Cavity Segmentation in X-ray Microscopy Scans of Mouse Tibiae

Gu M, Thies M, Wagner F, Pechmann S, Aust O, Weidner D, Neag G, Pan Z, Utz J, Schett G, Christiansen S, Uderhardt S, Maier A (2023)

Publication Type: Conference contribution

Publication year: 2023

Journal

Informatik aktuell Gesellschaft für Informatik (GI)

Publisher: Springer Science and Business Media Deutschland GmbH

Pages Range: 254-259

Conference Proceedings Title: Informatik aktuell

Event location: Braunschweig, DEU

ISBN: 9783658416560

DOI: 10.1007/978-3-658-41657-7_56

Abstract

Osteoporosis is a chronic disease that causes lower bone density and makes bones fragile. This severely impairs patient life qualities and increases the burden on the social and health care system. X-ray microscopy (XRM) allows tracking of osteoporosis-related changes at a microstructural level in the bone, entailing the characterization of osteocyte lacunae and blood vessel canals. Unfortunately, no segmentation methods for micro-structures in XRM images have yet been established. In this work, we compare the performance of a traditional thresholding-based method with three deep learning networks including 2D and 3D models in both binary and multi-class segmentation. We further propose a clustering method to automatically distinguish blood vessels from lacunae for the binary methods. The performance is evaluated with Dice score (F1 score). The thresholding-based method reaches a mean Dice score of 0.729, which the deep learning models improve by 0.129 - 0.168.

Authors with CRIS profile

Mingxuan Gu Lehrstuhl für Informatik 5 (Mustererkennung) Mareike Thies Lehrstuhl für Informatik 5 (Mustererkennung) Fabian Wagner Lehrstuhl für Informatik 5 (Mustererkennung) Oliver Aust Professur für Integrative Gewebeimmunologie Georgiana Neag Department of Medicine 3 – Rheumatology and Immunology Zhaoya Pan Lehrstuhl für Informatik 5 (Mustererkennung) Jonas Utz Lehrstuhl für Informatik 14 (Bild- und Sprachverarbeitung) Georg Schett Lehrstuhl für Innere Medizin III Stefan Uderhardt Department of Medicine 3 – Rheumatology and Immunology Andreas Maier Lehrstuhl für Informatik 5 (Mustererkennung)

Involved external institutions

Fraunhofer-Institut für Keramische Technologien und Systeme (IKTS) DE Germany (DE)

How to cite

APA:

Gu, M., Thies, M., Wagner, F., Pechmann, S., Aust, O., Weidner, D.,... Maier, A. (2023). Cavity Segmentation in X-ray Microscopy Scans of Mouse Tibiae. In Thomas M. Deserno, Heinz Handels, Andreas Maier, Klaus Maier-Hein, Christoph Palm, Thomas Tolxdorff (Eds.), Informatik aktuell (pp. 254-259). Braunschweig, DEU: Springer Science and Business Media Deutschland GmbH.

MLA:

Gu, Mingxuan, et al. "Cavity Segmentation in X-ray Microscopy Scans of Mouse Tibiae." Proceedings of the Bildverarbeitung für die Medizin Workshop, BVM 2023, Braunschweig, DEU Ed. Thomas M. Deserno, Heinz Handels, Andreas Maier, Klaus Maier-Hein, Christoph Palm, Thomas Tolxdorff, Springer Science and Business Media Deutschland GmbH, 2023. 254-259.

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