Home

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 am (happily) leading the team Processes in Pelagic EcosystemS (PEPS) of the Laboratoire d’Océanographie de Villefranche (LOV).

Recent publications

Gattuso J, Magnan AK, Bopp L, Cheung WWL, Duarte CM, Hinkel J, Mcleod E, Micheli F, Oschlies A, Williamson P, Billé R, Chalastani V, Gates RD, Irisson JO, Middelburg JJ, Poertner HO, Rau G. Ocean Solutions To Address Climate Change And Its Effects On Marine Ecosystems. Frontiers in Marine Science, in press.
Luo JY, Irisson JO, Graham B, Guigand C, Sarafraz A, Mader C, Cowen RK. [Automatic Plankton Image Analysis Using Convolutional Neural Networks]. Marine Ecology Progress Series, in press.
Faillettaz R, Paris CB, Irisson JO. Larval Fish Swimming Behavior Alters Dispersal Patterns From Marine Protected Areas In The North-Western Mediterranean Sea. Frontiers in Marine Science, 2018, PDF.
Ayata S, Irisson JO, Berline L, Dutay J, Mayot N, Nieblas A, D’Ortenzio F, Palmiéri J, Reygondeau G, Rossi V, Guieu C. Regionalisation Of The Mediterranean Basin, A Mermex Synthesis. Progress in Oceanography, 2018, PDF.
Faillettaz R, Durand E, Paris CB, Koubbi P, Irisson JO. Swimming Speeds Of Mediterranean Settlement-Stage Fish Larvae Nuance Hjort’s Aberrant Drift Hypothesis. Limnology and Oceanography, 2017, PDF.
Reygondeau G, Guieu C, Benedetti F, Irisson JO, Ayata S, Gasparini S, Koubbi P. Biogeochemical Regions Of The Mediterranean Sea: An Objective Multidimensional And Multivariate Environmental Approach. Progress in Oceanography, 2017, PDF.
Chust G, Vogt M, Benedetti F, Nakov T, Villéger S, Aubert A, Vallina SM, Righetti D, Not F, Biard T, Bittner L, Benoiston A, Guidi L, Villarino E, Gaborit C, Cornils A, Buttay L, Irisson JO, Chiarello M, Vallim AL, Blanco-Bercial L, Basconi L, Ayata S. Mare Incognitum: A Glimpse Into Future Plankton Diversity And Ecology Research. Frontiers in Marine Science, 2017, PDF.
Faillettaz R, Picheral M, Luo JY, Guigand C, Cowen RK, Irisson JO. Imperfect Automatic Image Classification Successfully Describes Plankton Distribution Patterns. Methods in Oceanography, 2016, PDF.
Ezzat L, Towle E, Irisson JO, Langdon C, Ferrier-Pagès C. The Relationship Between Heterotrophic Feeding And Inorganic Nutrient Availability In The Scleractinian Coral T. Reniformis Under A Short-Term Temperature Increase. Limnology and Oceanography, 2016, PDF.
Faillettaz R, Durand E, Paris CB, Koubbi P, Irisson JO. Swimming Speeds Of Mediterranean Settlement-Stage Fish Larvae Nuance Hjort’s Aberrant Drift Hypothesis. At SFEcologie 2016, Marseille, 2016. [Talk]
Irisson JO, Paris CB, Leis JM, Yerman MN. With A Little Help From My Friends: Group Orientation By Larvae Of A Coral Reef Fish. PLoS ONE, 2015, PDF.
Faillettaz R, Blandin A, Paris CB, Koubbi P, Irisson JO. Sun-Compass Orientation In Mediterranean Fish Larvae. PLoS ONE, 2015, PDF.
Sukhovich A, Bonnieux S, Hello Y, Irisson JO, Simons FJ, Nolet G. Seismic Monitoring In The Oceans By Autonomous Floats. Nature Communications, 2015, PDF.
Howes EL, Stemmann L, Assailly C, Irisson JO, Dima M, Bijma J, Gattuso J. Pteropod Time Series From The North Western Mediterranean (1967-2003): Impacts Of Ph And Climate Variability. Marine Ecology Progress Series, 2015, PDF.

Teaching

I am teaching mostly in the oceanography Masters degree of Sorbonne Université. I am particularly involved in the following classes:

5UM31 Instrumentation and Acquisition of Data in Oceanography
5UM32 Methods for the Exploitation of Data in Oceanography
5UM35 Modelling of Marine Environments
4UM55 Multivariate Analyses for Marine Ecology

Research projects

I am involved in various projects that have in common the use of advanced statistical techniques and machine learning to solve ecological problems.

BRIDGE: Development of the automatic classification algorithm in an intelligent plankton camera to equip autonomous gliders and floats. Funded by the EU, FP7 program.
DL-PIC - Deep Learning for Plankton Image Classification: Exploration of specific deep learning modifications to account for size, hierarchy in the classes, etc. in order to improve the accuracy of the classification of plankton images. Funded by CNRS-LEFE.
EcoTaxa: Web application for the collaborative storage and classification of ecological images. Various ongoing sources of funding.
ARTIFACTZ: Use of machine learning methods, in particular deep learning, to extract ecological traits from images.

I am also coordinating the continuation of the collection of the long term plankton time series of Villefranche-sur-Mer (dating form 1966).

Code

I love coding. All of my code is Open Source. Most of it is on github and coded in R. A few examples:

apeep Process ISIIS data without a peep.
atlasr Niche modelling code for the Biogeographic Atlast of the Southern Ocean.
castr R package to process CTD casts.
chroma R package to handle colors.
discr Process and analyse the data of the Drifting In Situ Chamber (DISC).
ecotaxar R package to query EcoTaxa databases and process the output.
morphr R (+ python) package to combine many images together and create a morphotype of an object.
nppen Non-Parametric Probabilistic Ecological Niche from Beaugrand et al 2011, in R.
soundclass Signal classifier for sounds.
wkmeans Observation Weighted K-Means in R (with a Fortran backend).
yssr Your Static Site in R.