IMIS - Marine Onderzoeksgroepen | Compendium Coast and Sea

Lagaisse, Rune
ORCID

Expertise
Previous institute
Publications (18)
Projects (8)
Datasets (16)

Thesaurus term: Marine ecology

Vlaams Instituut voor de Zee (VLIZ), more

Function: Researcher
Period: From 1st Mar 2021 till 26th Jan 2025

From sky to seafloor observation: Achieving eXcellence in Oceanic surveiLlance and cOnservation Through deep Learning , more
Genetic Tools for Ecosystem Health Assessment in the North Sea Region, more
Genomic Observatories under European Projects EMO BON and ARMS-MBON, more
Imaging data and services for aquatic science, more
Integration of biodiversity monitoring data into the Digital Twin Ocean, more
MARine COastal BiOdiversity Long-term Observations, more
Operational sensing life technologies for marine ecosystems, more
Post-brexit coastal pelagic fisheries, more

Data products [show]
Decrop, W., & Lagaisse, R. (2025). Pre-trained Phytoplankton species classifier Model. Zenodo., more Decrop, W., Lagaisse, R., Mortelmans, J., Muyle, J., Amadei Martínez, L., & Deneudt, K. (2025). LifeWatch observatory data: phytoplankton annotated trainingset by FlowCam imaging in the Belgian Part of the North Sea [Data set]. Zenodo., more
Data [show]
Decrop, W., Lagaisse, R., Jonas, M., Muyle, J., Amadei Martínez, L., & Deneudt, K. (2024). LifeWatch observatory data: phytoplankton annotated trainingset by FlowCam imaging in the Belgian Part of the North Sea (Versie v1). Zenodo., more Flanders Marine Institute (VLIZ), Belgium (2026): LifeWatch observatory data: phytoplankton observations by FlowCam imaging in the Belgian Part of the North Sea., more Lagaisse, R.; Flanders Marine Institute: Belgium; (2020): Phytoplankton biodiversity in the Belgian part of the North Sea: a microscopic and molecular inventory, more Lagaisse, Rune, R.; Amadei Martinez, Luz, L.; Decrop, Wout, W.; Deneudt, Klaas, K.; Muyle, Julie, J.; Mortelmans, Jonas, J.; Flanders Marine Institute (VLIZ): Belgium; (2024): LifeWatch observatory data: phytoplankton annotated image library by FlowCam imaging for the Belgian part of the North Sea. Marine Data Archive., more Mortelmans, J.; Lagaisse, R.; Rombouts, I., Artigas, F.; Hubert, Z.; Gallot, C.; Flanders Marine Institute: Belgium; Centre national de la recherce scientifique: France; (2020): Plankton biodiversity data from a LifeWatch/Jerico North Sea Cruise with R/V Simon Stevin in May 2022, more HBS GEANS: Obst M., Stæhr P., Sundberg P., Reiss H., Daraghmeh N., Axberg A., Deneudt K., Hablutzel P., Mortelmans J., Delacauw S., Lagaisse R. (2019) Hard Bottom Substrate pilot GEANS, more Pagnier J.; Allcock L.; Cancio I.; Chatzinikolaou E.; Chatzigeorgiou G.; Chrismas NAM.; Costantini F.; Dailianis T.; Deneudt K.; Diaz de Cerio, O.; Digenis M.; Exter K.; GerovasileiouV.; , González Fernández J.; Kauppi L.; Keklikoglou K.; Kristoffersen JB.; Lagaisse R.; Mavrič B.; Mortelmans J.; Paredes E.; Pavloudi C.; Piazza A.; Power AM.; Ramšak A.; Santi I.; Solbakken J.; Stavroulaki M.; Stæhr PAU.; Tajadura J.; Souza Troncoso J.; Vasileiadou K.; Vernadou E.; Obst M. (2025): ARMS-MBON data on long-term monitoring of hard-bottom communities: 18S results from 2020-2022, more Pagnier J.; Allcock L.; Cancio I.; Chatzinikolaou E.; Chatzigeorgiou G.; Chrismas NAM.; Costantini F.; Dailianis T.; Deneudt K.; Diaz de Cerio, O.; Digenis M.; Exter K.; GerovasileiouV.; , González Fernández J.; Kauppi L.; Keklikoglou K.; Kristoffersen JB.; Lagaisse R.; Mavrič B.; Mortelmans J.; Paredes E.; Pavloudi C.; Piazza A.; Power AM.; Ramšak A.; Santi I.; Solbakken J.; Stavroulaki M.; Stæhr PAU.; Tajadura J.; Souza Troncoso J.; Vasileiadou K.; Vernadou E.; Obst M. (2025): ARMS-MBON data on long-term monitoring of hard-bottom communities: COI results from 2020-2022, more Pagnier J.; Allcock L.; Cancio I.; Chatzinikolaou E.; Chatzigeorgiou G.; Chrismas NAM.; Costantini F.; Dailianis T.; Deneudt K.; Diaz de Cerio, O.; Digenis M.; Exter K.; GerovasileiouV.; , González Fernández J.; Kauppi L.; Keklikoglou K.; Kristoffersen JB.; Lagaisse R.; Mavrič B.; Mortelmans J.; Paredes E.; Pavloudi C.; Piazza A.; Power AM.; Ramšak A.; Santi I.; Solbakken J.; Stavroulaki M.; Stæhr PAU.; Tajadura J.; Souza Troncoso J.; Vasileiadou K.; Vernadou E.; Obst M. (2025): ARMS-MBON data on long-term monitoring of hard-bottom communities: ITS results from 2020-2022, more EMO BON: European Marine Omics Biodiversity Observation Network 2021 genomic observations (18S v4, COI, ITS1F, ITS2) in the Belgian Part of the North Sea, more EMO BON: European Marine Omics Biodiversity Observation Network 2022 genomic observations (18S v4, COI, ITS1F, ITS2) in the Belgian Part of the North Sea, more EMO BON: European Marine Omics Biodiversity Observation Network 2023 genomic observations (18S v4, COI, ITS1F, ITS2) in the Belgian Part of the North Sea, more
Other [show]
EMBRC-BE Joint Development Activity: Optimisation of in-situ sampling from ARMS in dynamic coastal environments, more EMO BON: European Marine Omics Biodiversity Observation Network 2024 genomic observations (18S v4, COI, ITS1F, ITS2) in the Belgian Part of the North Sea, more

A1 Publications (10) [show]
Santi, Ioulia; Pavloudi, Christina; Abagnale, Maria; Azua, Iñigo; Baña, Zuriñe; Bastianini, Mauro; Belser, Caroline; Berg, Kristel; Bilbao, Jone; Bird, Kimberley; Broudin, Caroline; Camusat, Mathieu; Cancio, Ibon; Caray-Counil, Louis; Casotti, Raffaella; Castel, Jade; Comtet, Thierry; Cox, Cymon; Cunliffe, Michael; Daguin, Claire; Deneudt, Klaas; Díaz de Cerio, Oihane; Exter, Katrina; Fauvelot, Cécile; Fontana, Yann; Frada, Miquel; Galand, Pierre; Gallia, Roberto; Garczarek, Laurence; González Fernández, Jose; Guillou, Laure; Heynderickx, Hanneloor; Koplovitz, Gil; Labrune, Celine; Lagaisse, Rune; Laroquette, Arnaud; Lescure, Lyvia; Lopes, Eva; Loulakaki, Melina; Louro, Bruno; Magalhães, Catarina; Margiotta, Francesca; Moal, Hannah; Moussy, Alice; Not, Fabrice; Percopo, Isabella; Paredes Rosendo, Estefanía; Péru, Erwan; Poulain, Julie; Praebel, Kim; Rigaut-Jalabert, Fabienne; Romac, Sarah; Rzeznik-Orignac, Jadwiga; Sarno, Diana; Souza Troncoso, Jesús; Thiébaut, Eric; Thomas, Wilfried; Tkacz, Andrzej; Tramontano, Ferdinando; Trano, Anna Chiara; Wincker, Patrick; Pade, Nicolas (2026). Next release of the European Marine Omics Biodiversity Observation Network (EMO BON) shotgun metagenomic data from water and sediment samples (Release 2). Biodiversity Data Journal 14: e178484. https://dx.doi.org/10.3897/bdj.14.e178484, more Azmi, E.; Alibabaei, K.; Kozlov, V.; Krijger, T.; Accarino, G.; Ayata, S.-D.; Calatrava, A.; De Carlo, M.M.; Decrop, W.; Elia, D.; Fiore, L.; Francescangeli, M.; Irisson, J.-O.; Lagaisse, R.; Laviale, M.; Lebeaud, A.; Leluschko, C.; Martínez, E.; Moltó, G.; Atake, I.R.; Antonio Augusto, S.N.; Damian, S.; Jesus, S.-G.; Tayyab, M.A.; Tosello, V.; López García, A.; Schaap, D.; Sipos, G. (2025). Best practices for AI-based image analysis applications in aquatic sciences: The iMagine case study. Ecological Informatics 91: 103306. https://dx.doi.org/10.1016/j.ecoinf.2025.103306, more Decrop, W.; Lagaisse, R.; Mortelmans, J.; Muñiz, C.; Heredia, I.; Calatrava, A.; Deneudt, K. (2025). Automated image classification workflow for phytoplankton monitoring. Front. Mar. Sci. 12: 1699781. https://dx.doi.org/10.3389/fmars.2025.1699781, more Lagaisse, R.; Dillen, N.; Bakeev, D.; Decrop, W.; Focke, P.; Mortelmans, J.; Muyle, J.; Deneudt, K. (2025). Advancing long-term phytoplankton biodiversity assessment in the North Sea using an imaging approach. Scientific Data 12: 1989. https://dx.doi.org/10.1038/s41597-025-06278-w, more Pagnier, Justine; Allcock, Louise; Cancio, Ibon; Chatzinikolaou, Eva; Chatzigeorgiou, Giorgos; Chrismas, Nathan; Costantini, Federica; Dailianis, Thanos; Deneudt, Klaas; Díaz de Cerio, Oihane; Digenis, Markos; Exter, Katrina; Gerovasileiou, Vasilis; González Fernández, Jose; Kauppi, Laura; Keklikoglou, Kleoniki; Kristoffersen, Jon Bent; Lagaisse, Rune; Mavrič, Borut; Mortelmans, Jonas; Paredes, Estefania; Pavloudi, Christina; Piazza, Alessandro; Power, Anne Marie; Ramšak, Andreja; Santi, Ioulia; Solbakken, Jostein; Stavroulaki, Melanthia; Stæhr, Peter; Tajadura, Javier; Souza Troncoso, Jesus; Vasileiadou, Katerina; Vernadou, Emmanouela; Obst, Matthias (2025). A long-term ecological research dataset from the marine genetic monitoring programme ARMS-MBON 2020-2021. Biodiversity Data Journal 13: e148981. https://dx.doi.org/10.3897/bdj.13.e148981, more Pavloudi, C.; Santi, I.; Azua, I.; Baña, Z.; Bastianini, M.; Belser, C.; Bilbao, J.; Bitz-Thorsen, J.; Broudin, C.; Camusat, M.; Cancio, I.; Caray-Counil, L.; Casotti, R.; Castel, J.; Comtet, T.; Cox, C.J.; Daguin, C.; Díaz, O.; Diaz de Cerio, O.; Exter, K.; Fauvelot, C.; Frada, M.J.; Galand, P.E.; Garczarek, L.; González Fernández, J.; Guillou, L.; Hablützel, P.I.; Heynderickx, H.; Houbin, C.; Kervella, A.E.; Krystallas, A.; Lagaisse, R.; Laroquette, A.; Lescure, L.; Lopes, E.; Loulakaki, M.; Louro, B.; Magalhães, C.; Maidanou, M.; Margiotta, F.; Montresor, M.; Not, F.; Paredes, E.; Percopo, I.; Péru, E.; Poulain, J.; Praebel, K.; Rigaut-Jalabert, F.; Romac, S.; Stavroulaki, M.; Troncoso, J.S.; Thiebaut, E.; Thomas, W.; Tkacz, A.; Trano, A.C.; Wincker, P.; Pade, N. (2025). First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples. Biodiversity Data Journal 13: e143585. https://dx.doi.org/10.3897/BDJ.13.e143585, more Mortelmans, J.; Semmouri, I.; Perneel, M.; Lagaisse, R.; Amadei Martínez, L.; Rommelaere, Z.; Hablützel, P.; Deneudt, K. (2024). Temperature-induced copepod depletion and the associated wax of Bellerochea in Belgian coastal waters: Implications and shifts in plankton dynamics. J. Sea Res. 201: 102523. https://dx.doi.org/10.1016/j.seares.2024.102523, more Perneel, M.; Lagaisse, R.; Mortelmans, J.; Maere, S.; Hablützel, P. (2024). Seasonal metabolic dynamics of microeukaryotic plankton: A year-long metatranscriptomic study in a temperate sea. mBio Online first(8): 1-17. https://dx.doi.org/10.1128/mbio.00383-24, more Santi, Ioulia; Beluche, Odette; Beraud, Mélanie; Buttigieg, Pier Luigi; Casotti, Raffaella; Cox, Cymon J.; Cunliffe, Michael; Davies, Neil; de Cerio, Oihane Diaz; Exter, Katrina; Kervella, Anne Emmanuelle; Kotoulas, Georgios; Lagaisse, Rune; Laroquette, Arnaud; Louro, Bruno; Not, Fabrice; Obst, Matthias; Pavloudi, Christina; Poulain, Julie; Præbel, Kim; Vanaverbeke, Jan; Pade, Nicolas (2023). European marine omics biodiversity observation network: A strategic outline for the implementation of omics approaches in ocean observation. Front. Mar. Sci. 10(1118120): 1-13. https://dx.doi.org/10.3389/fmars.2023.1118120, more Hablützel, P.I.; Rombouts, I.; Dillen, N.; Lagaisse, R.; Mortelmans, J.; Ollevier, A.; Perneel, M.; Deneudt, K. (2021). Exploring new technologies for plankton observations and monitoring of ocean health, in: Kappel, E.S. et al. Frontiers in ocean observing: Documenting ecosystems, understanding environmental changes, forecasting hazards. Oceanography, Suppl. 34(4): pp. 20-25. https://dx.doi.org/10.5670/oceanog.2021.supplement.02-09, more
Book [show]
Lagaisse, R. (2024). LifeWatch Belgium: FlowCam sampling and lab protocol for imaging microphytoplankton in the Belgian part of the North Sea. Flanders Marine Institute: Oostende. 10 pp. https://dx.doi.org/10.17504/protocols.io.6qpvr8e6zlmk/v1, more
Book chapters (2) [show]
De Cauwer, K.; Courtens, W.; De Witte, B.; De Schrijver, C.; Degraer, S.; Deneudt, K.; Desmidt, J.; Desmit, X.; Devos, K.; Everaert, G.; Francken, F.; Haelters, J.; Hostens, K.; Kapasakali, D.; Kerckhof, F.; Kerkhove, T.; Kint, L.; Knockaert, M.; Lagaisse, R.; Legrand, S.; Maes, J.; Montereale Gavazzi, G.; Moreau, K.; Norro, A.; Ochetti, F.E.; Parmentier, K.; Podholova, P.; Ponsar, S.; Rombouts, I.; Rumes, B.; Schallier, R.; Stienen, E.; Terseleer, N.; Vanavermaete, D.; Vanermen, N.; Van de walle, M.; Van der Zande, D.; Vanhalst, K.; Van Hoey, G.; Van Lancker, V.; Van Nieuwenhove, A.; Verlé, K.; Verstraete, H. (2025). Samenvatting van de staat van het marien milieu, in: Belgische Staat Mariene Strategie Deel 1 voor de Belgische mariene wateren. Staat van Belgische mariene wateren, goede milieutoestand en milieudoelen. Kaderrichtlijn Mariene Strategie - Artikel 8, 9 en 10. pp. 11-60, more Decrop, W.; Lagaisse, R.; Mortelmans, J.; Muñiz, C.; Deneudt, K. (2025). Design and implementation of an automated Image classification workflow for phytoplankton monitoring, in: Praet, N. et al. Particles in Europe 2025: Conference program and proceedings, 17 - 19 September 2025, Ostend, Belgium. pp. 62-70, more
Thesis [show]
Lagaisse, R. (2020). Phytoplankton biodiversity in the Belgian part of the North Sea: a microscopic and molecular inventory. MSc Thesis. Ghent University, Biology Department: Gent. 117 pp., more
Abstracts (4) [show]
Dujardin, J.; Perneel, M.; Lagaisse, R.; Larrinoa, N.; Mortelmans, J.; Theetaert, H.; Verbrugge, S.; Gkritzalis, T.; De Rijcke, M.; Maere, S.; Hablützel, P.I. (2024). From bloom to foam: Tracing the role of Phaeocystis in marine gel formation, in: Mees, J. et al. Book of abstracts – VLIZ Marine Science Day, 6 March 2024, Oostende. VLIZ Special Publication, 91: pp. 18-19, more Lagaisse, R.; Decrop, W.; Deneudt, K. (2024). AI in marine sciences: an open-access integrated environment for automated classification of phytoplankton images, in: Mees, J. et al. Book of abstracts – VLIZ Marine Science Day, 6 March 2024, Oostende. VLIZ Special Publication, 91: pp. 82, more Ollevier, A.; Ponsoni, L.; Develter, R.; Mortelmans, J.; Lagaisse, R.; De Troch, M.; Hablützel, P.; Boone, W. (2023). Oceanic drivers, nutrient dynamics and plankton communities in West-Greenland’s fjord system: A multidisciplinary study, in: Mees, J. et al. Book of abstracts – VLIZ Marine Science Day, 1 March 2023, Bruges. VLIZ Special Publication, 90: pp. 79, more Lagaisse, R.; Dillen, N.; Deneudt, K.; Hablützel, P. (2022). Working in a new era of automated classification in micro- (phyto)plankton monitoring: a FlowCAM case study, in: Mees, J. et al. Book of abstracts – VLIZ Marine Science Day, Online event 2 March 2022. VLIZ Special Publication, 88: pp. 58, more