Articles | Volume 39, issue 2
https://doi.org/10.5194/jm-39-183-2020
© Author(s) 2020. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/jm-39-183-2020
© Author(s) 2020. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
15 Oct 2020
Research article |
| 15 Oct 2020
| 15 Oct 2020
Automated analysis of foraminifera fossil records by image classification using a convolutional neural network
Aix-Marseille Université, CNRS, IRD, Coll. De France, INRAE, CEREGE, Technopôle de l'Arbois-Méditerranée, Aix-en-Provence, 13545, France
School of Electrical Engineering & Robotics, Queensland University of Technology, Brisbane, Australia
Martin Tetard
Aix-Marseille Université, CNRS, IRD, Coll. De France, INRAE, CEREGE, Technopôle de l'Arbois-Méditerranée, Aix-en-Provence, 13545, France
Adnya Pratiwi
Aix-Marseille Université, CNRS, IRD, Coll. De France, INRAE, CEREGE, Technopôle de l'Arbois-Méditerranée, Aix-en-Provence, 13545, France
Michael Adebayo
Aix-Marseille Université, CNRS, IRD, Coll. De France, INRAE, CEREGE, Technopôle de l'Arbois-Méditerranée, Aix-en-Provence, 13545, France
Thibault de Garidel-Thoron
Aix-Marseille Université, CNRS, IRD, Coll. De France, INRAE, CEREGE, Technopôle de l'Arbois-Méditerranée, Aix-en-Provence, 13545, France
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Martin Tetard, Ross Marchant, Giuseppe Cortese, Yves Gally, Thibault de Garidel-Thoron, and Luc Beaufort
Clim. Past, 16, 2415–2429, https://doi.org/10.5194/cp-16-2415-2020, https://doi.org/10.5194/cp-16-2415-2020, 2020
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Radiolarians are marine micro-organisms that produce a siliceous shell that is preserved in the fossil record and can be used to reconstruct past climate variability. However, their study is only possible after a time-consuming manual selection of their shells from the sediment followed by their individual identification. Thus, we develop a new fully automated workflow consisting of microscopic radiolarian image acquisition, image processing and identification using artificial intelligence.
Babette Hoogakker, Catherine Davis, Yi Wang, Stepanie Kusch, Katrina Nilsson-Kerr, Dalton Hardisty, Allison Jacobel, Dharma Reyes Macaya, Nicolaas Glock, Sha Ni, Julio Sepúlveda, Abby Ren, Alexandra Auderset, Anya Hess, Katrina Meissner, Jorge Cardich, Robert Anderson, Christine Barras, Chandranath Basak, Harold Bradbury, Inda Brinkmann, Alexis Castillo, Madelyn Cook, Kassandra Costa, Constance Choquel, Paula Diz, Jonas Donnenfield, Felix Elling, Zeynep Erdem, Helena Filipsson, Sebastian Garrido, Julia Gottschalk, Anjaly Govindankutty Menon, Jeroen Groeneveld, Christian Hallman, Ingrid Hendy, Rick Hennekam, Wanyi Lu, Jean Lynch-Stieglitz, Lelia Matos, Alfredo Martínez-García, Giulia Molina, Práxedes Muñoz, Simone Moretti, Jennifer Morford, Sophie Nuber, Svetlana Radionovskaya, Morgan Raven, Christopher Somes, Anja Studer, Kazuyo Tachikawa, Raúl Tapia, Martin Tetard, Tyler Vollmer, Shuzhuang Wu, Yan Zhang, Xin-Yuan Zheng, and Yuxin Zhou
EGUsphere, https://doi.org/10.5194/egusphere-2023-2981, https://doi.org/10.5194/egusphere-2023-2981, 2024
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Paleo-oxygen proxies can extend current records, bound pre-anthropogenic baselines, provide datasets necessary to test climate models under different boundary conditions, and ultimately understand how ocean oxygenation responds on longer timescales. Here we summarize current proxies used for the reconstruction of Cenozoic seawater oxygen levels. This includes an overview of the proxy's history, how it works, resources required, limitations, and future recommendations.
Martin Tetard, Laetitia Licari, Ekaterina Ovsepyan, Kazuyo Tachikawa, and Luc Beaufort
Biogeosciences, 18, 2827–2841, https://doi.org/10.5194/bg-18-2827-2021, https://doi.org/10.5194/bg-18-2827-2021, 2021
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Oxygen minimum zones are oceanic regions almost devoid of dissolved oxygen and are currently expanding due to global warming. Investigation of their past behaviour will allow better understanding of these areas and better prediction of their future evolution. A new method to estimate past [O2] was developed based on morphometric measurements of benthic foraminifera. This method and two other approaches based on foraminifera assemblages and porosity were calibrated using 45 core tops worldwide.
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Radiolarians are marine micro-organisms that produce a siliceous shell that is preserved in the fossil record and can be used to reconstruct past climate variability. However, their study is only possible after a time-consuming manual selection of their shells from the sediment followed by their individual identification. Thus, we develop a new fully automated workflow consisting of microscopic radiolarian image acquisition, image processing and identification using artificial intelligence.
Related subject area
Planktic foraminifera
Pliocene–Pleistocene warm-water incursions and water mass changes on the Ross Sea continental shelf (Antarctica) based on foraminifera from IODP Expedition 374
Rediscovering Globigerina bollii Cita and Premoli Silva 1960
Biochronology and evolution of Pulleniatina (planktonic foraminifera)
Globigerinoides rublobatus – a new species of Pleistocene planktonic foraminifera
Analysing planktonic foraminiferal growth in three dimensions with foram3D: an R package for automated trait measurements from CT scans
Spine-like structures in Paleogene muricate planktonic foraminifera
Taxonomic review of living planktonic foraminifera
Upper Eocene planktonic foraminifera from northern Saudi Arabia: implications for stratigraphic ranges
Jurassic planktic foraminifera from the Polish Basin
Middle Jurassic (Bajocian) planktonic foraminifera from the northwest Australian margin
Ontogenetic disparity in early planktic foraminifers
Seasonal and interannual variability in population dynamics of planktic foraminifers off Puerto Rico (Caribbean Sea)
Calcification depth of deep-dwelling planktonic foraminifera from the eastern North Atlantic constrained by stable oxygen isotope ratios of shells from stratified plankton tows
Reproducibility of species recognition in modern planktonic foraminifera and its implications for analyses of community structure
Factors affecting consistency and accuracy in identifying modern macroperforate planktonic foraminifera
Julia L. Seidenstein, R. Mark Leckie, Robert McKay, Laura De Santis, David Harwood, and IODP Expedition 374 Scientists
J. Micropalaeontol., 43, 211–238, https://doi.org/10.5194/jm-43-211-2024, https://doi.org/10.5194/jm-43-211-2024, 2024
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Warmer waters in the Southern Ocean have led to the loss of Antarctic ice during past interglacial times. The shells of foraminifera are preserved in Ross Sea sediment, which is collected in cores. Benthic species from Site U1523 inform us about changing water masses and current activity, including incursions of Circumpolar Deep Water. Warm water planktic species were found in sediment samples from four intervals within 3.72–1.82 million years ago, indicating warmer than present conditions.
Alessio Fabbrini, Maria Rose Petrizzo, Isabella Premoli Silva, Luca M. Foresi, and Bridget S. Wade
J. Micropalaeontol., 43, 121–138, https://doi.org/10.5194/jm-43-121-2024, https://doi.org/10.5194/jm-43-121-2024, 2024
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We report on the rediscovery of Globigerina bollii, a planktonic foraminifer described by Cita and Premoli Silva (1960) in the Mediterranean Basin. We redescribe G. bollii as a valid species belonging to the genus Globoturborotalita. We report and summarise all the recordings of the taxon in the scientific literature. Then we discuss how the taxon might be a palaeogeographical indicator of the intermittent gateways between the Mediterranean Sea, Paratethys, and Indian Ocean.
Paul N. Pearson, Jeremy Young, David J. King, and Bridget S. Wade
J. Micropalaeontol., 42, 211–255, https://doi.org/10.5194/jm-42-211-2023, https://doi.org/10.5194/jm-42-211-2023, 2023
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Planktonic foraminifera are marine plankton that have a long and continuous fossil record. They are used for correlating and dating ocean sediments and studying evolution and past climates. This paper presents new information about Pulleniatina, one of the most widespread and abundant groups, from an important site in the Pacific Ocean. It also brings together a very large amount of information on the fossil record from other sites globally.
Marcin Latas, Paul N. Pearson, Christopher R. Poole, Alessio Fabbrini, and Bridget S. Wade
J. Micropalaeontol., 42, 57–81, https://doi.org/10.5194/jm-42-57-2023, https://doi.org/10.5194/jm-42-57-2023, 2023
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Planktonic foraminifera are microscopic single-celled organisms populating world oceans. They have one of the most complete fossil records; thanks to their great abundance, they are widely used to study past marine environments. We analysed and measured series of foraminifera shells from Indo-Pacific sites, which led to the description of a new species of fossil planktonic foraminifera. Part of its population exhibits pink pigmentation, which is only the third such case among known species.
Anieke Brombacher, Alex Searle-Barnes, Wenshu Zhang, and Thomas H. G. Ezard
J. Micropalaeontol., 41, 149–164, https://doi.org/10.5194/jm-41-149-2022, https://doi.org/10.5194/jm-41-149-2022, 2022
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Foraminifera are sand-grain-sized marine organisms that build spiral shells. When they die, the shells sink to the sea floor where they are preserved for millions of years. We wrote a software package that automatically analyses the fossil spirals to learn about evolution of new shapes in the geological past. With this software we will be able to analyse larger datasets than we currently can, which will improve our understanding of the evolution of new species.
Paul N. Pearson, Eleanor John, Bridget S. Wade, Simon D'haenens, and Caroline H. Lear
J. Micropalaeontol., 41, 107–127, https://doi.org/10.5194/jm-41-107-2022, https://doi.org/10.5194/jm-41-107-2022, 2022
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The microscopic shells of planktonic foraminifera accumulate on the sea floor over millions of years, providing a rich archive for understanding the history of the oceans. We examined an extinct group that flourished between about 63 and 32 million years ago using scanning electron microscopy and show that they were covered with needle-like spines in life. This has implications for analytical methods that we use to determine past seawater temperature and acidity.
Geert-Jan A. Brummer and Michal Kučera
J. Micropalaeontol., 41, 29–74, https://doi.org/10.5194/jm-41-29-2022, https://doi.org/10.5194/jm-41-29-2022, 2022
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To aid researchers working with living planktonic foraminifera, we provide a comprehensive review of names that we consider appropriate for extant species. We discuss the reasons for the decisions we made and provide a list of species and genus-level names as well as other names that have been used in the past but are considered inappropriate for living taxa, stating the reasons.
Bridget S. Wade, Mohammed H. Aljahdali, Yahya A. Mufrreh, Abdullah M. Memesh, Salih A. AlSoubhi, and Iyad S. Zalmout
J. Micropalaeontol., 40, 145–161, https://doi.org/10.5194/jm-40-145-2021, https://doi.org/10.5194/jm-40-145-2021, 2021
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We examined the planktonic foraminifera (calcareous zooplankton) from a section in northern Saudi Arabia. We found the assemblages to be diverse, well-preserved and of late Eocene age. Our study provides new insights into the stratigraphic ranges of many species and indicates that the late Eocene had a higher tropical/subtropical diversity of planktonic foraminifera than previously reported.
Maria Gajewska, Zofia Dubicka, and Malcolm B. Hart
J. Micropalaeontol., 40, 1–13, https://doi.org/10.5194/jm-40-1-2021, https://doi.org/10.5194/jm-40-1-2021, 2021
Marjorie Apthorpe
J. Micropalaeontol., 39, 93–115, https://doi.org/10.5194/jm-39-93-2020, https://doi.org/10.5194/jm-39-93-2020, 2020
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Three well-preserved new species of Middle Jurassic (Bajocian) planktonic foraminifera from the continental margin of northwest Australia are described. This is on the southern shelf of the Tethys Ocean, and these planktonics are the first to be reported from the Jurassic Southern Hemisphere. Described as new are Globuligerina bathoniana australiana n. ssp., G. altissapertura n. sp. and Mermaidogerina loopae n. gen. n. sp. The research is part of a study of regional Jurassic foraminifera.
Sophie Kendall, Felix Gradstein, Christopher Jones, Oliver T. Lord, and Daniela N. Schmidt
J. Micropalaeontol., 39, 27–39, https://doi.org/10.5194/jm-39-27-2020, https://doi.org/10.5194/jm-39-27-2020, 2020
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Changes in morphology during development can have profound impacts on an organism but are hard to quantify as we lack preservation in the fossil record. As they grow by adding chambers, planktic foraminifera are an ideal group to study changes in growth in development. We analyse four different species of Jurassic foraminifers using a micro-CT scanner. The low morphological variability suggests that strong constraints, described in the modern ocean, were already acting on Jurassic specimens.
Anna Jentzen, Joachim Schönfeld, Agnes K. M. Weiner, Manuel F. G. Weinkauf, Dirk Nürnberg, and Michal Kučera
J. Micropalaeontol., 38, 231–247, https://doi.org/10.5194/jm-38-231-2019, https://doi.org/10.5194/jm-38-231-2019, 2019
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The study assessed the population dynamics of living planktic foraminifers on a weekly, seasonal, and interannual timescale off the coast of Puerto Rico to improve our understanding of short- and long-term variations. The results indicate a seasonal change of the faunal composition, and over the last decades. Lower standing stocks and lower stable carbon isotope values of foraminifers in shallow waters can be linked to the hurricane Sandy, which passed the Greater Antilles during autumn 2012.
Andreia Rebotim, Antje Helga Luise Voelker, Lukas Jonkers, Joanna J. Waniek, Michael Schulz, and Michal Kucera
J. Micropalaeontol., 38, 113–131, https://doi.org/10.5194/jm-38-113-2019, https://doi.org/10.5194/jm-38-113-2019, 2019
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To reconstruct subsurface water conditions using deep-dwelling planktonic foraminifera, we must fully understand how the oxygen isotope signal incorporates into their shell. We report δ18O in four species sampled in the eastern North Atlantic with plankton tows. We assess the size and crust effect on the isotopic δ18O and compared them with predictions from two equations. We reveal different patterns of calcite addition with depth, highlighting the need to perform species-specific calibrations.
Nadia Al-Sabouni, Isabel S. Fenton, Richard J. Telford, and Michal Kučera
J. Micropalaeontol., 37, 519–534, https://doi.org/10.5194/jm-37-519-2018, https://doi.org/10.5194/jm-37-519-2018, 2018
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In this study we investigate consistency in species-level identifications and whether disagreements are predictable. Overall, 21 researchers from across the globe identified sets of 300 specimens or digital images of planktonic foraminifera. Digital identifications tended to be more disparate. Participants trained by the same person often had more similar identifications. Disagreements hardly affected transfer-function temperature estimates but produced larger differences in diversity metrics.
Isabel S. Fenton, Ulrike Baranowski, Flavia Boscolo-Galazzo, Hannah Cheales, Lyndsey Fox, David J. King, Christina Larkin, Marcin Latas, Diederik Liebrand, C. Giles Miller, Katrina Nilsson-Kerr, Emanuela Piga, Hazel Pugh, Serginio Remmelzwaal, Zoe A. Roseby, Yvonne M. Smith, Stephen Stukins, Ben Taylor, Adam Woodhouse, Savannah Worne, Paul N. Pearson, Christopher R. Poole, Bridget S. Wade, and Andy Purvis
J. Micropalaeontol., 37, 431–443, https://doi.org/10.5194/jm-37-431-2018, https://doi.org/10.5194/jm-37-431-2018, 2018
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In this study we investigate consistency in species-level identifications and whether disagreements are predictable. Twenty-three scientists identified a set of 100 planktonic foraminifera, noting their confidence in each identification. The median accuracy of students was 57 %; 79 % for experienced researchers. Where they were confident in the identifications, the values are 75 % and 93 %, respectively. Accuracy was significantly higher if the students had been taught how to identify species.
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Short summary
Foraminifera are marine microorganisms with a calcium carbonate shell. Their fossil remains build up on the seafloor, forming kilometres of sediment over time. From analysis of the foraminiferal record we can estimate past climate conditions and the geological history of the Earth. We have developed an artificial intelligence system for automatically identifying foraminifera species, replacing the time-consuming manual approach and thus helping to make these analyses more efficient and accurate.
Foraminifera are marine microorganisms with a calcium carbonate shell. Their fossil remains...
