Electron Microscopy Image Reconstruction Research Articles

Physics-Based Regularizer for Joint Soft Segmentation and Reconstruction of Electron Microscopy Images of Polycrystalline Microstructures

For Bayesian image reconstruction applications in which the measured image follows from physical considerations, it is desirable to incorporate the corresponding physics into the prior model. In this paper, we use a phase-field as the physics-based prior model to implement the soft segmentation and reconstruction of noisy microstructural images of a polycrystalline, covalent material (SiC). The functional form of this prior is based on a coarse-grained Ginzburg–Landau free energy that embodies the underlying physics, and its phenomenological parameters are obtained from atomistic computer simulation. In particular, we compare an existing functional form developed by Fan and Chen for microstructural simulations with one developed here that is better suited to noise reduction in image reconstruction, and find that the latter form is indeed superior in this context. Numerical and experimental results demonstrate that the proposed method performs successful soft segmentation and reconstruction of microscopy images, even at very low signal levels. In addition, the superior performance of the proposed model for several case studies in comparison with state-of-the-art methods, such as BM3D and one using a MRF-based prior, is demonstrated.

A comparative study on the application of SIFT, SURF, BRIEF and ORB for 3D surface reconstruction of electron microscopy images

Image feature detector and descriptor algorithms have made a big advance in almost every area of computer vision applications including object localisation, object tracking, mobile robot mapping, watermarking, panorama stitching and 3D surface reconstruction by assisting the detection and description of feature points in a set of given images. In this paper, we evaluate the performance of four robust feature detection algorithms namely SIFT, SURF, BRIEF and ORB on multi-view 3D surface reconstruction of microscopic samples obtained by a scanning electron microscope (SEM), a widely used equipment in biological and materials sciences for determining the surface attributes of micro objects. To this end, we first develop an optimised multi-view framework for SEM extrinsic calibration and its 3D surface reconstruction. We design a Differential Evolutionary-based algorithm to solve the problem in a global optimisation platform. Several qualitative and quantitative comparisons such as reliability on SEM extrinsic calibration and validity on 3D visualisation performed on real microscopic objects as well as a synthetic model. The present evaluation is expected to provide better insights and consideration to determine which algorithm is well deserved for multi-view 3D SEM surface reconstruction.

Subunit–subunit interactions and overall topology of the dimeric mitochondrial ATP synthase of Polytomella sp.

Mitochondrial F 1F 0-ATP synthase of chlorophycean algae is a dimeric complex of 1600 kDa constituted by 17 different subunits with varying stoichiometries, 8 of them conserved in all eukaryotes and 9 that seem to be unique to the algal lineage (subunits ASA1–9). Two different models proposing the topological assemblage of the nine ASA subunits in the ATP synthase of the colorless alga Polytomella sp. have been put forward. Here, we readdressed the overall topology of the enzyme with different experimental approaches: detection of close vicinities between subunits based on cross-linking experiments and dissociation of the enzyme into subcomplexes, inference of subunit stoichiometry based on cysteine residue labelling, and general three-dimensional structural features of the complex as obtained from small-angle X-ray scattering and electron microscopy image reconstruction. Based on the available data, we refine the topological arrangement of the subunits that constitute the mitochondrial ATP synthase of Polytomella sp.

Membrane association induces a conformational change in the Ebola virus matrix protein.

The matrix protein VP40 from Ebola virus is targeted to the plasma membrane, where it is thought to induce assembly and budding of virions through its association with the lipid bilayer. Ebola virus VP40 is expressed as a monomeric molecule in solution, consisting of two loosely associated domains. Here we show that a C-terminal truncation of seven residues destabilizes the monomeric closed conformation and induces spontaneous hexamerization in solution, as indicated by chemical cross-linking and electron microscopy. Three-dimensional reconstruction of electron microscopy images shows ring-like structures consisting of the N-terminal domain along with evidence for flexibly attached C-terminal domains. In vitro destabilization of the monomer by urea treatment results in similar hexameric molecules in solution. In addition, we demonstrate that membrane association of wild-type VP40 also induces the conformational switch from monomeric to hexameric molecules that may form the building blocks for initiation of virus assembly and budding. Such a conformational change induced by bilayer targeting may be a common feature of many viral matrix proteins and its potential inhibition may result in new anti-viral therapies.