title: Electron tomography simulator with realistic 3D phantom for evaluation of acquisition, alignment and reconstruction methods.
abstract: Because of the significance of electron microscope tomography in the investigation of biological structure at nanometer scales, ongoing improvement efforts have been continuous over recent years. This is particularly true in the case of software developments. Nevertheless, verification of improvements delivered by new algorithms and software remains difficult. Current analysis tools do not provide adaptable and consistent methods for quality assessment. This is particularly true with images of biological samples, due to image complexity, variability, low contrast and noise. We report an electron tomography (ET) simulator with accurate ray optics modeling of image formation that includes curvilinear trajectories through the sample, warping of the sample and noise. As a demonstration of the utility of our approach, we have concentrated on providing verification of the class of reconstruction methods applicable to wide field images of stained plastic-embedded samples. Accordingly, we have also constructed digital phantoms derived from serial block face scanning electron microscope images. These phantoms are also easily modified to include alignment features to test alignment algorithms. The combination of more realistic phantoms with more faithful simulations facilitates objective comparison of acquisition parameters, alignment and reconstruction algorithms and their range of applicability. With proper phantoms, this approach can also be modified to include more complex optical models, including distance-dependent blurring and phase contrast functions, such as may occur in cryotomography.
authors.affiliation: Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China; National Center for Microscopy and Imaging Research, University of California, San Diego, USA.
authors.forename: Xiaohua
authors.initials: X
authors.lastname: Wan
authors.affiliation: National Center for Microscopy and Imaging Research, University of California, San Diego, USA.
authors.forename: Tsvi
authors.initials: T
authors.lastname: Katchalski
authors.affiliation: National Center for Microscopy and Imaging Research, University of California, San Diego, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Churas
authors.affiliation: National Center for Microscopy and Imaging Research, University of California, San Diego, USA.
authors.forename: Sreya
authors.initials: S
authors.lastname: Ghosh
authors.affiliation: National Center for Microscopy and Imaging Research, University of California, San Diego, USA.
authors.forename: Sebastien
authors.initials: S
authors.lastname: Phan
authors.affiliation: National Center for Microscopy and Imaging Research, University of California, San Diego, USA. Electronic address: albert.rick.lawrence@gmail.com.
authors.forename: Albert
authors.initials: A
authors.lastname: Lawrence
authors.affiliation: Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Hao
authors.affiliation: Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China; Beijing Institute of Technology, Beijing, China.
authors.forename: Ziying
authors.initials: Z
authors.lastname: Zhou
authors.affiliation: School of Electronic and Information Engineering, Tianjin Polytechnic University, Tianjin, China; National Center for Microscopy and Imaging Research, University of California, San Diego, USA.
authors.forename: Ruijuan
authors.initials: R
authors.lastname: Chen
authors.affiliation: Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Fa
authors.initials: F
authors.lastname: Zhang
authors.affiliation: National Center for Microscopy and Imaging Research, University of California, San Diego, USA; Departments of Neurosciences and Bioengineering, University of California, San Diego, USA.
authors.forename: Mark H
authors.initials: MH
authors.lastname: Ellisman
mesh_terms: D000465:Algorithms; D055032:Electron Microscope Tomography / Q000295:instrumentation / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods; D019047:Phantoms, Imaging / Q000592:standards*; D012984:Software
keywords: Alignment; Block face; Curvilinear; Electron; Inversion; Microscope; Reconstruction; Series; Simulator; Tilt; Tomography; Tracking; Warping