Enhancing synchrotron radiation micro-CT images using deep learning: an application of Noise2Inverse on bone imaging

Journal of Synchrotron Radiation, vol. 32, pp. 690–699

Abstract

In bone-imaging research, in situ synchrotron radiation micro-computed tomography (SRµCT) mechanical tests are used to investigate the mechanical properties of bone in relation to its microstructure. Low-dose computed tomography (CT) is used to preserve bone's mechanical properties from radiation damage, though it increases noise. To reduce this noise, the self-supervised deep learning method Noise2Inverse was used on low-dose SRµCT images where segmentation using traditional thresholding techniques was not possible. Simulated-dose datasets were created by sampling projection data at full, one-half, one-third, one-fourth and one-sixth frequencies of an in situ SRµCT mechanical test. After convolutional neural networks were trained, Noise2Inverse performance on all dose simulations was assessed visually and by analyzing bone microstructural features. Visually, high image quality was recovered for each simulated dose. Lacunae volume, lacunae aspect ratio and mineralization distributions shifted slightly in full, one-half and one-third dose network results, but were distorted in one-fourth and one-sixth dose network results. Following this, new models were trained using a larger dataset to determine differences between full dose and one-third dose simulations. Significant changes were found for all parameters of bone microstructure, indicating that a separate validation scan may be necessary to apply this technique for microstructure quantification. Noise present during data acquisition from the testing setup was determined to be the primary source of concern for Noise2Inverse viability. While these limitations exist, incorporating dose calculations and optimal imaging parameters enables self-supervised deep learning methods such as Noise2Inverse to be integrated into existing experiments to decrease radiation dose.

Authors 4

1. Yoshihiro Obata corresponding

   University of California San Diego

   Affiliation as printed

   Department of Mechanical and Aerospace Engineering, University of California San Diego, San Diego, CA 92161, USA

2. Dilworth Y. Parkinson corresponding

   Lawrence Berkeley National Laboratory · Advanced Light Source

   Affiliation as printed

   Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

3. Daniël M. Pelt corresponding Aachen Leiden Institute of Advanced Computer Science

   Leiden University

   Affiliation as printed

   Leiden Institute of Advanced Computer Science (LIACS), Universiteit Leiden, 2333 CA Leiden, The Netherlands

4. Claire Acevedo corresponding

   University of California San Diego

   Affiliation as printed

   Department of Mechanical and Aerospace Engineering, University of California San Diego, San Diego, CA 92161, USA