Automated analysis of foraminifera fossil records by image classification using a convolutional neural network

• Published in: Journal of micropalaeontology Vol. 39; no. 2; pp. 183 - 202
• Main Authors: Marchant, Ross, Tetard, Martin, Pratiwi, Adnya, Adebayo, Michael, de Garidel-Thoron, Thibault
• Format: Journal Article
• Language: English
• Published: Bath Copernicus GmbH 15.10.2020; Geological Society; Copernicus Publications
• Subjects: Applied research; Artificial neural networks; Automatic; Automation; Biodiversity and Ecology; Classification; Datasets; Earth Sciences; Engineering Sciences; Environmental Sciences; Fossil foraminifera; Geology; Human performance; Image processing; Machine Learning; Methods; Microscopes; Morphology; Neural networks; Paleontology; Physiological aspects; Sciences of the Universe; Sediments; Statistics; RECOGNITION; IDENTIFICATION; PLANKTIC FORAMINIFERA
• ISSN: 2041-4978; 0262-821X; 2041-4978
• DOI: 10.5194/jm-39-183-2020

Manual identification of foraminiferal morphospecies or morphotypes under stereo microscopes is time consuming for micropalaeontologists and not possible for nonspecialists. Therefore, a long-term goal has been to automate this process to improve its efficiency and repeatability. Recent advances in computation hardware have seen deep convolutional neural networks emerge as the state-of-the-art technique for image-based automated classification. Here, we describe a method for classifying large foraminifera image sets using convolutional neural networks. Construction of the classifier is demonstrated on the publicly available Endless Forams image set with a best accuracy of approximately 90 %. A complete automatic analysis is performed for benthic species dated to the last deglacial period for a sediment core from the north-eastern Pacific and for planktonic species dated from the present until 180 000 years ago in a core from the western Pacific warm pool. The relative abundances from automatic counting based on more than 500 000 images compare favourably with manual counting, showing the same signal dynamics. Our workflow opens the way to automated palaeoceanographic reconstruction based on computer image analysis and is freely available for use.