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Machine learning techniques to characterize functional traits of plankton from image data
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 unprecedentedl...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley & Sons, Inc.
2022
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Materias: | |
Acceso en línea: | 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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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. |
format | Online Article Text |
id | pubmed-9543351 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | John Wiley & Sons, Inc. |
record_format | MEDLINE/PubMed |
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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