Saved in:
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Dataset Open Access |
| Language: | en |
| Published: |
PANGAEA
2021
|
| Subjects: | |
| Online Access: | https://doi.org/10.1594/PANGAEA.931784 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1867168210843860992 |
|---|---|
| author | Granse, Dirk Titschack, Jürgen Suchrow, Sigrid Wendt, Paul Salmon, Armel Ainouche, Malika Jensen, Kai Koop-Jakobsen, Ketil Timann, Christian Lemke, Arne-Jörn |
| author_facet | Granse, Dirk Titschack, Jürgen Suchrow, Sigrid Wendt, Paul Salmon, Armel Ainouche, Malika Jensen, Kai Koop-Jakobsen, Ketil Timann, Christian Lemke, Arne-Jörn |
| collection | Datos científicos de ciencias marinas y ambientales |
| contents | 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. |
| format | Dataset Open Access |
| id | pangaea_https___doi_org_10_1594_PANGAEA_931784 |
| institution | PANGAEA |
| language | en |
| publishDate | 2021 |
| publisher | PANGAEA |
| record_format | pangaea |
| spellingShingle | 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 Granse, Dirk Titschack, Jürgen Suchrow, Sigrid Wendt, Paul Salmon, Armel Ainouche, Malika Jensen, Kai Koop-Jakobsen, Ketil Timann, Christian Lemke, Arne-Jörn aerenchyma gas-flow air-flow resistance; Binary Object; Binary Object (Character Set); Binary Object (File Size); Binary Object (Media Type); Hybrids; Hybrids - Chances and Challenges of New Genetic Combinations; 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 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. |
| title | 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 |
| topic | aerenchyma gas-flow air-flow resistance; Binary Object; Binary Object (Character Set); Binary Object (File Size); Binary Object (Media Type); Hybrids; Hybrids - Chances and Challenges of New Genetic Combinations; 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 |
| url | https://doi.org/10.1594/PANGAEA.931784 |