Joint iterative reconstruction and 3D rigid alignment for X-ray tomography

Journal Article · Thu Mar 03 00:00:00 UTC 2022 · Optics Express

DOI: https://doi.org/10.1364/OE.443248 · OSTI ID:1847186

Pande, K. ; Donatelli, J. J.; Parkinson, D. Y.; Yan, H.; Sethian, J. A.

X-ray tomography is widely used for three-dimensional structure determination in many areas of science, from the millimeter to the nanometer scale. The resolution and quality of the 3D reconstruction is limited by the availability of alignment parameters that correct for the mechanical shifts of the sample or sample stage for the images that constitute a scan. In this paper we describe an algorithm for marker-free, fully automated and accurately aligned and reconstructed X-ray tomography data. Our approach solves the tomographic reconstruction jointly with projection data alignment based on a rigid-body deformation model. We demonstrate the robustness of our method on both synthetic phantom and experimental data and show that our method is highly efficient in recovering relatively large alignment errors without prior knowledge of a low resolution approximation of the 3D structure or a reasonable estimate of alignment parameters.

• Research Organization: Brookhaven National Laboratory (BNL), Upton, NY (United States)
• Sponsoring Organization: National Institutes of Health (NIH); USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR); USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER)
• Grant/Contract Number: AC02-05CH11231; AC02-76SF00515; SC0012704
• OSTI ID: 1847186
• Report Number(s): BNL-223314-2022-JAAM
• Journal Information: Optics Express, Journal Name: Optics Express Journal Issue: 6 Vol. 30; ISSN 1094-4087; ISSN OPEXFF
• Publisher: Optical Society of AmericaCopyright Statement
• Country of Publication: United States
• Language: English