Removal of vesicle structures from transmission electron microscope images

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 - 2016/2

Y1 - 2016/2

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

SN - 1057-7149

VL - 25

SP - 540

EP - 552

JO - IEEE Transactions on Image Processing

JF - IEEE Transactions on Image Processing

IS - 2

ER -