title: Three-dimensional reconstruction of highly complex microscopic samples using scanning electron microscopy and optical flow estimation.
abstract: Scanning Electron Microscope (SEM) as one of the major research and industrial equipment for imaging of micro-scale samples and surfaces has gained extensive attention from its emerge. However, the acquired micrographs still remain two-dimensional (2D). In the current work a novel and highly accurate approach is proposed to recover the hidden third-dimension by use of multi-view image acquisition of the microscopic samples combined with pre/post-processing steps including sparse feature-based stereo rectification, nonlocal-based optical flow estimation for dense matching and finally depth estimation. Employing the proposed approach, three-dimensional (3D) reconstructions of highly complex microscopic samples were achieved to facilitate the interpretation of topology and geometry of surface/shape attributes of the samples. As a byproduct of the proposed approach, high-definition 3D printed models of the samples can be generated as a tangible means of physical understanding. Extensive comparisons with the state-of-the-art reveal the strength and superiority of the proposed method in uncovering the details of the highly complex microscopic samples.
authors.affiliation: Department of Electrical Engineering, University of Wisconsin-Milwaukee, Milwaukee, WI, United States of America.
authors.forename: Ahmadreza
authors.identifier: http://orcid.org/0000-0002-4496-8940
authors.initials: A
authors.lastname: Baghaie
authors.affiliation: Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, WI, United States of America.
authors.forename: Ahmad
authors.initials: A
authors.lastname: Pahlavan Tafti
authors.affiliation: Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States of America.
authors.forename: Heather A
authors.initials: HA
authors.lastname: Owen
authors.affiliation: Department of Mechanical Engineering, University of Wisconsin-Milwaukee, Milwaukee, WI, United States of America.
authors.forename: Roshan M
authors.initials: RM
authors.lastname: D'Souza
authors.affiliation: Departments of Electrical Engineering and Computer Science, University of Wisconsin-Milwaukee, Milwaukee, WI, United States of America.
authors.forename: Zeyun
authors.initials: Z
authors.lastname: Yu
mesh_terms: D000465:Algorithms; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008855:Microscopy, Electron, Scanning / Q000379:methods*