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Granse, Dirk; Titschack, Jürgen; Suchrow, Sigrid; Wendt, Paul; Salmon, Armel; Ainouche, Malika; Jensen, Kai; Koop-Jakobsen, Ketil; Timann, Christian; Lemke, Arne-Jörn (2021): 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. PANGAEA, https://doi.org/10.1594/PANGAEA.931784

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Abstract:
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; http://amira.zib.de). 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 air-filled aerenchyma and > -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.
Keyword(s):
aerenchyma gas-flow air-flow resistance; marker controlled watershed CT-scan image segmentation; polyploidization, hybridization, polyploidy, plant hybrid; skeleton analysis; Sporobolus, Spartina × townsendii, Spartina anglica, Spartina alterniflora, Spartina maritima; tidal salt marsh ecosystem; whole genome duplication WGD
Supplement to:
Granse, Dirk; Titschack, Jürgen; Ainouche, Malika; Jensen, Kai; Koop-Jakobsen, Ketil (accepted): Subsurface aeration of tidal wetland soils: Root-system structure and aerenchyma connectivity in Spartina (Poaceae). Science of the Total Environment, 149771, https://doi.org/10.1016/j.scitotenv.2021.149771
Related to:
Hounsfield, Godfrey N (1980): Computed Medical Imaging. Journal of Computer Assisted Tomography, 4(5), 665-674, https://doi.org/10.1097/00004728-198010000-00017
Stalling, Detlev; Westerhoff, Malte; Hege, Hans-Christian (2005): Amira: A Highly Interactive System for Visual Data Analysis. In: Hansen, C.D., Johnson, C.R. (Eds.), Visualization Handbook. Butterworth-Heinemann, Burlington, 749-767, https://doi.org/10.1016/B978-012387582-2/50040-X
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1Binary ObjectBinaryGranse, Dirk
2Binary Object (Media Type)Binary (Type)Granse, Dirk
3Binary Object (Character Set)Binary (Charset)Granse, Dirk
4Binary Object (File Size)Binary (Size)BytesGranse, Dirk
Size:
288 data points

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