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High-resolution three-dimensional images of deep-sea bamboo corals Acanella arbuscula and Keratoisis sp. collected in the Baffin Bay and Davis Strait during the CCGS Amundsen expedition in 2021

High-resolution X-ray computed tomography images of two deep-sea bamboo corals (Acanella arbuscula, Johnson, 1862; Keratoisis sp., Wright, 1869) collected from Baffin Bay and Davis Strait during a research expedition on board the CCGS Amundsen in July-August 2021. Corals were imaged using Micro-Focused X-Ray Computed Tomography at the Micro-Vis X-ray Imaging Centre (Southampton, UK) to non-destructively investigate their skeletal architecture, calcification strategies and growth patterns.

Supported by a National Environmental Research Council Funded (INSPIRE) PhD [grant number NE/S007210/1, 2019-2027, awarded to T.J.W] and the National Research Facility for Lab X-ray CT (NXCT) [EPSRC grant number EP/T02593X/1].

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Date (Creation)
2023-06-29
Date (Revision)
2023-06-29
Date (Publication)
2023-06-29
Date (released)
2023-06-29
Edition
1.0
Unique resource identifier
https://doi.org/10.5285/76534d05-ba4e-47b7-9685-0a8c88404ef2
Codespace
doi
Unique resource identifier
GB/NERC/BAS/PDC/01752
Codespace
https://data.bas.ac.uk/
Unique resource identifier
NE/S007210/1
Codespace
award
Unique resource identifier
EP/T02593X/1
Codespace
award
Other citation details
Please cite this item as: Williams, T.J., Katsamenis, O.L., Basford, P.J., Solan, M., Foster, G.L., Standish, C., Godbold, J.A., & Archambault, P. (2023). High-resolution three-dimensional images of deep-sea bamboo corals Acanella arbuscula and Keratoisis sp. collected in the Baffin Bay and Davis Strait during the CCGS Amundsen expedition in 2021 (Version 1.0) [Data set]. NERC EDS UK Polar Data Centre. https://doi.org/10.5285/76534d05-ba4e-47b7-9685-0a8c88404ef2
Credit
No credit.
Status
completed Completed
Author
  University of Southampton - Williams, Thomas J. ( Researcher )
Author
  University of Southampton - Katsamenis, Orestis L. ( Researcher )
Author
  University of Southampton - Basford, Philip J. ( Researcher )
Author
  University of Southampton - Solan, Martin ( Researcher )
Author
  University of Southampton - Foster, Gavin L. ( Researcher )
Author
  University of Southampton - Standish, Christopher ( Researcher )
Author
  University of Southampton - Godbold, Jasmin A. ( Researcher )
Author
  Universite Laval - Archambault, Philippe ( Researcher )
Point of contact
  NERC EDS UK Polar Data Centre
British Antarctic Survey, High Cross, Madingley Road , Cambridge , Cambridgeshire , CB3 0ET , United Kingdom
+44 (0)1223 221400
https://www.bas.ac.uk/team/business-teams/information-services/uk-polar-data-centre/
Maintenance and update frequency
asNeeded As needed
Maintenance note
completed Completed
Global Change Master Directory (GCMD) Science Keywords
  • EARTH SCIENCE > Biosphere > Ecological Dynamics > Biodiversity
  • EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates
  • EARTH SCIENCE > Oceans > Marine Sediments > Bioturbation
  • EARTH SCIENCE > Oceans > Marine Sediments > Sediment Chemistry
  • EARTH SCIENCE > Oceans > Marine Biology
Theme
  • Acanella
  • Bamboo coral
  • Keratoisis
  • calcite
  • microCT
  • skeleton
Place
  • Baffin Bay, Disko Fan Arctic
  • Davis Strait Arctic
GEMET - INSPIRE themes, version 1.0
  • Habitats and biotopes
  • Oceanographic geographical features
Access constraints
otherRestrictions Other restrictions
Other constraints
no limitations to public access
Access constraints
otherRestrictions Other restrictions
Other constraints
no limitations
Use constraints
license License
Other constraints
Open Government Licence v3.0
Use constraints
otherRestrictions Other restrictions
Other constraints
None.
Unique resource identifier
url
Codespace
url
Association Type
crossReference Cross reference
Unique resource identifier
url
Codespace
url
Association Type
crossReference Cross reference
Unique resource identifier
doi
Codespace
doi
Association Type
crossReference Cross reference
Spatial representation type
textTable Text, table
Metadata language
engEnglish
Character set
utf8 UTF8
Topic category
  • Biota
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Begin date
2021-07-29
End date
2021-07-29
Supplemental Information
It is recommended that careful attention be paid to the contents of any data, and that the author be contacted with any questions regarding appropriate use. If you find any errors or omissions, please report them to polardatacentre@bas.ac.uk.
Date (Publication)
2008-11-12
Publisher
  European Petroleum Survey Group
https://www.epsg-registry.org/
Unique resource identifier
urn:ogc:def:crs:EPSG::3031
Version
6.18.3

Distributor

Distributor
  NERC EDS UK Polar Data Centre
British Antarctic Survey, High Cross, Madingley Road , Cambridge , Cambridgeshire , CB3 0ET , United Kingdom
+44 (0)1223 221400
https://www.bas.ac.uk/team/business-teams/information-services/uk-polar-data-centre/
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dataset Dataset
Statement

Methodology:

Five specimens of Acanella arbuscula and four specimens of Keratoisis sp. were collected from two stations (Davis Strait; 63.34533 degrees N; 58.19571 degrees W, 1311 m, 29th July 2021, Disko Fan; 67.96631 degrees N, 59.49381 degrees W, 889 m, 2nd August 2021) using a remotely operated submersible (Sub-Atlantic® Comanche, Forum Energy TechnologiesTM, USA) during the 2021 Amundsen expedition (AMD21 Leg 2; 15th July 2021 - 12th August 2021, CCGS Amundsen). Where possible, corals were sampled at or close to the basal internode (near the base of the specimen at the sediment surface). Any external debris and residing fauna were carefully removed from the collected colonies using tweezers before each specimen was sealed in a plastic Ziplock bag and frozen at -20 degrees Celsius. After 72 hours, the specimens were removed from the freezer and carefully cleaned with jets of re-circulated 0.45 micrometer membrane-filtered seawater (FSW) at 4 degrees Celsius using a WaterPikTM (Johannes & Wiebe 1970) before being placed back in -20 degrees Celsius. The cleaned skeleton portions were then sealed in new Ziplock plastic sample bags enclosed in Tupperware (Acanella arbuscula) or PVC vinyl tubing (Keratoisis sp.) before being transported to the University of Southampton, UK.

Reconstruction of biogenic structures was achieved using a Nikon XT custom designed micro-focus computed tomography system (based on the XT H 225 ST, Nikon Tring, UK) housed within the 3D X-ray Histology (XRH) facility (www.muvis.org). Coral specimens were securely positioned vertically in Perspex holding tubes with polystyrene bungs to ensure stability during rotation and scanning. Scans were conducted at 80 KVp using a Molybdenum target. Lower resolution scans (50 micrometer) used a 12 W power, while higher resolution scans (15 micrometer) reduced it to 6.9 W for a sharper X-ray focal spot. A water tube was also scanned under the same conditions as the samples to serve as a density reference. CT Pro 3D 6.6 or 6.7 software (Nikon Xtek, Tring UK) was used for all reconstructions. Due to the limited scanner field of view, multiple overlapping scan positions were used and merged after reconstruction to remove cone beam artifacts. This merging process was facilitated by a custom macro in Fiji, allowing alignment of the scans based on the same slice. The script could also adjust image contrast to compensate for any heel effect in the absence of density calibration. The final 32-bit volume was converted to an 8-bit volume using Fiji/ImageJ (v 1.53c; Schindelin, Arganda-Carreras, Frise et al., 2012) and then converted to stacked tagged image file format (TIFF) images to reduce data size and facilitate further processing.

More detailed methodology surrounding sampling and scanning can be found in Williams, Standish, Archambault et al. [in prep] and Williams, Katsamenis, Basford, et al. [in prep], respectively.

Data collection:

Nikon XT custom designed micro-focus computed tomography system (based on the XT H 225 ST, Nikon Tring, UK

Remotely operated submersible (Sub-Atlantic Comanche, Forum Energy TechnologiesTM, USA)

WaterPikTM (Johannes & Wiebe 1970)

CT Pro software (6.6/6.7; Nikon Xtek, Tring UK)

Fiji/ImageJ software (v 1.53c; Schindelin et al., 2012)

Data quality:

Coral specimens were securely positioned vertically in Perspex holding tubes with polystyrene bungs to ensure stability during rotation and scanning.

A water tube was also scanned under the same conditions as the samples to serve as a density reference. CT Pro 3D 6.6 or 6.7 software (Nikon Xtek, Tring UK) was used for all reconstructions.

During concatenation of separate scans, image contrast was adjusted to compensate for any heel effect in the absence of density calibration.

Conversion to stacked tagged image file format (TIFF) images was lossless.

File identifier
76534d05-ba4e-47b7-9685-0a8c88404ef2 XML
Metadata language
engEnglish
Character set
utf8 UTF8
Hierarchy level
dataset Dataset
Hierarchy level name
dataset
Date stamp
2023-06-29
Metadata standard name
ISO 19115 Geographic Information - Metadata
Metadata standard version
ISO 19115:2003(E)
Point of contact
  NERC EDS UK Polar Data Centre
British Antarctic Survey, High Cross, Madingley Road , Cambridge , Cambridgeshire , CB3 0ET , United Kingdom
+44 (0)1223 221400
https://www.bas.ac.uk/team/business-teams/information-services/uk-polar-data-centre/
 
 

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Keywords

Acanella Bamboo coral Keratoisis calcite microCT skeleton
GEMET - INSPIRE themes, version 1.0
Habitats and biotopes Oceanographic geographical features
Global Change Master Directory (GCMD) Science Keywords
EARTH SCIENCE > Biosphere > Ecological Dynamics > Biodiversity EARTH SCIENCE > Oceans > Marine Biology EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates EARTH SCIENCE > Oceans > Marine Sediments > Bioturbation EARTH SCIENCE > Oceans > Marine Sediments > Sediment Chemistry

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