TUTCRIS - Tampereen teknillinen yliopisto

TUTCRIS

Compensation of Missing Wedge Effects with Sequential Statistical Reconstruction in Electron Tomography

Tutkimustuotosvertaisarvioitu

Standard

Compensation of Missing Wedge Effects with Sequential Statistical Reconstruction in Electron Tomography. / Paavolainen, Lassi; Acar, Erman; Tuna, Uygar; Peltonen, Sari; Moriya, Toshio; Soonsawad, Pan; Marjomaki, Varpu; Cheng, R. Holland; Ruotsalainen, Ulla.

julkaisussa: PLoS ONE, Vuosikerta 9, Nro 10, 108978, 03.10.2014.

Tutkimustuotosvertaisarvioitu

Harvard

Paavolainen, L, Acar, E, Tuna, U, Peltonen, S, Moriya, T, Soonsawad, P, Marjomaki, V, Cheng, RH & Ruotsalainen, U 2014, 'Compensation of Missing Wedge Effects with Sequential Statistical Reconstruction in Electron Tomography', PLoS ONE, Vuosikerta. 9, Nro 10, 108978. https://doi.org/10.1371/journal.pone.0108978

APA

Paavolainen, L., Acar, E., Tuna, U., Peltonen, S., Moriya, T., Soonsawad, P., ... Ruotsalainen, U. (2014). Compensation of Missing Wedge Effects with Sequential Statistical Reconstruction in Electron Tomography. PLoS ONE, 9(10), [108978]. https://doi.org/10.1371/journal.pone.0108978

Vancouver

Author

Paavolainen, Lassi ; Acar, Erman ; Tuna, Uygar ; Peltonen, Sari ; Moriya, Toshio ; Soonsawad, Pan ; Marjomaki, Varpu ; Cheng, R. Holland ; Ruotsalainen, Ulla. / Compensation of Missing Wedge Effects with Sequential Statistical Reconstruction in Electron Tomography. Julkaisussa: PLoS ONE. 2014 ; Vuosikerta 9, Nro 10.

Bibtex - Lataa

@article{da02160308eb41e4ba3883ccc0b64e15,
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.",
keywords = "IMAGE-RECONSTRUCTION, EMISSION-TOMOGRAPHY, BAYESIAN-APPROACH, AXIS TOMOGRAPHY, ALGORITHM, RESOLUTION, MAXIMUM",
author = "Lassi Paavolainen and Erman Acar and Uygar Tuna and Sari Peltonen and Toshio Moriya and Pan Soonsawad and Varpu Marjomaki and Cheng, {R. Holland} and Ulla Ruotsalainen",
note = "Contribution: organisation=sgn,FACT1=1<br/>Portfolio EDEND: 2014-10-30<br/>Publisher name: Public Library of Science<br /> publication_forum: 65163",
year = "2014",
month = "10",
day = "3",
doi = "10.1371/journal.pone.0108978",
language = "English",
volume = "9",
journal = "PLoS ONE",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "10",

}

RIS (suitable for import to EndNote) - Lataa

TY - JOUR

T1 - Compensation of Missing Wedge Effects with Sequential Statistical Reconstruction in Electron Tomography

AU - Paavolainen, Lassi

AU - Acar, Erman

AU - Tuna, Uygar

AU - Peltonen, Sari

AU - Moriya, Toshio

AU - Soonsawad, Pan

AU - Marjomaki, Varpu

AU - Cheng, R. Holland

AU - Ruotsalainen, Ulla

N1 - Contribution: organisation=sgn,FACT1=1<br/>Portfolio EDEND: 2014-10-30<br/>Publisher name: Public Library of Science<br /> publication_forum: 65163

PY - 2014/10/3

Y1 - 2014/10/3

N2 - 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.

AB - 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.

KW - IMAGE-RECONSTRUCTION

KW - EMISSION-TOMOGRAPHY

KW - BAYESIAN-APPROACH

KW - AXIS TOMOGRAPHY

KW - ALGORITHM

KW - RESOLUTION

KW - MAXIMUM

U2 - 10.1371/journal.pone.0108978

DO - 10.1371/journal.pone.0108978

M3 - Article

VL - 9

JO - PLoS ONE

JF - PLoS ONE

SN - 1932-6203

IS - 10

M1 - 108978

ER -