| 1. |
- Elder, Leanne, et al.
(författare)
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Sixty-one thousand recent planktonic foraminifera from the Atlantic Ocean
- 2018
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 5, s. 180109-
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Tidskriftsartikel (refereegranskat)abstract
- Marine microfossils record the environmental, ecological, and evolutionary dynamics of past oceans in temporally expanded sedimentary archives. Rapid imaging approaches provide a means of exploiting the primary advantage of this archive, the vast number of fossils, for evolution and ecology. Here we provide the first large scale image and 2D and 3D shape dataset of modern planktonic foraminifera, a major microfossil group, from 34 Atlantic Ocean sediment samples. Information on more than 124,000 objects is provided, including general object classification for 4/5ths of the dataset (~ 99,000 objects). Of the ~ 99,000 classifications provided, more than 61,000 are complete or damaged planktonic foraminifera. Objects also include benthic foraminifera, ostracods, pteropods, spicules, and planktonic foraminifera test fragments, among others. This dataset is the first major microfossil output of a new high-throughput imaging method (AutoMorph) developed to extract 2D and 3D data from photographic images of fossils. Our sample preparation and imaging techniques are described in detail. The data provided here comprises the most extensive publically available archive of planktonic foraminiferal morphology and morphological variation to date.
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| 2. |
- Hsiang, Allison
(författare)
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AutoMorph: Accelerating morphometrics with automated 2D and 3D image processing and shape extraction
- 2017
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Ingår i: Methods in Ecology and Evolution. - 2041-210X.
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Tidskriftsartikel (refereegranskat)abstract
- Large-scale, comparative studies of morphological variation are rare due to the time-intensive nature of shape quantification. This data gap is important to address, as intraspecific and interspecific morphological variation underpins and reflects ecological and evolutionary processes.Here, we detail a novel software package, AutoMorph, for high-throughput object and shape extraction. AutoMorph can batch image many types of organisms (e.g. foraminifera, molluscs and fish teeth), allowing for rapid generation of assemblage- scale morphological data.We used AutoMorph to image and generate 2D and 3D morphological data for >100,000 marine microfossils in about a year. Our collaborators have used AutoMorph to process >12,000 patellogastropod shells and >50,000 fish teeth.AutoMorph allows users to rapidly produce large amounts of morphological data, facilitating community-scale evolutionary and ecological studies. To hasten the adoption of automated approaches, we have made AutoMorph freely available and open source. AutoMorph runs on all UNIX-like systems; future versions will run across all platforms.
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| 3. |
- Kahanamoku, Sara, et al.
(författare)
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Twelve thousand recent patellogastropods from a northeastern Pacific latitudinal gradient
- 2018
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 5, s. 170197-
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Tidskriftsartikel (refereegranskat)abstract
- Marine microfossils record the environmental, ecological, and evolutionary dynamics of past oceans in temporally expanded sedimentary archives. Rapid imaging approaches provide a means of exploiting the primary advantage of this archive, the vast number of fossils, for evolution and ecology. Here we provide the first large scale image and 2D and 3D shape dataset of modern planktonic foraminifera, a major microfossil group, from 34 Atlantic Ocean sediment samples. Information on more than 124,000 objects is provided, including general object classification for 4/5ths of the dataset (~ 99,000 objects). Of the ~ 99,000 classifications provided, more than 61,000 are complete or damaged planktonic foraminifera. Objects also include benthic foraminifera, ostracods, pteropods, spicules, and planktonic foraminifera test fragments, among others. This dataset is the first major microfossil output of a new high-throughput imaging method (AutoMorph) developed to extract 2D and 3D data from photographic images of fossils. Our sample preparation and imaging techniques are described in detail. The data provided here comprises the most extensive publically available archive of planktonic foraminiferal morphology and morphological variation to date.
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| 4. |
- Schiebel, Ralf, et al.
(författare)
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Advances in planktonic foraminifer research : New perspectives for paleoceanography
- 2018
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Ingår i: Revue de Micropaleontologie. - : Elsevier BV. - 0035-1598 .- 1873-4413. ; 61:3-4, s. 113-138
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Forskningsöversikt (refereegranskat)abstract
- Planktonic foraminifer tests are major archives of environmental change and provide a multitude of proxies in paleoceanography and paleoclimatology. The application of such proxies is contingent upon a collaborative effort to better understand how the living organisms record the properties of their environment and how the resulting signals are recorded in marine sediments. In this contribution, we provide a review of the rapidly developing sub-fields of research, where new advances have been made possibleby technological developments, and by cross-disciplinary work of the scientific community. Following brief historical overviews of the sub-fields, we discuss the latest advances in planktonic foraminifer research and highlight the resulting new perspectives in ocean and climate research. Natural classification based on consistent species concepts forms the basis for analysis of any foraminifer-derived proxy. New approaches in taxonomy and phylogeny of Cenozoic planktonic foraminifers (Section 2) are presented, highlighting new perspectives on sensitivity and response of planktonic foraminifers to the changing climate and environment (Section 4). Calibration of foraminifer-specific data and environmental parameters is improving along with the technical development of probes and the access to samples from the natural environment (Section 3), enhancing our understanding of the ever-changing climate and ocean system. Comprehension of sedimentation and flux dynamics facilitates maximum gain of information from fossil assemblages (Section 5). Subtle changes in the physical (e.g., temperature), chemical (e.g., pH), and biological (e.g., food) conditions of ambient seawater affect the abundance of species and composition of assemblages as well as the chemical composition of the foraminifer shell and provide increasingly-detailed proxy data on paleoenvironments (Section 6).
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