Removal of vesicle structures from transmission electron microscope images
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Removal of vesicle structures from transmission electron microscope images. / Jensen, Katrine Hommelhoff; Sigworth, Fred J.; Brandt, Sami Sebastian.
In: IEEE Transactions on Image Processing, Vol. 25, No. 2, 2016, p. 540-552.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Removal of vesicle structures from transmission electron microscope images
AU - Jensen, Katrine Hommelhoff
AU - Sigworth, Fred J.
AU - Brandt, Sami Sebastian
PY - 2016
Y1 - 2016
N2 - In this paper, we address the problem of imaging membrane proteins for single-particle cryo-electron microscopy reconstruction of the isolated protein structure. More precisely, we propose a method for learning and removing the interfering vesicle signals from the micrograph, prior to reconstruction. In our approach, we estimate the subspace of the vesicle structures and project the micrographs onto the orthogonal complement of this subspace. We construct a 2D statistical model of the vesicle structure, based on higher order singular value decomposition (HOSVD), by considering the structural symmetries of the vesicles in the polar coordinate plane. We then propose to lift the HOSVD model to a novel hierarchical model by summarizing the multidimensional HOSVD coefficients by their principal components. Along with the model, a solid vesicle normalization scheme and model selection criterion are proposed to make a compact and general model. The results show that the vesicle structures are accurately separated from the background by the HOSVD model that is also able to adapt to the asymmetries of the vesicles. This is a promising result and suggests even wider applicability of the proposed approach in learning and removal of statistical structures.
AB - In this paper, we address the problem of imaging membrane proteins for single-particle cryo-electron microscopy reconstruction of the isolated protein structure. More precisely, we propose a method for learning and removing the interfering vesicle signals from the micrograph, prior to reconstruction. In our approach, we estimate the subspace of the vesicle structures and project the micrographs onto the orthogonal complement of this subspace. We construct a 2D statistical model of the vesicle structure, based on higher order singular value decomposition (HOSVD), by considering the structural symmetries of the vesicles in the polar coordinate plane. We then propose to lift the HOSVD model to a novel hierarchical model by summarizing the multidimensional HOSVD coefficients by their principal components. Along with the model, a solid vesicle normalization scheme and model selection criterion are proposed to make a compact and general model. The results show that the vesicle structures are accurately separated from the background by the HOSVD model that is also able to adapt to the asymmetries of the vesicles. This is a promising result and suggests even wider applicability of the proposed approach in learning and removal of statistical structures.
KW - Algorithms
KW - Cytoplasmic Vesicles
KW - Image Processing, Computer-Assisted
KW - Membrane Proteins
KW - Microscopy, Electron, Transmission
KW - Models, Biological
KW - Models, Statistical
KW - Signal Processing, Computer-Assisted
KW - Journal Article
U2 - 10.1109/TIP.2015.2504901
DO - 10.1109/TIP.2015.2504901
M3 - Journal article
C2 - 26642456
VL - 25
SP - 540
EP - 552
JO - IEEE Transactions on Image Processing
JF - IEEE Transactions on Image Processing
SN - 1057-7149
IS - 2
ER -
ID: 168252184