Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage (Supplementary Material)

  • Supplementary data to reproduce and understand key results from the related publication, including original image data and processed data. In particular, sections from hyomandibulae harvested from specimens of round stingray Urobatis halleri, donated from another study (DOI: 10.1002/etc.2564). Specimens were from sub-adults/adults collected by beach seine from collection sites in San Diego and Seal Beach, California, USA. The hyomandibulae were mounted in clay, sealed in ethanol-humidified plastic tubes and scanned with a Skyscan 1172 desktop μCT scanner (Bruker μCT, Kontich, Belgium) in association with another study (DOI: 10.1111/joa.12508). Scans for all samples were performed with voxel sizes of 4.89 μm at 59 kV source voltage and 167 μA source current, over 360◦ sample 120 rotation. For our segmentations, the datasets were resampled to a voxel size of 9.78 μm to reduce the size of the images and speed up processing. In addition, the processed data that was generated with the visualization software Amira with techniques described in the related publication based on the mentioned specimens.
Metadaten
Author:David Knötel, Ronald Seidel, Paul Zaslansky, Steffen Prohaska, Mason N. Dean, Daniel Baum
Document Type:Research data
ResourceTypeGeneral:Dataset
Year of first publication:2017
Notes to research data :Supplementary data to reproduce and understand key results from the related publication, including original image data and processed data.
Date data created:2017
Geolocation:San Diego and Seal Beach, California, USA
Scientific name :Urobatis halleri
Related identifier:https://doi.org/10.1371/journal.pone.0188018
Software description :The data was processed with the visualization software Amira. See http://www.zib.de/software/tesserae-segmentation for information about Amira and how to download the Amira extension package created for this publication. See https://github.com/zibamira/tesserae-segmentation.git for the source code of the Amira extension package.
Research data download:http://www.zib.de/ext-data/2017_Knoetel_PLOSONE-Supplementary-Material.zip
DOI:https://doi.org/10.12752/4.DKN.1.0
Licence (German):License LogoCreative Commons - Namensnennung