A Micro-computed Tomography Database and Reference Implementation for Parallel Computations of Trabecular Thickness and Spacing

Journal of Open Research Software, vol. 10, pp. 4

Abstract

We provide a well-defined accurate brute force implementation without approximations as a reference to support future development of correct and fast algorithms to measure the trabecular thickness and spacing. Using artificial ellipsoid examples, the systematic error is shown to be related to the voxelization, which can be reduced by upsampling. Furthermore, we collected a database of 40 three-dimensional micro-computed tomography images of trabecular bone regions of a sheep femur. With the coverage of a broad range of trabecular thickness and spacing, the database is suitable for assessing the correctness of algorithms for the measurements of trabecular thickness and spacing. The bone data is shared publicly in the online repository ‘Figshare’ and the brute force code is freely available in Code Ocean. Scientists are encouraged to implement faster algorithms, e.g., graphic processing unit-accelerated, with accurate or controlled approximate behaviour to compute trabecular thickness and spacing. Especially, the provided data can be re-employed together with the reference algorithm to evaluate their accuracies.

Authors 8

1. Thi-Ngoc-Thu Nguyen corresponding

   King Mongkut's University of Technology North Bangkok

   Affiliation as printed

   Student, The Sirindhorn International Thai-German Graduate School of Engineering, King Mongkut’s University of Technology North Bangkok, Bangkok, TH; Intern, Gremse-IT GmbH, Aachen

   Intern, Gremse-IT GmbH, Aachen

   Student, The Sirindhorn International Thai-German Graduate School of Engineering, King Mongkut’s University of Technology North Bangkok, Bangkok, TH

2. Andreas Höfter
   Affiliation as printed

   Developer, Gremse-IT GmbH, Aachen

3. Kevin Leonardic
   Affiliation as printed

   Developer, Gremse-IT GmbH, Aachen

4. Stefanie Rosenhain Aachen Institute for Experimental Molecular Imaging Researcher

   Universitätsklinikum Aachen

   Affiliation as printed

   Researcher, Gremse-IT GmbH, Aachen; Researcher, Institute for Experimental Molecular Imaging, University Hospital Aachen, Aachen

   Researcher, Gremse-IT GmbH, Aachen

   Researcher, Institute for Experimental Molecular Imaging, University Hospital Aachen, Aachen

5. Fabian M. Kiessling Aachen Institute for Experimental Molecular Imaging Fraunhofer MEVIS Institute for Medical Image Computing Professor Comprehensive Diagnostics Center Aachen

   Universitätsklinikum Aachen · Fraunhofer Institute for Digital Medicine

   Affiliation as printed

   Professor, Institute for Experimental Molecular Imaging, University Hospital Aachen, Aachen; Fraunhofer MEVIS, Institute for Medical Image Computing, Aachen; Comprehensive Diagnostics Center Aachen, Aachen

   Comprehensive Diagnostics Center Aachen, Aachen

   Fraunhofer MEVIS, Institute for Medical Image Computing, Aachen

   Professor, Institute for Experimental Molecular Imaging, University Hospital Aachen, Aachen

6. Wannida Sae-Tang

   King Mongkut's University of Technology North Bangkok

   Affiliation as printed

   Assistant Professor, The Sirindhorn International Thai-German Graduate School of Engineering, King Mongkut’s University of Technology North Bangkok, Bangkok

7. Uwe Naumann Aachen Professor

   RWTH Aachen University

   Affiliation as printed

   Professor, Software and Tools for Computational Engineering, RWTH Aachen University, Aachen

8. Felix Gremse Aachen Institute for Experimental Molecular Imaging Software and Tools for Computational Engineering Researcher Director Software and Tools for Computational Engineering

   RWTH Aachen University · Universitätsklinikum Aachen

   Affiliation as printed

   Director, Gremse-IT GmbH, Aachen; Researcher, Institute for Experimental Molecular Imaging, University Hospital Aachen, Aachen; Software and Tools for Computational Engineering, RWTH Aachen University, Aachen

   Director, Gremse-IT GmbH, Aachen

   Researcher, Institute for Experimental Molecular Imaging, University Hospital Aachen, Aachen

   Software and Tools for Computational Engineering, RWTH Aachen University, Aachen