demadron

A. McDonnel

E. Boss

FP7 (EUROCEAN, SESAME, EuroBasin), FP8 (Perseus, GROOM, JERICO), H2020 (BRIDGES, JERICOnext),

PROOF, PNEC, ANR POTES, OCEANOMICS et MAORY, Services d’Observation RADEZOO and MOOSE

Lars Stemmann (Professor),

Lionel Guidi (CNRS Researcher),

Fabien Lombard (Associate Professor),

Jean Olivier Irisson (Associate Professor),

Gabriel Gorsky (CNRS Emeritus)

Marc Picheral (Research Engineer),

Mami Uneo (Research Engineer)

Amanda Elineau (Assistant Engineer),

Corinne Desnos (Technician)

PERMANENT

PostDoc, PhDs,

Masters

and we are looking for more interested people (Marie Curie Fellowships, …)

Then we are ready for a networkof octopus eyes.

UVP

VPR

ISIS

ISIS

UVP

LOKI

ZOOVIS SIPPERLOPC

Plankton

Particle

WWW Plankton: BIG DATA ?

o AGREED PROCEDURES (image format, treatment, semi-

automatic recognition, intercalibration)

o AGREED DATA MANAGEMENT

o AGREED DATA DISTRIBUTION

o AGREED MODELING FRAMEWORKS

o SUMMER SCHOOLS FOR THE USERS

These are propositions that we could discuss.