Abstract:
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].
Keywords:
Acanella, Bamboo coral, Keratoisis, calcite, microCT, skeleton
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
| Access Constraints: | None. |
|---|---|
| Use Constraints: | This data is covered by a UK Open Government Licence (http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/) |
| Creation Date: | 2023-06-29 |
|---|---|
| Dataset Progress: | Complete |
| Dataset Language: | English |
| ISO Topic Categories: |
|
| Parameters: |
|
| Personnel: | |
| Name | UK Polar Data Centre |
| Role(s) | Metadata Author |
| Organisation | British Antarctic Survey |
| Name | Thomas J Williams |
| Role(s) | Investigator, Technical Contact |
| Name | Orestis L Katsamenis |
| Role(s) | Investigator |
| Organisation | University of Southampton |
| Name | Philip J Basford |
| Role(s) | Investigator |
| Organisation | University of Southampton |
| Name | Martin Solan |
| Role(s) | Investigator |
| Organisation | University of Southampton |
| Name | Gavin L Foster |
| Role(s) | Investigator |
| Organisation | University of Southampton |
| Name | Christopher Standish |
| Role(s) | Investigator |
| Organisation | University of Southampton |
| Name | Jasmin A Godbold |
| Role(s) | Investigator |
| Organisation | University of Southampton |
| Name | Philippe Archambault |
| Role(s) | Investigator |
| Organisation | Universite Laval |
| Parent Dataset: | N/A |
| Reference: | Johannes, R. E. & Wiebe, W. J. Method for determination of coral tissue biomass and composition. (1970). Schindelin, J., Arganda-Carreras, I., Frise, E. et al. Fiji: an open-source platform for biological-image analysis. Nat Methods 9, 676-682 (2012). https://doi.org/10.1038/nmeth.2019 Williams, T. J., Standish, C. D., Archambault, P., et al. Geochemical proxies for deep-sea temperature and nutrient content in cold-water bamboo corals. Chem Geol 654, 122053 (2024). https://doi.org/10.1016/j.chemgeo.2024.122053 Williams, T. J., Katsamenis, O. L., Basford, P. J., et al. Three-dimensional reconstruction of high latitude bamboo coral via X-ray microfocus Computed Tomography. Sci Data (in press). |
|
|---|---|---|
| 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. |
|
| Lineage: | 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. |
|
| Temporal Coverage: | |
|---|---|
| Start Date | 2021-08-02 |
| End Date | 2021-08-02 |
| Start Date | 2021-07-29 |
| End Date | 2021-07-29 |
| Spatial Coverage: | |
| Latitude | |
| Southernmost | 63.34533 |
| Northernmost | 63.34533 |
| Longitude | |
| Westernmost | 58.19571 |
| Easternmost | 58.19571 |
| Altitude | |
| Min Altitude | N/A |
| Max Altitude | N/A |
| Depth | |
| Min Depth | 1311 m |
| Max Depth | 1311 m |
| Latitude | |
| Southernmost | 67.96631 |
| Northernmost | 67.96631 |
| Longitude | |
| Westernmost | 59.49381 |
| Easternmost | 59.49381 |
| Altitude | |
| Min Altitude | N/A |
| Max Altitude | N/A |
| Depth | |
| Min Depth | 889 m |
| Max Depth | 889 m |
| Data Resolution: | |
| Latitude Resolution | N/A |
| Longitude Resolution | N/A |
| Horizontal Resolution Range | N/A |
| Vertical Resolution | 15 micrometer (central scan) |
| Vertical Resolution Range | N/A |
| Temporal Resolution | N/A |
| Temporal Resolution Range | N/A |
| Latitude Resolution | N/A |
| Longitude Resolution | N/A |
| Horizontal Resolution Range | N/A |
| Vertical Resolution | 50 micrometer (overview scan) |
| Vertical Resolution Range | N/A |
| Temporal Resolution | N/A |
| Temporal Resolution Range | N/A |
| Latitude Resolution | N/A |
| Longitude Resolution | N/A |
| Horizontal Resolution Range | N/A |
| Vertical Resolution | 15 micrometer (concat. scan) |
| Vertical Resolution Range | N/A |
| Temporal Resolution | N/A |
| Temporal Resolution Range | N/A |
| Location: | |
| Location | Arctic |
| Detailed Location | Baffin Bay, Disko Fan |
| Location | Arctic |
| Detailed Location | Davis Strait |
| 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 Storage: | Data structure [Species]; e.g. ACANELLA arbuscula |-- [XRH-ID]; e.g. DEMO02019-FFPE |-- [Scan name]; e.g. 20210129 XRH 1234 OLK DEMO02019-FFPE notes * |-- Refined raw volume files (.tif) * |-- [extra]; e.g. extra files related to CTscan |-- Scan report (.pdf) * |-- Scan fly-through along the XY plane of the volume (.mp4) * * in a standardised format YYYYMMDD ScanerID JobID OperatorInitials SampleID note-1 note-2 Key [folder] (file type) Data files - TOTAL SIZE 103.51 GB README FORMAT OF DATA (.txt) - 1 file (921 B) .../20211006 XRH 2833 PJB MVIS04311-NFDRY 0015mm [2021-10-06 11.40.01]/ Refined raw 8-bit scaled volume files (.tif) - 2850 files (918 KB each) /extra/ MVIS04311-NFDRY 0015mm report (.pdf) - 1 file (2 MB) 20211006 XRH 2833 PJB MVIS04311-NFDRY 0015mm (.mp4) - 1 file (3.9 MB) .../20211006 XRH 2833 PJB MVIS04311-NFDRY overview [2021-10-06 11.16.00]/ Refined raw 8-bit scaled volume files (.tif) - 2850 files (3 MB each) /extra/ MVIS04311-NFDRY overview report (.pdf) - 1 file (2 MB) 20211006 XRH 2833 PJB MVIS04311-NFDRY overview 01 (.mp4) - 1 file (22 MB) .../20211006 XRH 2833 PJB MVIS04322-NFDRY 0015mm [2021-10-06 12.33.17]/ Refined raw 8-bit scaled volume files (.tif) - 2850 files (792 KB each) /extra/ MVIS04322-NFDRY 0015mm report (.pdf) - 1 file (1.1 MB) 20211006 XRH 2833 PJB MVIS04322-NFDRY 0015mm (.mp4) - 1 file (2 MB) .../20211006 XRH 2833 PJB MVIS04322-NFDRY overview [2021-10-06 12.12.59]/ Refined raw 8-bit scaled volume files (.tif) - 2160 files (1.7 MB each) /extra/ 20211006 XRH 2833 PJB MVIS04322-NFDRY overview 01 (.mp4) - 1 file (28.6 MB) .../20211006 XRH 2833 PJB MVIS04333-NFDRY 0015mm [2021-10-06 14.53.57]/ Refined raw 8-bit scaled volume files (.tif) - 2850 files (1.2 MB each) /extra/ 20211006 XRH 2833 PJB MVIS04333-NFDRY 0015mm 01 (.mp4) - 1 file (4.6 MB) .../20211006 XRH 2833 PJB MVIS04333-NFDRY overview [2021-10-06 14.31.51]/ Refined raw 8-bit scaled volume files (.tif) - 2130 files (2.4 MB each) /extra/ MVIS04333-NFDRY overview report (.pdf) - 1 file (380 KB) 20211006 XRH 2833 PJB MVIS04333-NFDRY overview (.mp4) - 1 file (25 MB) .../20211006 XRH 2833 PJB MVIS04340-NFDRY 0015mm [2021-10-06 13.21.40]/ Refined raw 8-bit scaled volume files (.tif) - 2850 files (1.2 MB each) /extra/ MVIS04340-NFDRY 0015mm report (.pdf) - 1 file (2 MB) 20211006 XRH 2833 PJB MVIS04340-NFDRY 0015mm (.mp4) - 1 file (2.5 MB) .../20211006 XRH 2833 PJB MVIS04340-NFDRY overview [2021-10-06 13.00.34]/ Refined raw 8-bit scaled volume files (.tif) - 2282 files (2.4 MB each) /extra/ MVIS04340-NFDRY overview report (.pdf) - 1 file (389 KB) 20211006 XRH 2833 PJB MVIS04340-NFDRY overview (.mp4) - 1 file (14.5 MB) .../20211006 XRH 2833 PJB MVIS04354-NFDRY 0015mm [2021-10-06 14.07.04]/ Refined raw 8-bit scaled volume files (.tif) - 2850 files (1.2 MB each) /extra/ MVIS04354-NFDRY 0015mm report (.pdf) - 1 file (2 MB) 20211006 XRH 2833 PJB MVIS04354-NFDRY 0015mm (.mp4) - 1 file (3.2 MB) .../20211006 XRH 2833 PJB MVIS04354-NFDRY overview [2021-10-06 13.48.44]/ Refined raw 8-bit scaled volume files (.tif) - 1744 files (1.8 MB each) /extra/ MVIS04354-NFDRY overview report (.pdf) - 1 file (354 KB) 20211006 XRH 2833 PJB MVIS04354-NFDRY overview (.mp4) - 1 file (23.6 MB) .../20211006 XRH 2833 PJB MVIS04365-NFDRY Btm 00 01 02 concat [2021-10-06 18.04.39]/ Refined raw 8-bit scaled volume files (.tif) - 6851 files (2.8 MB each) /extra/ MVIS04365-NFDRY Btm 00 report (.pdf) - 1 file (1.6 MB) MVIS04365-NFDRY Btm 01 report (.pdf) - 1 file (1.5 MB) MVIS04365-NFDRY Btm 02 report (.pdf) - 1 file (1.5 MB) 20211006 XRH 2833 PJB MVIS04365-NFDRY Btm 00 (.mp4) - 1 file (12.7 MB) 20211006 XRH 2833 PJB MVIS04365-NFDRY Btm 01 (.mp4) - 1 file (8.6 MB) 20211006 XRH 2833 PJB MVIS04365-NFDRY Btm 02 (.mp4) - 1 file (7.6 MB) .../20211006 XRH 2833 PJB MVIS04379-NFDRY Btm 00 01 02 concat [2021-10-07 07.32.36]/ Refined raw 8-bit scaled volume files (.tif) - 6855 files (3.8 MB each) /extra/ MVIS04379-NFDRY Btm 00 report (.pdf) - 1 file (1.5 MB) MVIS04379-NFDRY Btm 01 report (.pdf) - 1 file (1.5 MB) MVIS04379-NFDRY Btm 02 report (.pdf) - 1 file (1.5 MB) 20211006 XRH 2833 PJB MVIS04379-NFDRY Btm 00 (.mp4) - 1 file (7.4 MB) 20211006 XRH 2833 PJB MVIS04379-NFDRY Btm 01 (.mp4) - 1 file (6.6 MB) 20211006 XRH 2833 PJB MVIS04379-NFDRY Btm 02 (.mp4) - 1 file (6.2 MB) .../20211006 XRH 2833 PJB MVIS04387-NFDRY Btm 00 01 02 concat [2021-10-07 03.03.17]/ Refined raw 8-bit scaled volume files (.tif) - 6853 files (1.4 MB each) /extra/ MVIS04387-NFDRY Btm 00 report (.pdf) - 1 file (1.6 MB) MVIS04387-NFDRY Btm 01 report (.pdf) - 1 file (1.6 MB) MVIS04387-NFDRY Btm 02 report (.pdf) - 1 file (1.6 MB) 20211006 XRH 2833 PJB MVIS04387-NFDRY Btm 00 (.mp4) - 1 file (32.4 MB) 20211006 XRH 2833 PJB MVIS04387-NFDRY Btm 01 (.mp4) - 1 file (42.1 MB) 20211006 XRH 2833 PJB MVIS04387-NFDRY Btm 02 (.mp4) - 1 file (66.6 MB) .../20211006 XRH 2833 PJB MVIS04398-NFDRY Btm 00 01 02 concat [2021-10-06 22.33.58]/ Refined raw 8-bit scaled volume files (.tif) - 6851 files (974 KB each) /extra/ MVIS04398-NFDRY Btm 00 report (.pdf) - 1 file (1.6 MB) MVIS04398-NFDRY Btm 01 report (.pdf) - 1 file (1.5 MB) MVIS04398-NFDRY Btm 02 report (.pdf) - 1 file (1.5 MB) 20211006 XRH 2833 PJB MVIS04398-NFDRY Btm 00 (.mp4) - 1 file (13.7MB) 20211006 XRH 2833 PJB MVIS04398-NFDRY Btm 01 (.mp4) - 1 file (10.2 MB) 20211006 XRH 2833 PJB MVIS04398-NFDRY Btm 02 (.mp4) - 1 file (8.9 MB) /20211006 XRH 2833 PJB MVIS04311-NFDRY 0015mm [2021-10-06 11.40.01]/ |
|---|