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

Point of contact

Organisation name	Individual name	Electronic mail address	Role
University of Southampton	Williams, Thomas J.		Author
University of Southampton	Katsamenis, Orestis L.		Author
University of Southampton	Basford, Philip J.		Author
University of Southampton	Solan, Martin		Author
University of Southampton	Foster, Gavin L.		Author
University of Southampton	Standish, Christopher		Author
University of Southampton	Godbold, Jasmin A.		Author
Universite Laval	Archambault, Philippe		Author
NERC EDS UK Polar Data Centre		PDCServiceDesk@bas.ac.uk	Point of contact

Maintenance and update frequency

As needed

Maintenance note

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

Other restrictions

Other constraints

no limitations to public access

Access constraints

Other restrictions

Other constraints

no limitations

Use constraints

License

Other constraints

Open Government Licence v3.0

Use constraints

Other restrictions

Other constraints

None.

Unique resource identifier

url

Codespace

url

Association Type

Cross reference

Unique resource identifier

url

Codespace

url

Association Type

Cross reference

Unique resource identifier

doi

Codespace

doi

Association Type

Cross reference

Spatial representation type

Text, table

Language

English

Character set

UTF8

Topic category

• Biota

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.

Title

European Petroleum Survey Group (EPSG) Geodetic Parameter Registry

Date (Publication)

2008-11-12

Cited responsible party

Organisation name	Individual name	Electronic mail address	Role
European Petroleum Survey Group		EPSGadministrator@iogp.org	Publisher

Unique resource identifier

urn:ogc:def:crs:EPSG::3031

Version

6.18.3

Hierarchy level

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.

Metadata

File identifier

76534d05-ba4e-47b7-9685-0a8c88404ef2 XML

Metadata language

English

Character set

UTF8

Hierarchy level

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)

Metadata author

Organisation name	Individual name	Electronic mail address	Role
NERC EDS UK Polar Data Centre		polardatacentre@bas.ac.uk	Point of contact