Camille Godbillot, Ross Marchant, Luc Beaufort, Karine Leblanc, Yves Gally, Thang D. Q. Le, Cristele Chevalier, Thibault de Garidel-Thoron
{"title":"利用卷积神经网络检测沉积物显微切片上硅质微化石的新方法","authors":"Camille Godbillot, Ross Marchant, Luc Beaufort, Karine Leblanc, Yves Gally, Thang D. Q. Le, Cristele Chevalier, Thibault de Garidel-Thoron","doi":"10.1029/2024JG008047","DOIUrl":null,"url":null,"abstract":"<p>Diatom communities preserved in sediment samples are valuable indicators for understanding the past and present dynamics of phytoplankton communities, and their response to environmental changes. These studies are traditionally achieved by counting methods using optical microscopy, a time-consuming process that requires taxonomic expertise. With the advent of automated image acquisition workflows, large image data sets can now be acquired, but require efficient preprocessing methods. Detecting diatom frustules on microscope images is a challenge due to their low relief, diverse shapes, and tendency to aggregate, which prevent the use of traditional thresholding techniques. Deep learning algorithms have the potential to resolve these challenges, more particularly for the task of object detection. Here we explore the use of a Faster Region-based Convolutional Neural Network model to detect siliceous biominerals, including diatoms, in microscope images of a sediment trap series from the Mediterranean Sea. Our workflow demonstrates promising results, achieving a precision score of 0.72 and a recall score of 0.74 when applied to a test set of Mediterranean diatom images. Our model performance decreases when used to detect fragments of these microfossils; it also decreases when particles are aggregated or when images are out of focus. Microfossil detection remains high when the model is used on a microscope image set of sediments from a different oceanic basin, demonstrating its potential for application in a wide range of contemporary and paleoenvironmental studies. This automated method provides a valuable tool for analyzing complex samples, particularly for rare species under-represented in training data sets.</p>","PeriodicalId":16003,"journal":{"name":"Journal of Geophysical Research: Biogeosciences","volume":"129 9","pages":""},"PeriodicalIF":3.7000,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1029/2024JG008047","citationCount":"0","resultStr":"{\"title\":\"A New Method for the Detection of Siliceous Microfossils on Sediment Microscope Slides Using Convolutional Neural Networks\",\"authors\":\"Camille Godbillot, Ross Marchant, Luc Beaufort, Karine Leblanc, Yves Gally, Thang D. Q. Le, Cristele Chevalier, Thibault de Garidel-Thoron\",\"doi\":\"10.1029/2024JG008047\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>Diatom communities preserved in sediment samples are valuable indicators for understanding the past and present dynamics of phytoplankton communities, and their response to environmental changes. These studies are traditionally achieved by counting methods using optical microscopy, a time-consuming process that requires taxonomic expertise. With the advent of automated image acquisition workflows, large image data sets can now be acquired, but require efficient preprocessing methods. Detecting diatom frustules on microscope images is a challenge due to their low relief, diverse shapes, and tendency to aggregate, which prevent the use of traditional thresholding techniques. Deep learning algorithms have the potential to resolve these challenges, more particularly for the task of object detection. Here we explore the use of a Faster Region-based Convolutional Neural Network model to detect siliceous biominerals, including diatoms, in microscope images of a sediment trap series from the Mediterranean Sea. Our workflow demonstrates promising results, achieving a precision score of 0.72 and a recall score of 0.74 when applied to a test set of Mediterranean diatom images. Our model performance decreases when used to detect fragments of these microfossils; it also decreases when particles are aggregated or when images are out of focus. Microfossil detection remains high when the model is used on a microscope image set of sediments from a different oceanic basin, demonstrating its potential for application in a wide range of contemporary and paleoenvironmental studies. 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A New Method for the Detection of Siliceous Microfossils on Sediment Microscope Slides Using Convolutional Neural Networks
Diatom communities preserved in sediment samples are valuable indicators for understanding the past and present dynamics of phytoplankton communities, and their response to environmental changes. These studies are traditionally achieved by counting methods using optical microscopy, a time-consuming process that requires taxonomic expertise. With the advent of automated image acquisition workflows, large image data sets can now be acquired, but require efficient preprocessing methods. Detecting diatom frustules on microscope images is a challenge due to their low relief, diverse shapes, and tendency to aggregate, which prevent the use of traditional thresholding techniques. Deep learning algorithms have the potential to resolve these challenges, more particularly for the task of object detection. Here we explore the use of a Faster Region-based Convolutional Neural Network model to detect siliceous biominerals, including diatoms, in microscope images of a sediment trap series from the Mediterranean Sea. Our workflow demonstrates promising results, achieving a precision score of 0.72 and a recall score of 0.74 when applied to a test set of Mediterranean diatom images. Our model performance decreases when used to detect fragments of these microfossils; it also decreases when particles are aggregated or when images are out of focus. Microfossil detection remains high when the model is used on a microscope image set of sediments from a different oceanic basin, demonstrating its potential for application in a wide range of contemporary and paleoenvironmental studies. This automated method provides a valuable tool for analyzing complex samples, particularly for rare species under-represented in training data sets.
期刊介绍:
JGR-Biogeosciences focuses on biogeosciences of the Earth system in the past, present, and future and the extension of this research to planetary studies. The emerging field of biogeosciences spans the intellectual interface between biology and the geosciences and attempts to understand the functions of the Earth system across multiple spatial and temporal scales. Studies in biogeosciences may use multiple lines of evidence drawn from diverse fields to gain a holistic understanding of terrestrial, freshwater, and marine ecosystems and extreme environments. Specific topics within the scope of the section include process-based theoretical, experimental, and field studies of biogeochemistry, biogeophysics, atmosphere-, land-, and ocean-ecosystem interactions, biomineralization, life in extreme environments, astrobiology, microbial processes, geomicrobiology, and evolutionary geobiology