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author Orenstein, Eric C.
Ayata, Sakina‐Dorothée
Maps, Frédéric
Becker, Érica C.
Benedetti, Fabio
Biard, Tristan
de Garidel‐Thoron, Thibault
Ellen, Jeffrey S.
Ferrario, Filippo
Giering, Sarah L. C.
Guy‐Haim, Tamar
Hoebeke, Laura
Iversen, Morten Hvitfeldt
Kiørboe, Thomas
Lalonde, Jean‐François
Lana, Arancha
Laviale, Martin
Lombard, Fabien
Lorimer, Tom
Martini, Séverine
Meyer, Albin
Möller, Klas Ove
Niehoff, Barbara
Ohman, Mark D.
Pradalier, Cédric
Romagnan, Jean‐Baptiste
Schröder, Simon‐Martin
Sonnet, Virginie
Sosik, Heidi M.
Stemmann, Lars S.
Stock, Michiel
Terbiyik‐Kurt, Tuba
Valcárcel‐Pérez, Nerea
Vilgrain, Laure
Wacquet, Guillaume
Waite, Anya M.
Irisson, Jean‐Olivier
author_facet Orenstein, Eric C.
Ayata, Sakina‐Dorothée
Maps, Frédéric
Becker, Érica C.
Benedetti, Fabio
Biard, Tristan
de Garidel‐Thoron, Thibault
Ellen, Jeffrey S.
Ferrario, Filippo
Giering, Sarah L. C.
Guy‐Haim, Tamar
Hoebeke, Laura
Iversen, Morten Hvitfeldt
Kiørboe, Thomas
Lalonde, Jean‐François
Lana, Arancha
Laviale, Martin
Lombard, Fabien
Lorimer, Tom
Martini, Séverine
Meyer, Albin
Möller, Klas Ove
Niehoff, Barbara
Ohman, Mark D.
Pradalier, Cédric
Romagnan, Jean‐Baptiste
Schröder, Simon‐Martin
Sonnet, Virginie
Sosik, Heidi M.
Stemmann, Lars S.
Stock, Michiel
Terbiyik‐Kurt, Tuba
Valcárcel‐Pérez, Nerea
Vilgrain, Laure
Wacquet, Guillaume
Waite, Anya M.
Irisson, Jean‐Olivier
author_sort Orenstein, Eric C.
collection PubMed
description Plankton imaging systems supported by automated classification and analysis have improved ecologists' ability to observe aquatic ecosystems. Today, we are on the cusp of reliably tracking plankton populations with a suite of lab‐based and in situ tools, collecting imaging data at unprecedentedly fine spatial and temporal scales. But these data have potential well beyond examining the abundances of different taxa; the individual images themselves contain a wealth of information on functional traits. Here, we outline traits that could be measured from image data, suggest machine learning and computer vision approaches to extract functional trait information from the images, and discuss promising avenues for novel studies. The approaches we discuss are data agnostic and are broadly applicable to imagery of other aquatic or terrestrial organisms.
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spelling pubmed-95433512022-10-14 Machine learning techniques to characterize functional traits of plankton from image data Orenstein, Eric C. Ayata, Sakina‐Dorothée Maps, Frédéric Becker, Érica C. Benedetti, Fabio Biard, Tristan de Garidel‐Thoron, Thibault Ellen, Jeffrey S. Ferrario, Filippo Giering, Sarah L. C. Guy‐Haim, Tamar Hoebeke, Laura Iversen, Morten Hvitfeldt Kiørboe, Thomas Lalonde, Jean‐François Lana, Arancha Laviale, Martin Lombard, Fabien Lorimer, Tom Martini, Séverine Meyer, Albin Möller, Klas Ove Niehoff, Barbara Ohman, Mark D. Pradalier, Cédric Romagnan, Jean‐Baptiste Schröder, Simon‐Martin Sonnet, Virginie Sosik, Heidi M. Stemmann, Lars S. Stock, Michiel Terbiyik‐Kurt, Tuba Valcárcel‐Pérez, Nerea Vilgrain, Laure Wacquet, Guillaume Waite, Anya M. Irisson, Jean‐Olivier Limnol Oceanogr Review Plankton imaging systems supported by automated classification and analysis have improved ecologists' ability to observe aquatic ecosystems. Today, we are on the cusp of reliably tracking plankton populations with a suite of lab‐based and in situ tools, collecting imaging data at unprecedentedly fine spatial and temporal scales. But these data have potential well beyond examining the abundances of different taxa; the individual images themselves contain a wealth of information on functional traits. Here, we outline traits that could be measured from image data, suggest machine learning and computer vision approaches to extract functional trait information from the images, and discuss promising avenues for novel studies. The approaches we discuss are data agnostic and are broadly applicable to imagery of other aquatic or terrestrial organisms. John Wiley & Sons, Inc. 2022-06-30 2022-08 /pmc/articles/PMC9543351/ /pubmed/36247386 http://dx.doi.org/10.1002/lno.12101 Text en © 2022 The Authors. Limnology and Oceanography published by Wiley Periodicals LLC on behalf of Association for the Sciences of Limnology and Oceanography. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Review
Orenstein, Eric C.
Ayata, Sakina‐Dorothée
Maps, Frédéric
Becker, Érica C.
Benedetti, Fabio
Biard, Tristan
de Garidel‐Thoron, Thibault
Ellen, Jeffrey S.
Ferrario, Filippo
Giering, Sarah L. C.
Guy‐Haim, Tamar
Hoebeke, Laura
Iversen, Morten Hvitfeldt
Kiørboe, Thomas
Lalonde, Jean‐François
Lana, Arancha
Laviale, Martin
Lombard, Fabien
Lorimer, Tom
Martini, Séverine
Meyer, Albin
Möller, Klas Ove
Niehoff, Barbara
Ohman, Mark D.
Pradalier, Cédric
Romagnan, Jean‐Baptiste
Schröder, Simon‐Martin
Sonnet, Virginie
Sosik, Heidi M.
Stemmann, Lars S.
Stock, Michiel
Terbiyik‐Kurt, Tuba
Valcárcel‐Pérez, Nerea
Vilgrain, Laure
Wacquet, Guillaume
Waite, Anya M.
Irisson, Jean‐Olivier
Machine learning techniques to characterize functional traits of plankton from image data
title Machine learning techniques to characterize functional traits of plankton from image data
title_full Machine learning techniques to characterize functional traits of plankton from image data
title_fullStr Machine learning techniques to characterize functional traits of plankton from image data
title_full_unstemmed Machine learning techniques to characterize functional traits of plankton from image data
title_short Machine learning techniques to characterize functional traits of plankton from image data
title_sort machine learning techniques to characterize functional traits of plankton from image data
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9543351/
https://www.ncbi.nlm.nih.gov/pubmed/36247386
http://dx.doi.org/10.1002/lno.12101
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