Computed tomography (CT) scan image analysis: Data of CT-scan images, root system structure, and root aerenchyma connectivity of Spartina (Poaceae) soil cores from tidal wetlands


Soil cores from tidal Spartina-marshes were sampled in 2018 in the European Wadden Sea, Sönke-Nissen-Koog, Germany, as well as at the Atlantic coast, Brittany, France, and scanned by a Toshiba Aquilion 64 computer tomograph (CT) at the Klinikum Bremen-Mitte (Bremen, Germany) using an X-ray source voltage of 120 kV and a current of 600 mA. Images were reconstructed using Toshiba's patented helical cone beam reconstruction technique and are provided as grey-scale image in DICOM-format that contains the X-ray attenuation of the sample material measured in standardized Hounsfield Units (HU; Hounsfield, 1979). The resulting CT-image stacks (d = 18 cm, h = 23 cm) have a resolution of 0.35 mm in x-direction and y-direction and of 0.5 mm in z-direction (0.3 mm reconstruction unit). The CT-scan images were analyzed by processing the data with the ZIB edition of the Amira software (version 2019.35; Stalling et al., 2005; The root-systems of Spartina plants were reconstructed by means of marker-controlled watershed segmentation followed by automated skeleton analysis. The root-tissue and root-aerenchyma were distinguished using a segmentation threshold of -500 HU for root-tissue. The volumes of root-tissue and root-aerenchyma were quantified (MaterialStatistics module; statistics per slice per label) and aerenchyma fragment volumes inside larger rhizomes (minimum radius of 0.7 mm and minimum of 70 mm length) were calculated.

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Creator Granse, Dirk ORCID logo; Titschack, Jürgen ORCID logo; Suchrow, Sigrid; Wendt, Paul; Salmon, Armel; Ainouche, Malika; Jensen, Kai (ORCID: 0000-0002-0543-070X); Koop-Jakobsen, Ketil ORCID logo; Timann, Christian; Lemke, Arne-Jörn
Publisher PANGAEA
Publication Year 2021
Rights Creative Commons Attribution 4.0 International;
OpenAccess true
Resource Type Dataset
Format text/tab-separated-values
Size 288 data points
Discipline Earth System Research