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Titschack, Jürgen; Schmitt, Kira; Baum, Daniel; Büscher, Janina; Form, Armin; Tracey, Dianne M; Mills, Sadie; Wienberg, Claudia; Timann, Christian; Lemke, Arne-Jörn: CT-based calices segmentation (in DICOM format) of cold-water coral colony samples and spreadsheet containing the directed edges of the colony skeleton graph [dataset bundled publication]. PANGAEA, https://doi.pangaea.de/10.1594/PANGAEA.969578 (dataset in review)

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Abstract:
Dendroid stony corals build highly complex colonies that develop from a single coral polyp sitting in a cup-like skeleton, called corallite, by asexual reproduction, resulting in a tree-like branching pattern of its skeleton. This dataset bundle contains computed tomography data of five coral colonies belonging to three reef-forming cold-water coral species: Lophelia pertusa (also known under the name Desmophyllum pertusum), Madrepora coulata and Goniocorella dumosa. For each colony the CT raw data (in DICOM format), the polyp cavity instance segmentation, the calices segmentation (given as unique label values) and a spreadsheet containing the (directed) edges of the colony skeleton graph (each label in the calices dataset represents a vertex in this graph; the edges are given by their start label Node ID #1 and the label of their target Node ID #2) are provided. This decomposition of dendroid coral colonies into their building stones (corallites with the respective calice) and subsequent determination of colony skeleton graphs provide the basis to study their ontogenetic development and morphoplasticity.
Keyword(s):
calices segmentation; Computed Tomography; Goniocorella dumosa; polyp-cavity segmentation
Supplement to:
Schmitt, Kira; Titschack, Jürgen; Baum, Daniel (preprint): CoDA: Interactive Segmentation and Morphological Analysis of Dendroid Structures Exemplified on Stony Cold-Water Corals. arXiv, https://doi.org/10.48550/ARXIV.2406.18236
Funding:
German Research Foundation (DFG), grant/award no. Ba5042/6-1; Ti706/6-1; project 490665120: CTcoral – CyberTaxonomische Klassifizierung und morphologische Charakterisierung von Kaltwasserkorallen
Ministry of Business, Innovation and Employment (MBIE), grant/award no. COIX1614: Resilience Of deep-sea Benthic fauna to the Effects of Sedimentation (ROBES)
Coverage:
Median Latitude: 35.111321 * Median Longitude: 38.361853 * South-bound Latitude: -43.368833 * West-bound Longitude: -7.073333 * North-bound Latitude: 64.111000 * East-bound Longitude: 179.452167
Date/Time Start: 2006-10-15T07:11:00 * Date/Time End: 2008-03-01T13:57:00
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0) (License comes into effect after moratorium ends)
Size:
11 datasets

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Download ZIP file containing all datasets as tab-delimited text — use the following character encoding:

Datasets listed in this bundled publication

  1. Titschack, J; Schmitt, K; Baum, D et al. (in review): CT raw data, polyp-cavity segmentation and calices segmentation (all DICOM format) of Lophelia pertusa colony POS455-A2W. https://doi.pangaea.de/10.1594/PANGAEA.969465
  2. Titschack, J; Schmitt, K; Baum, D et al. (in review): Directed edges of the colony skeleton graph from Lophelia pertusa colony sample POS455-A2W. https://doi.pangaea.de/10.1594/PANGAEA.969464
  3. Titschack, J; Schmitt, K; Baum, D (in review): Calices segmentation (DICOM format) of Lophelia pertusa colony fragment POS455-C1W. https://doi.pangaea.de/10.1594/PANGAEA.974315
  4. Titschack, J; Schmitt, K; Baum, D et al. (2022): CT raw data and polyp-cavity segmentation (both DICOM format) of Lophelia pertusa colony fragment POS455-C1W. https://doi.org/10.1594/PANGAEA.947276
  5. Titschack, J; Schmitt, K; Baum, D (in review): Directed edges of the colony skeleton graph from Lophelia pertusa colony sample POS455-C1W. https://doi.pangaea.de/10.1594/PANGAEA.969442
  6. Titschack, J; Schmitt, K; Baum, D et al. (in review): CT raw data, polyp-cavity segmentation and calices segmentation (all DICOM format) of Madrepora oculata colony sample GeoB12747-1. https://doi.pangaea.de/10.1594/PANGAEA.969565
  7. Titschack, J; Schmitt, K; Baum, D et al. (in review): Directed edges of the colony skeleton graph from Madrepora oculata colony sample GeoB12747-1. https://doi.pangaea.de/10.1594/PANGAEA.969550
  8. Titschack, J; Schmitt, K; Baum, D (in review): Directed edges of the colony skeleton graph from Lophelia pertusa colony sample SaM-ID43148. https://doi.pangaea.de/10.1594/PANGAEA.969455
  9. Titschack, J; Schmitt, K; Baum, D et al. (in review): CT raw data, polyp-cavity segmentation and calices segmentation (all DICOM format) of Goniocorella dumosa colony sample NIWA148046. https://doi.pangaea.de/10.1594/PANGAEA.969572
  10. Titschack, J; Schmitt, K; Baum, D et al. (in review): Directed edges of the colony skeleton graph from Goniocorella dumosa colony sample NIWA148046. https://doi.pangaea.de/10.1594/PANGAEA.969566
  11. Titschack, J; Schmitt, K; Baum, D et al. (2022): CT raw data and polyp-cavity segmentation (both DICOM format) of Lophelia pertusa colony fragment SaM_ID43148. https://doi.org/10.1594/PANGAEA.947300