Data-archive to "Imaging the internal structure of Borelis schlumbergeri Reichel (1937): Advances by high-resolution hard X-ray tomography". PANGAEA

Kellner, Siri K. and Knappertsbusch, Michael W. and Costeur, Loic and Müller, Bert and Schulz, Georg. (2018) Data-archive to "Imaging the internal structure of Borelis schlumbergeri Reichel (1937): Advances by high-resolution hard X-ray tomography". PANGAEA. [Research Data]

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Official URL: https://edoc.unibas.ch/82143/

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The internal structure of the extant larger benthic foraminifer Borelis schlumbergeri Reichel (1937) (Alveolinidae Ehrenberg, 1839) was investigated by high resolution hard x-ray computer tomography. Scanning was carried out using a single specimen using a Phoenix nanotom m from GE Sensing & Inspection Technologies GmbH. Exposure to hard x-rays was during about 4 hours and 1440 equiangular radiographs were taken along 360°. From the 2108 virtual slices through the stack visualizations of internal microstructures of the calcareous test and sarcode reconstruction were generated after segmentation and rendering in AVIZO7 software from FEI Visualization Sciences Group and using Voxler2 software from Golden Software, LLC. The 2.6 GB set including raw images, derived stacks of AVIZO labels, and video representations illustrating the interior of the Borelis specimen is put on line in form of a zipped archive for further experimentation by the community and for usage in micropaleontological training classes. The archive comprises the original stack of dicom images generated by the nanotom device, a reduced stack of derived AVIZO7 files and labels illustrating the reconstructed inner structures and rendered surfaces, a second reduced data stack of dicom images for loading and experimentation with ImageJ and Voxler2 software, an Excel-sheet containing volume measurements of individual segmented chambers and chamberlets. In addition, several videos (GIF, AVI, MPEG) are provided illustrating the growth of the sarcode body from embryonic stage to adult stage, and showing the shell architecture of the investigated Borelis specimen in animated series of vertical slices. Using the presented data requires access to AVIZO7 and / or Voxler2, which are commercial software. Alternatively, the provided stack of dicom images can also loaded and analyzed using open source Java plugins to ImageJ, which is in the public domain ( https://imagej.net/ ). For visualization image stacks three-dimensionally and for volume rendering the ImageJ 3D Viewer plugin can be applied ( http://3dviewer.neurofly.de ), and segmentation of inner structures can be done using the Segmentation Editor in ImageJ from Johannes Schindelin, Francois Kusztos and Benjamin Schmid ( https://imagej.net/Segmentation_Editor ).
Faculties and Departments:05 Faculty of Science > Departement Umweltwissenschaften > Ehemalige Einheiten Umweltwissenschaften > Paläontologie (Meyer)
UniBasel Contributors:Knappertsbusch, Michael W. and Müller, Bert and Schulz, Georg
Item Type:Research Data
Publisher:Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research (AWI)
Note:Publication type according to Uni Basel Research Database: Discussion paper / Internet publication
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Last Modified:29 Jun 2021 09:54
Deposited On:12 May 2021 07:13

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