Jean-Olivier Irisson

I am a computational ecologist, which means that I combine data, algorithms, and software implementations on computers to tackle ecological questions. I work in marine ecosystems, where I study plankton (all the organisms drifting with ocean currents).

As an associate professor, at Sorbonne Université, I spend half of my time teaching, mostly data science (multivariate and spatial statistics, signal processing, programming) and a bit of larval fish ecology. On the research side, I use machine learning to process large volumes of plankton images, extract data from them, and finally relate the structure of plankton communities to the conditions in their environment.

Since 2016, I have been leading the Computational Plankton Ecology (COMPLEx) team of the Laboratoire d’Océanographie de Villefranche (LOV).

For a detailed overview of my past and current research, my Habilitation à Diriger des Recherches is the most complete document you can read.

Publications

In the works

Panaïotis T, Amblard E, Boniface-Chang G, Dulac-Arnold G, Woodward B, Irisson J-O. Benchmark of plankton images classification approaches: feature quality matters more than classifier complexity. Submitted to Earth System Science and Data.
Panaïotis T, Biard T, Caray–Counil L, Faillettaz R, Luo JY, Guigand CM, Cowen RK, Irisson J-O. High throughput in situ imaging reveals complex ecological behavior of giant marine mixotrophic protists. To be submitted to PNAS.
Dugenne M, Corrales-Ugalde M, Luo J, Stemmann L, Irisson J-O, Lombard F, O’Brien T, Stock C, Kiko R (2024). Key link between iron and the size structure of three main mesoplanktonic groups (Crustaceans, Rhizarians, and colonial N2-fixers) in the Global Ocean. bioRxiv:2024–03.
Schickele A, Clerc C, Benedetti F, De Angelis D, Hofmann Elizondo U, Muennich M, Irisson J-O, Vogt M (2024). Standardizing marine habitat modelling practices to enhance inter-comparability across biological observations. bioRxiv:2024–09

Recently published

Fabri-Ruiz S, Berdalet E, Ulses C, Somot S, Vila M, Lemée R, Irisson J-O (2024). Harmful Ostreopsis cf. ovata blooms could extend in time span with climate change in the Western Mediterranean Sea. Science of The Total Environment 947:174726. 10.1016/j.scitotenv.2024.174726 [PDF]
Di Stefano M, Nerini D, Alvarez I, Ardizzone G, Astruch P, Basterretxea G, Blanfuné A, Bonhomme D, Calò A, Catalan I, Cattano C, Cheminée A, Crec’hriou R, Cuadros A, Di Franco A, Diaz-Gil C, Estaque T, Faillettaz R, Félix-Hackradt FC, Garcia-Charton JA, Guidetti P, Guilloux L, Harmelin J-G, Harmelin-Vivien M, Hidalgo M, Hinz H, Irisson J-O, La Mesa G, Le Diréach L, Lenfant P, Macpherson E, Matić-Skoko S, Mercader M, Milazzo M, Monfort T, Moranta J, Muntoni M, Murenu M, Nunez L, Olivar MP, Pastor J, Pérez-Ruzafa Á, Planes S, Raventos N, Richaume J, Rouanet E, Roussel E, Ruitton S, Sabatés A, Thibaut T, Ventura D, Vigliola L, Vrdoljak D, Rossi V (2024). Early-life dispersal traits of coastal fishes: an extensive database combining observations and growth models. Earth System Science Data 16:3851–3871. 10.5194/essd-16-3851-2024 [PDF]
Schickele A, Debeljak P, Ayata S-D, Bittner L, Pelletier E, Guidi L, Irisson J-O (2024). The genomic potential of photosynthesis in piconanoplankton is functionally redundant but taxonomically structured at a global scale. Science Advances 10:eadl0534. 10.1126/sciadv.adl0534 [PDF]
Dugenne M, Corrales-Ugalde M, Luo JY, Kiko R, O’Brien TD, Irisson J-O, Lombard F, Stemmann L, Stock C, Anderson CR, Babin M, Bhairy N, Bonnet S, Carlotti F, Cornils A, Crockford ET, Daniel P, Desnos C, Drago L, Elineau A, Fischer A, Grandrémy N, Grondin P-L, Guidi L, Guieu C, Hauss H, Hayashi K, Huggett JA, Jalabert L, Karp-Boss L, Kenitz KM, Kudela RM, Lescot M, Marec C, McDonnell A, Mériguet Z, Niehoff B, Noyon M, Panaïotis T, Peacock E, Picheral M, Riquier E, Roesler C, Romagnan J-B, Sosik HM, Spencer G, Taucher J, Tilliette C, Vilain M (2024). First release of the Pelagic Size Structure database: global datasets of marine size spectra obtained from plankton imaging devices. Earth System Science Data 16:2971–2999. 10.5194/essd-16-2971-2024 [PDF]
Panaïotis T, Poteau A, Riquier ÉD, Catalano C, Courchet L, Motreuil S, Coppola L, Picheral M, Irisson J (2024). Temporal evolution of plankton and particles distribution across a mesoscale front during the spring bloom. Limnology & Oceanography:lno.12566. 10.1002/lno.12566 [PDF]
Laget M, Drago L, Panaïotis T, Kiko R, Stemmann L, Rogge A, Llopis-Monferrer N, Leynaert A, Irisson J-O, Biard T (2024). Global census of the significance of giant mesopelagic protists to the marine carbon and silicon cycles. Nature Communications 15:3341. 10.1038/s41467-024-47651-4 [PDF]
Masoudi M, Giering SLC, Eftekhari N, Massot-Campos M, Irisson J-O, Thornton B (2024). Optimizing Plankton Image Classification With Metadata-Enhanced Representation Learning. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing 17:17117–17133. 10.1109/JSTARS.2024.3424498 [PDF]
Beck M, Cailleton C, Guidi L, Desnos C, Jalabert L, Elineau A, Stemmann L, Ayata S-D, Irisson J-O (2023). Morphological diversity increases with decreasing resources along a zooplankton time series. Proc R Soc B 290:20232109. 10.1098/rspb.2023.2109 [PDF]
Panaïotis T, Babin M, Biard T, Carlotti F, Coppola L, Guidi L, Hauss H, Karp‐Boss L, Kiko R, Lombard F, McDonnell AMP, Picheral M, Rogge A, Waite AM, Stemmann L, Irisson J-O (2023). Three major mesoplanktonic communities resolved by in situ imaging in the upper 500 m of the global ocean. Global Ecol Biogeogr 32:1991–2005. 10.1111/geb.13741 [PDF]
Rubbens P, Brodie S, Cordier T, Destro Barcellos D, Devos P, Fernandes-Salvador JA, Fincham JI, Gomes A, Handegard NO, Howell K, Jamet C, Kartveit KH, Moustahfid H, Parcerisas C, Politikos D, Sauzède R, Sokolova M, Uusitalo L, Van den Bulcke L, van Helmond ATM, Watson JT, Welch H, Beltran-Perez O, Chaffron S, Greenberg DS, Kühn B, Kiko R, Lo M, Lopes RM, Möller KO, Michaels W, Pala A, Romagnan J-B, Schuchert P, Seydi V, Villasante S, Malde K, Irisson J-O (2023). Machine learning in marine ecology: an overview of techniques and applications. ICES Journal of Marine Science:fsad100. 10.1093/icesjms/fsad100 [PDF]

All my publications

Main projects

As leader

2023 - 2026 FORMAL “From observing to modelling ocean life” (Sorbonne Université, Fr; 500k€, coPI). Bring together oceanographers and applied mathematicians to foster improved use of data and models of the marine environment. Involves six kinds of data (omics, imaging, biologging, acoustics, biogeochemical profiles, satellite images), four types of models (biogeochemical, niche, interaction, lagrangian), and leverages machine learning techniques for data processing, analysis, assimilation into models.

2022 - 2023 LOVNOWER “Machine learning and computer vision for plankton imagery” (France Relance, Fr; 220k€, PI).
Partnership with a computer vision company to develop machine learning-based tools for classification and visual search in the EcoTaxa plankton imagery platform.

2019 - 2023 WWWPIC World Wide Web of Plankton Image Curation (Belmont Forum; 1M€, PI).
Setup an international infrastructure for the classification of plankton images assisted by machine learning and the sharing of the resulting datasets; use this infrastructure to tackle questions about the distribution of plankton from the mesoscale to the global ocean.

As contributor

2023 - 2026 Blue-Cloud 2026 “A federated European FAIR and Open Research Ecosystem for oceans, seas, coastal and inland waters”: (Horizon EU; 360k€, PI for Sorbonne Université).
Integrate plankton imagery data as a FAIR data source into international data infrastructure; leverage these infrastructures and cloud computing to define operational species distribution modelling pipeline and map biodiversity at global scale.

DTO-Bioflow, WP3 “Enabling sustained flows of biodiversity monitoring data into the DTO”: (Horizon EU; 445k€, PI for Sorbonne Université).
Define and implement automated flows of data from plankton imagery instruments to the Digital Twin of the Ocean. Exploit this data to better constrain carbon flux at global scale.

BiOcean5D, WP3 “Data to knowledge, a digital foundation for holistic marine biodiversity assessment” (Horizon EU; 250k€, task PI).
Study biodiversity along coast to offshore gradients along the coast of Europe through the Tara Europa cruise, in association with the coastal TREC sampling campaign of EMBL. Beyond scientific exploitation of the data, my role is also to ensure the proper flow of plankton imagery data towards international databases.

ANERIS “operAtional seNsing lifE technologies for maRIne ecosystemS” WP3 Imagery (Horizon EU; 170k€, participant).
Deploy imaging instruments on moored platforms and process their data on-the-fly to study high frequency changes in marine plankton ecosystems.

2022 - 2026 TraitZoo “Trait biogeography and functional diversity of marine mesozooplankton” (ANR, Fr; 134k€, PI for LOV).
Extract traits (size, pigment concentration, reproduction potential, energy reserves) from images of plankton and use this data to describe the biogeography and functional implications of those traits.

2022 - 2025 iMagine “Imaging data and services for aquatic science” (Horizon EU; 360k€, PI for Sorbonne Université).
Develop a new version of the image processing pipeline for the ZooScan instrument, using artificial intelligence; release this as a cloud service; leverage it to process a 50 years long time series of plankton imagery data and analyse it to detect potential effects of climate change.

PopNCo, WP5 “Data integration and synthesis” (ANR, Fr; 130k€, WP PI).
Assess the spatio-temporal variability of connectivity between biological populations from genetic and modelling data, through graph-based approaches.

2021 - 2024 TechOceanS, Theme 2 “Imaging and optics” (H2020, EU; 300k€, participant).
Investigate image compression through auto-encoders and unsupervised image selection for optimal use of low-bandwidth transmission from autonomous in situ plankton imagers.

JERICO-S3, Tasks 6.3.1 “Biological imagery data” and 7.5 “JERICO infrastructure” (H2020, EU; 62k€, task PI).
Define international standards for quantitative imagery of plankton, implement those standards in data processing pipelines from several instruments, provide access to an infrastructure hosting the resulting data.

All my projects

Main classes

I mostly teach in the Master of Marine Sciences at Sorbonne Université. I coordinate three classes and I participate in three others:

Instrumentation and Acquisition of Data in Oceanography (coordinator). I teach Scientific cruise planning (4.5h), Databases for oceanography (6h), Plankton imaging (3h), Data processing (3h), I supervise student projects (6h) and participate in the oceanographic cruise (2 days).

Methods for Data Exploitation in Oceanography (coordinator). I teach R for data science (9h), Mapping and interpolation with practical (3+6h), Introduction to multivariate data analysis with practical (3+1.5h), Signal processing with practical (3+3h), Data processing (4.5h), and I supervise student projects (6h).

Multivariate Statistics Summer school (coordinator). I teach a course and a computer lab for each topic: Introduction to programming with R (6h), Data series (6+6h), Redundancy analysis (3+3h), and Tree‐based learning (3+3h).

Introduction to modelling. I teach an introduction to population dynamics that joins a course and a computer lab (8h).

Modelling of the Marine Environment. I teach a course and a computer lab for Lagrangian models (2+3h) and Advanced population dynamics (2+3h); I also supervise student projects (3h).

Plankton diversity Summer school. I teach Ichthyoplankton ecology and taxonomy, with a identification of specimen (3h)

Full list of present and past classes in progress

Code

Coding _is_ fun!

I love coding. All of my code is Open Source. Most of it is hosted on github and coded in R. Relevant repositories are:

apeep Process ISIIS data without a peep.
atlasr Habitat modelling for the Biogeographic Atlas of the Southern Ocean.
autoplot Automatic plots for multivariate analyses with ggplot2.
castr Process CTD casts (or any other series-like data for that matter).
chroma Handle colours: transform, convert, create perceptually correct colour scales, etc.
discr Process and analyse the data of the Drifting In Situ Chamber (DISC).
jihoml Fluidify the process of fitting, evaluating, and using Machine Learning models. The package is close in spirit to caret and tidymodels albeit much less featurefull… but faaast!
morphr R package to combine many images together and create a morphotype of an object.
nbssr Compute Normalised Biomass Size Spectra.
nppen Non-Parametric Probabilistic Ecological Niche from Beaugrand et al 2011, in R.
soundclass Signal classifier for sounds.
shoreliner Shoreline extractor from the GSHHG database.
wkmeans Observation Weighted K-Means in R (with a Fortran backend).
yssr Static website generator, in R.

When I am not coding myself, I also supervise the development of scientific applications that serve the community. Those include EcoTaxa and, with a lower involvement, EcoPart, for plankton imaging and particles size spectra. They generated an ecosystem of associated software such as:

AQC Quality check tool for the ZooScan.
ecotaxar Query the EcoTaxa database and process the output.
ecotaxarapi R client to access the API of EcoTaxa.
ecotaxa_py_client Python client to access the API of EcoTaxa.
ecotaxa_ML_template Code to train image classification models for EcoTaxa.
uvpec Python package to train image classification models to be embedded in the UVP6.

Datasets

I strive publish the data that I use openly and encourage others to do the same through the development of the tools described above. So far, I have contributed to the following datasets.

Panaïotis T, Caray-Counil L, Jalabert L, Irisson J-O (2024). ISIISNet : plankton images captured with the ISIIS (In-situ Ichthyoplankton Imaging System). 10.17882/101950
Elineau A, Desnos C, Jalabert L, Olivier M, Romagnan J-B, Costa Brandao M, Lombard F, Llopis N, Courboulès J, Caray-Counil L, Serranito B, Irisson J-O, Picheral M, Gorsky G, Stemmann L (2024). ZooScanNet: plankton images captured with the ZooScan. 10.17882/55741
Jalabert L, Signoret G, Caray-Counil L, Vilain M, Martins E, Lombard F, Picheral M, Irisson J-O (2024). FlowCAMNet : plankton images captured with the FlowCAM. 10.17882/101961
Romagnan J-B, Panaïotis T, Bourriau P, Danielou M-M, Doray M, Dupuy C, Forest B, Grandremy N, Huret M, Le Mestre S, Nowaczyk A, Petitgas P, Pineau P, Rouxel J, Tardivel M, Irisson J-O (2024). ZooCAMNet : plankton images captured with the ZooCAM. 10.17882/101928
Di Stefano M, Nerini D, Alvarez Ellacuria I, Ardizzone G, Astruch P, Basterretxea G, Blanfuné A, Bonhomme D, Calò A, Catalan I, Cattano C, Cheminée A, Crec’Hriou R, Cuadros A, Di Franco A, Diaz-Gil C, Estaque T, Faillettaz R, Félix-Hackradt FC, Garcia-Charton JA, Guidetti P, Guilloux L, Harmelin J-G, Harmelin-Vivien M, Hidalgo M, Hinz H, Irisson J-O, La Mesa G, Le Diréach L, Lenfant P, Macpherson E, Matić-Skoko S, Mercader M, Milazzo M, Monfort T, Moranta J, Muntoni M, Murenu M, Nunez L, Olivar MP, Pastor J, Pérez-Ruzafa Á, Planes S, Raventos N, Richaume J, Rouanet E, Roussel E, Ruitton S, Sabatés A, Thibaut T, Ventura D, Vigliola L, Vrdoljak D, Rossi V (2024). Compilation of locations, larval durations and dates of spawning and settlement for coastal fishes in the Mediterranean Sea. 10.17882/91148
Jalabert L, Amblard E, Berrenger H, Bourhis A, Desnos C, Llopis N, Martins E, Merland C, Serranito B, Elineau A, Irisson J-O (2024). Segmentation masks of ZooScan images focusing on images with several objects separated by a human operator. 10.17882/99663
Panaïotis T, Biard T, Caray–Counil L, Faillettaz R, Luo JY, Guigand CM, Cowen RK, Irisson J-O (2023). Data for High throughput in situ imaging reveals complex ecological behavior of giant marine mixotrophic protists. 10.17882/96266
Panaïotis T, Poteau A, Diamond Riquier É, Catalano C, Courchet L, Motreuil S, Coppola L, Picheral M, Irisson J-O (2023). Plankton and particles from Seaexplorer glider and UVP6 across the Ligurian Front. 10.17882/95806
Romagnan J-B, Jalabert L, Llopis Monferrer N, Merland C, Trudnowska E, Brandão MC, Elineau A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans Consortium Coordinators, Karsenti E, Pesant S, Irisson J-O, Lombard F, Stemmann L, Gorsky G (2021). Occurrence of Eukaryotes in the size fraction >300 micrometres, collected worldwide during the Tara Oceans expedition (2009-2013) using a Multinet and analysed on a ZooScan imaging platform. 10.14284/517
Romagnan J-B, Jalabert L, Llopis Monferrer N, Elineau A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans Consortium Coordinators, Karsenti E, Pesant S, Irisson J-O, Lombard F, Stemmann L, Gorsky G (2021). Occurrence of Eukaryotes in the size fraction >300 micrometres, collected worldwide during the Tara Oceans expedition (2009-2013) using a Bongo net and analysed on a ZooScan imaging platform. 10.14284/518
Romagnan J-B, Jalabert L, Olivier M, Elineau A, Brandão MC, Caray-Counil L, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans Consortium Coordinators, Karsenti E, Pesant S, Irisson J-O, Lombard F, Stemmann L, Gorsky G (2020). Occurrence of Eukaryotes in the size fraction >200 micrometres, collected worldwide during the Tara Oceans expedition (2009-2013) using a WPII net and analysed on a ZooScan imaging platform. 10.14284/521
Romagnan J-B, Jalabert L, Brandão MC, Caray-Counil L, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans Consortium Coordinators, Karsenti E, Pesant S, Irisson J-O, Lombard F, Stemmann L, Gorsky G (2020). Occurrence of Eukaryotes in the size fraction >680 micrometres, collected worldwide during the Tara Oceans expedition (2009-2013) using a Régent net and analysed on a ZooScan imaging platform. 10.14284/522
Sorbonne Université/CNRS, Institut de la Mer de Villefranche, Sorbonne Université/CNRS, Laboratoire d’Océanographie de Villefranche (2020). Plankton community in Régent (680µm) net, Point B, Villefranche-sur-Mer, France. 10.14284/477
Sorbonne Université/CNRS, Institut de la Mer de Villefranche, Sorbonne Université/CNRS, Laboratoire d’Océanographie de Villefranche (2020). Plankton community in WP2 net (200µm), Point B, Villefranche-sur-Mer, France. 10.14284/473
Sorbonne Université/CNRS, Institut De La Mer de Villefranche, Sorbonne Université/CNRS, Laboratoire d’Océanographie de Villefranche (2020). Plankton community in Juday-Bogorov (330µm) net, Point B, Villefranche-sur-Mer, France. 10.14284/478
Sorbonne Université/CNRS, Institut de la Mer de Villefranche, Sorbonne Université/CNRS, Laboratoire d’Océanographie de Villefranche (2020). Plankton community in WP2 net (200µm), DYFAMED point, Ligurian Sea, France. 10.14284/479
Irisson J-O, Faillettaz R, Petit F, De Liège G (2018). RadeICHTHYO : Abundance of settlement-stage fish larvae (ichthyoplankton) in the bay of Villefranche-sur-mer. 10.17882/52943
Irisson J-O, D’Ortenzio F, Testor P, Mortier L (2017). Visufront deployment (EGO glider : milou) (Mediterranean Sea - Western basin). 10.17882/51429

Bio

Here is short bio and a picture for official purposes:

Jean-Olivier Irisson is a computational ecologist. After graduating from the École Normale Supérieure in Paris, he studied the behaviour of tropical fish larvae and its implication for population connectivity for his Masters and PhD at the École Pratique des Hautes Études in Perpignan (France) as well as for his post-doc at the University of Miami. Since 2009, he is an associate professor at Sorbonne Université, in the Laboratoire d’Océanographie de Villefranche (Southern France). He leads the plankton ecology team and is involved in long term monitoring programs as well as research on plankton ecology, at the interface between environmental and computer sciences.

Full curriculum vitae in PDF