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dc.contributor.authorJohansen, Thomas Haugland
dc.contributor.authorSørensen, Steffen Aagaard
dc.contributor.authorMøllersen, Kajsa
dc.contributor.authorGodtliebsen, Gustav
dc.date.accessioned2021-08-13T10:34:20Z
dc.date.available2021-08-13T10:34:20Z
dc.date.issued2021-07-16
dc.description.abstractForaminifera are single-celled marine organisms that construct shells that remain as fossils in the marine sediments. Classifying and counting these fossils are important in paleo-oceanographic and -climatological research. However, the identification and counting process has been performed manually since the 1800s and is laborious and time-consuming. In this work, we present a deep learning-based instance segmentation model for classifying, detecting, and segmenting microscopic foraminifera. Our model is based on the Mask R-CNN architecture, using model weight parameters that have learned on the COCO detection dataset. We use a fine-tuning approach to adapt the parameters on a novel object detection dataset of more than 7000 microscopic foraminifera and sediment grains. The model achieves a (COCO-style) average precision of 0.78 on the classification and detection task, and 0.80 on the segmentation task. When the model is evaluated without challenging sediment grain images, the average precision for both tasks increases to 0.84 and 0.86, respectively. Prediction results are analyzed both quantitatively and qualitatively and discussed. Based on our findings we propose several directions for future work and conclude that our proposed model is an important step towards automating the identification and counting of microscopic foraminiferaen_US
dc.identifier.citationJohansen T, Sørensen SA, Møllersen K, Godtliebsen G. Instance Segmentation of Microscopic Foraminifera. Applied Sciences. 2021;11(14)en_US
dc.identifier.cristinIDFRIDAID 1924674
dc.identifier.doi10.3390/app11146543
dc.identifier.issn2076-3417
dc.identifier.urihttps://hdl.handle.net/10037/22041
dc.language.isoengen_US
dc.publisherMDPIen_US
dc.relation.journalApplied Sciences
dc.relation.projectIDTromsø forskningsstiftelse: 16_TF_FGen_US
dc.rights.accessRightsopenAccessen_US
dc.rights.holderCopyright 2021 The Author(s)en_US
dc.subjectVDP::Mathematics and natural science: 400en_US
dc.subjectVDP::Matematikk og Naturvitenskap: 400en_US
dc.titleInstance Segmentation of Microscopic Foraminiferaen_US
dc.type.versionpublishedVersionen_US
dc.typeJournal articleen_US
dc.typeTidsskriftartikkelen_US
dc.typePeer revieweden_US


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