Investigation of iterative image reconstruction in three-dimensional optoacoustic tomography

Iterative image reconstruction algorithms for optoacoustic tomography (OAT), also known as photoacoustic tomography, have the ability to improve image quality over analytic algorithms due to their ability to incorporate accurate models of the imaging physics, instrument response, and measurement noise. However, to date, there have been few reported attempts to employ advanced iterative image reconstruction algorithms for improving image quality in three-dimensional (3D) OAT. In this work, we implement and investigate two iterative image reconstruction methods for use with a 3D OAT small animal imager: namely, a penalized least-squares (PLS) method employing a quadratic smoothness penalty and a PLS method employing a total variation norm penalty. The reconstruction algorithms employ accurate models of the ultrasonic transducer impulse responses. Experimental data sets are employed to compare the performances of the iterative reconstruction algorithms to that of a 3D filtered backprojection (FBP) algorithm. By use of quantitative measures of image quality, we demonstrate that the iterative reconstruction algorithms can mitigate image artifacts and preserve spatial resolution more effectively than FBP algorithms. These features suggest that the use of advanced image reconstruction algorithms can improve the effectiveness of 3D OAT while reducing the amount of data required for biomedical applications

Could face-centered cubic titanium in cold-rolled commercially-pure titanium only be a Ti-hydride?

A face-centered cubic (FCC) phase in electro-polished specimens for transmission electron microscopy of commercially pure titanium has sometimes been reported. Here, a combination of atom-probe tomography, scanning transmission electron microscopy and low-loss electron energy loss spectroscopy is employed to study both the crystal structural and chemical composition of this FCC phase. Our results prove that the FCC phase is actually a TiHx (x>1) hydride, and not a new allotrope of Ti, in agreement with previous reports. The formation of the hydride is discussed

The Geometrical Structure of Disordered Sphere Packings

The three dimensional structure of large packings of monosized spheres with volume fractions ranging between 0.58 and 0.64 has been studied with X-ray Computed Tomography. We search for signatures of organization, we classify local arrangements and we explore the effects of local geometrical constrains on the global packing. This study is the largest and the most accurate empirical analysis of disordered packings at the grain-scale to date with over 140,000 sphere coordinates mapped. We discuss topological and geometrical ways to characterize and classify these systems, and discuss implications that local geometry can have on the mechanisms of formation of these amorphous structures.Comment: 15 pages; 16 figure

Time-resolved and three-dimensional study of dislocation-particle interactions in aluminum and copper alloys

Dislocation-particle interactions in three alloys systems, Al-Cu, Al-Mg-Sc, and Cu-Co have been investigated using in situ straining experiments inside the transmission electron microscope, post mortem analysis, and electron tomographic reconstructions. Specifically, diffraction-contrast electron tomography was developed during the course of this work as a 3D imaging technique for crystalline systems such that the dislocation and defect arrangement could be fully characterized and spatially-resolved. Micrographs imaged using two-beam and kinematical bright-field and weak-beam dark-field conditions were acquired over an angular range then used to reconstruct the tomograms. Supplemental advances to the technique include: Visualization of dislocations in color based on Burgers vector or other relevant characteristics; determination of the specimen coordinate system in the tomogram; and overcoming the g ∙ b invisibility condition by dual-axes tomography. In the Al-Cu system, which contained Al2Cu plate-shaped particles residing on {001}Al habit planes, in situ straining experiments revealed glide of lattice dislocations in the coherent side of the particle-matrix interface. The confined dislocations escaped the interface by cross-slip after reaching one end of the Al2Cu plate or by shearing the particle, as observed during post mortem analysis. Dislocations bypassed the particles by shear at multiple locations along their length, suggesting that a shearing site becomes more unfavorable with each dislocation passage such that adjacent slip systems must be activated in order to continue shear. When highly deformed, the inter-particle region was shown by electron tomography to be populated with a complex configuration of lattice dislocations pinned at both ends on a particle interface as well as debris created from dislocation-dislocation interactions. In the Cu-Co system, semicoherent Co-rich octahedral particles normally unshearble by lattice dislocations were observed to be sheared by small twins emanating from the Cu matrix. This new deformation behavior was attributed to the high strain rates associated with twinning and a small increase in interfacial energy associated with shearing of Co particles, which has the same stacking as the Cu matrix. Interactions with lattice dislocations, on the other hand, exhibited similar behavior during in situ and post mortem observations as the Al-Mg-Sc system, which contained Al3Sc particles. In the semi-coherent regime, between 40 nm and up to around 200 nm for Al3Sc and 100 nm for Co, an initial elastic interaction from the misfit strain field gave way to a novel bypass mechanism involving the creation of half-loops attached on one side to the particle interface via bowing and cross-slip while locally pinned at on the particle interface. Bypass of such a particle also involved interfacial dislocations, which increased the complexity of the particle-matrix interface and impeded subsequent bypass of the same particle. In all cases, multiple interactions with lattice dislocations resulted in the evolution of defect structures around a particle over time and the interactions examined were more complex than single dislocation-single particle interactions depicted in classical theoretical models

Towards in cellulo virus crystallography

Viruses are a significant threat to both human health and the economy, and there is an urgent need for novel anti-viral drugs and vaccines. High-resolution viral structures inform our understanding of the virosphere, and inspire novel therapies. Here we present a method of obtaining such structural information that avoids potentially disruptive handling, by collecting diffraction data from intact infected cells. We identify a suitable combination of cell type and virus to accumulate particles in the cells, establish a suitable time point where most cells contain virus condensates and use electron microscopy to demonstrate that these are ordered crystalline arrays of empty capsids. We then use an X-ray free electron laser to provide extremely bright illumination of sub-micron intracellular condensates of bacteriophage phiX174 inside living Escherichia coli at room temperature. We have been able to collect low resolution diffraction data. Despite the limited resolution and completeness of these initial data, due to a far from optimal experimental setup, we have used novel methodology to determine a putative space group, unit cell dimensions, particle packing and likely maturation state of the particles.Peer reviewe

Extraction of physically-realistic pore network properties from three-dimensional synchrotron microtomography images of unconsolidated porous media

Algorithms were implemented to obtain high resolution three-dimensional images using synchrotron microtomography. Morphological algorithms were developed to extract physically-realistic pore-network structure from unconsolidated porous media systems imaged using synchrotron microtomography. The structure can be used to correlate pore-scale phenomena with the pore structure and can also be incorporated into a pore-network model to verify existing models, understand, or predict transport and flow processes and phenomena in complex porous media systems. The algorithms are based on the three-dimensional skeletonization of the pore space in the form of nodes connected to paths. Dilation algorithms were developed to generate inscribed spheres on the nodes and paths of the medial axis to represent pore-bodies and pore-throats of the network, respectively. Pore-network structure is captured by three-dimensional spatial distribution of pore-bodies and pore-throats, pore-body and pore-throat size distributions, and the connectivity. Theoretical packings were used to verify the algorithms. Systems of glass bead and natural sand were used in this study to investigate the applicability of the algorithms. Additionally, porosity, specific surface area, and representative elementary volume (REV) analysis of porosity were calculated. The impact of resolution was investigated using perfect glass bead and natural sand systems. Finally, semivariograms and integral scale concepts were used as a tool to investigate the spatial correlation of the network. Results showed that microtomography is an effective tool to provide quantitative analysis of three-dimensional systems. The quality of the datasets depends on photon energy, photon flux, size and type of the sample, and the number of projections. The resolution has a significant impact on the construction of the medial axis and extraction of pore network parameters. This impact varies in its significance based on the system and the properties being calculated. Results highlighted the difficulty of creating a unique network from a complex, continuum pore space. Results showed that the algorithms developed are general in use and can be applied to any three-dimensional unconsolidated porous media system. Spatial correlation results showed that systems have different correlation behavior; therefore, it might be not correct if a correlation model is assigned a priori into a pore-network model

Stiffening of nanoporous gold: experiment, simulation and theory

By combining electron microscopy measurements, atomistic simulations and elastic homogenization theory, we theoretically investigate the Young's modulus of nanoporous Au structures. Based on atomistic replicas generated starting from experimental tomographic evidence, atomistic simulations reveal that nanoporous Au stiffens as ligaments become finer, reproducing experimental findings obtained by nanoindentation of dealloyed samples. We argue that such a stiffening is neither due to surface stress nor to grain boundaries. Instead, we observe a direct quantitative correlation between the density of dislocations found in the material phase of the nanoporous structures and their Young's modulus and we propose a microscopic explanation of the observed stiffening. In particular, we show that local stress and strain fields in the neighborhood of dislocation cores allow dislocations to work as reinforcing solutes