title: Compensation of missing wedge effects with sequential statistical reconstruction in electron tomography.
abstract: Electron tomography (ET) of biological samples is used to study the organization and the structure of the whole cell and subcellular complexes in great detail. However, projections cannot be acquired over full tilt angle range with biological samples in electron microscopy. ET image reconstruction can be considered an ill-posed problem because of this missing information. This results in artifacts, seen as the loss of three-dimensional (3D) resolution in the reconstructed images. The goal of this study was to achieve isotropic resolution with a statistical reconstruction method, sequential maximum a posteriori expectation maximization (sMAP-EM), using no prior morphological knowledge about the specimen. The missing wedge effects on sMAP-EM were examined with a synthetic cell phantom to assess the effects of noise. An experimental dataset of a multivesicular body was evaluated with a number of gold particles. An ellipsoid fitting based method was developed to realize the quantitative measures elongation and contrast in an automated, objective, and reliable way. The method statistically evaluates the sub-volumes containing gold particles randomly located in various parts of the whole volume, thus giving information about the robustness of the volume reconstruction. The quantitative results were also compared with reconstructions made with widely-used weighted backprojection and simultaneous iterative reconstruction technique methods. The results showed that the proposed sMAP-EM method significantly suppresses the effects of the missing information producing isotropic resolution. Furthermore, this method improves the contrast ratio, enhancing the applicability of further automatic and semi-automatic analysis. These improvements in ET reconstruction by sMAP-EM enable analysis of subcellular structures with higher three-dimensional resolution and contrast than conventional methods.
authors.affiliation: Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland.
authors.forename: Lassi
authors.initials: L
authors.lastname: Paavolainen
authors.affiliation: Department of Signal Processing, Tampere University of Technology, Tampere, Finland; BioMediTech, Tampere University of Technology, Tampere, Finland.
authors.forename: Erman
authors.initials: E
authors.lastname: Acar
authors.affiliation: Department of Signal Processing, Tampere University of Technology, Tampere, Finland.
authors.forename: Uygar
authors.initials: U
authors.lastname: Tuna
authors.affiliation: Department of Signal Processing, Tampere University of Technology, Tampere, Finland; BioMediTech, Tampere University of Technology, Tampere, Finland.
authors.forename: Sari
authors.initials: S
authors.lastname: Peltonen
authors.affiliation: Department of Signal Processing, Tampere University of Technology, Tampere, Finland; BioMediTech, Tampere University of Technology, Tampere, Finland.
authors.forename: Toshio
authors.initials: T
authors.lastname: Moriya
authors.affiliation: Department of Molecular and Cellular Biology, University of California Davis, Davis, California, United States of America; Department of Anatomy, Faculty of Dentistry, Mahidol University, Bangkok, Thailand.
authors.forename: Pan
authors.initials: P
authors.lastname: Soonsawad
authors.affiliation: Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland.
authors.forename: Varpu
authors.initials: V
authors.lastname: Marjomäki
authors.affiliation: Department of Molecular and Cellular Biology, University of California Davis, Davis, California, United States of America.
authors.forename: R Holland
authors.initials: RH
authors.lastname: Cheng
authors.affiliation: Department of Signal Processing, Tampere University of Technology, Tampere, Finland; BioMediTech, Tampere University of Technology, Tampere, Finland.
authors.forename: Ulla
authors.initials: U
authors.lastname: Ruotsalainen
mesh_terms: D000465:Algorithms; D016477:Artifacts; D055032:Electron Microscope Tomography / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods*