Jean-Olivier Irisson

Welcome !

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.


In the works

  • Fabri-Ruiz S, Berdalet E, Ulses C, Somot S, Vila M, Lemée R, Irisson J-O. Harmful Ostreopsis cf. ovata blooms could extend in time span with climate change in the Western Mediterranean Sea. To be submitted to Ecography.
  • Panaïotis T, Poteau A, Diamond-Riquier E, Catalano C, Courchet L, Motreuil S, Coppola L, Picheral M, Irisson J-O. Temporal evolution of plankton and particles distribution across a mesoscale front during the spring bloom. Accepted in Limnology & Oceanography.
  • 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. To be submitted to Limnology & Oceanography: Methods.
  • 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.
  • Schickele A, Debeljak P, Ayata S-D, Bittner L, Pelletier E, Guidi L, Irisson J-O. Exploring the functional biogeography of photosynthesis in picoeukaryotes. bioRxiv preprint, submitted to Science Advances.

Recently published

  • 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]
  • 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]
  • Fabri-Ruiz S, Baudena A, Moullec F, Lombard F, Irisson J-O, Pedrotti ML (2023). Mistaking plastic for zooplankton: Risk assessment of plastic ingestion in the Mediterranean sea. Science of The Total Environment 856:159011. 10.1016/j.scitotenv.2022.159011 [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 (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]
  • Dugenne M, Corrales-Ugalde M, Luo J, Kiko R, O’Brien T, Irisson J-O, Lombard F, Stemmann L, Stock C, Anderson CR (2023). First release of the Pelagic Size Structure database: Global datasets of marine size spectra obtained from plankton imaging devices. Earth System Science Data Discussions 2023:1–41.
  • Berenshtein I, Faillettaz R, Irisson J-O, Kiflawi M, Siebeck UE, Leis JM, Paris CB (2022). Evidence for a consistent use of external cues by marine fish larvae for orientation. Commun Biol 5:1–9. 10.1038/s42003-022-04137-7 [PDF]
  • Kiko R, Picheral M, Antoine D, Babin M, Berline L, Biard T, Boss E, Brandt P, Carlotti F, Christiansen S, Coppola L, de la Cruz L, Diamond-Riquier E, Durrieu de Madron X, Elineau A, Gorsky G, Guidi L, Hauss H, Irisson J-O, Karp-Boss L, Karstensen J, Kim D, Lekanoff RM, Lombard F, Lopes RM, Marec C, McDonnell AMP, Niemeyer D, Noyon M, O’Daly SH, Ohman M, Pretty JL, Rogge A, Searson S, Shibata M, Tanaka Y, Tanhua T, Taucher J, Trudnowska E, Turner JS, Waite A, Stemmann L (2022). A global marine particle size distribution dataset obtained with the Underwater Vision Profiler 5. Earth System Science Data Discussions 14:4315–4337. 10.5194/essd-2022-51 [PDF]
  • Soviadan YD, Benedetti F, Brandão MC, Ayata S-D, Irisson J-O, Jamet JL, Kiko R, Lombard F, Gnandi K, Stemmann L (2022). Patterns of mesozooplankton community composition and vertical fluxes in the global ocean. Progress in Oceanography 200:102717. 10.1016/j.pocean.2021.102717 [PDF]
  • Picheral M, Catalano C, Brousseau D, Claustre H, Coppola L, Leymarie E, Coindat J, Dias F, Fevre S, Guidi L, Irisson J-O, Legendre L, Lombard F, Mortier L, Penkerch C, Rogge A, Schmechtig C, Thibault S, Tixier T, Waite A, Stemmann L (2022). The Underwater Vision Profiler 6: an imaging sensor of particle size spectra and plankton, for autonomous and cabled platforms. Limnology & Ocean Methods 20:115–129. 10.1002/lom3.10475 [PDF]
  • Drago L, Panaïotis T, Irisson J-O, Babin M, Biard T, Carlotti F, Coppola L, Guidi L, Hauss H, Karp-Boss L, Lombard F, McDonnell AMP, Picheral M, Rogge A, Waite AM, Stemmann L, Kiko R (2022). Global Distribution of Zooplankton Biomass Estimated by In Situ Imaging and Machine Learning. Frontiers in Marine Science 9. 10.3389/fmars.2022.894372 [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


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:

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:


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