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Metadata Files

Data Publication

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

Williams, Thomas J. | Katsamenis, Orestis L. | Basford, Philip J. | Solan, Martin | Foster, Gavin L. | Standish, Christopher | Godbold, Jasmin A. | Archambault, Philippe

NERC EDS UK Polar Data Centre

(2023)

Descriptions

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].
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-Atlanticµ 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.
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.
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)

Keywords


Originally assigned keywords
"EARTH SCIENCE","BIOSPHERE","ECOLOGICAL DYNAMICS","COMMUNITY DYNAMICS","BIODIVERSITY FUNCTIONS"
"EARTH SCIENCE","BIOLOGICAL CLASSIFICATION","ANIMALS/INVERTEBRATES"
"EARTH SCIENCE","OCEANS","MARINE SEDIMENTS","BIOTURBATION"
"EARTH SCIENCE","OCEANS","MARINE SEDIMENTS","SEDIMENT CHEMISTRY"
Acanella
Bamboo coral
Keratoisis
calcite
microCT
skeleton

Corresponding MSL vocabulary keywords
calcite
X-ray tomography

MSL enriched keywords
minerals
carbonate minerals
calcite
Apparatus
X-ray tomography
Technique
imaging (3D)
computed tomography (CT)
measured property
molybdenum

MSL enriched sub domains i

microscopy and tomography
geochemistry

Source

https://data.bas.ac.uk/full-record.php?id=GB/NERC/BAS/PDC/01752

Source publisher

NERC EDS UK Polar Data Centre


DOI

10.5285/76534d05-ba4e-47b7-9685-0a8c88404ef2


Creators

Williams, Thomas J.

University of Southampton

ORCID:

https://orcid.org/0000-0002-6616-955X

Katsamenis, Orestis L.

University of Southampton

ORCID:

https://orcid.org/0000-0003-4367-4147

Basford, Philip J.

University of Southampton

ORCID:

https://orcid.org/0000-0001-6058-8270

Solan, Martin

University of Southampton

ORCID:

https://orcid.org/0000-0001-9924-5574

Foster, Gavin L.

University of Southampton

ORCID:

https://orcid.org/0000-0003-3688-9668

Standish, Christopher

University of Southampton

ORCID:

https://orcid.org/0000-0002-9726-295X

Godbold, Jasmin A.

University of Southampton

ORCID:

https://orcid.org/0000-0001-5558-8188

Archambault, Philippe

Universite Laval

ORCID:

https://orcid.org/0000-0001-5986-6149


Contributors

Williams, Thomas J.

ContactPerson

University of Southampton

ORCID:

https://orcid.org/0000-0002-6616-955X

Williams, Thomas J.

Researcher

University of Southampton

ORCID:

https://orcid.org/0000-0002-6616-955X

Katsamenis, Orestis L.

Researcher

University of Southampton

ORCID:

https://orcid.org/0000-0003-4367-4147

Basford, Philip J.

Researcher

University of Southampton

ORCID:

https://orcid.org/0000-0001-6058-8270

Solan, Martin

Researcher

University of Southampton

ORCID:

https://orcid.org/0000-0001-9924-5574

Foster, Gavin L.

Researcher

University of Southampton

ORCID:

https://orcid.org/0000-0003-3688-9668

Standish, Christopher

Researcher

University of Southampton

ORCID:

https://orcid.org/0000-0002-9726-295X

Godbold, Jasmin A.

Researcher

University of Southampton

ORCID:

https://orcid.org/0000-0001-5558-8188

Archambault, Philippe

Researcher

Universite Laval

ORCID:

https://orcid.org/0000-0001-5986-6149

UK Polar Data Centre

DataManager

Natural Environment Research Council

UK Polar Data Centre

Distributor

Natural Environment Research Council

UK Polar Data Centre

HostingInstitution

Natural Environment Research Council


References

10.1038/nmeth.2019


Citation

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


Dates

Collected:

2021-07-29/2021-07-29

Collected:

2021-08-02/2021-08-02

Accepted:

2023-06-29

Created:

2023-06-26

Submitted:

2023-06-29

Issued:

2023-07-11


Language

en


Funding References

Funder name: Natural Environment Research Council

Funder identifier: https://ror.org/02b5d8509

Funder identifier type: ROR

Award number: NE/S007210/1

Award uri: https://gtr.ukri.org/projects?ref=NE/S007210/1

Award title: INSPIRE: Interdisciplinary Southampton Partnership for Investigators Researching the Environment

Funder name: Engineering and Physical Sciences Research Council

Funder identifier: https://ror.org/0439y7842

Funder identifier type: ROR

Award number: EP/T02593X/1

Award uri: https://gtr.ukri.org/projects?ref=EP/T02593X/1

Award title: National Research Facility for Lab X-ray CT


Rights

Open Government Licence V3.0


Datacite version

1.0


Geo location(s)

Davis Strait Arctic

Baffin Bay, Disko Fan Arctic


Spatial coordinates