GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging

Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. In many scientific applications, however, the number of projections that can be measured is limited due to geometric constraints, tolerable radiation dose and/or acquisition speed. Thus it becomes an important problem to obtain the best-possible reconstruction from a limited number of projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE). By iterating between real and reciprocal space, GENFIRE searches for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques by numerical simulations, and by experimentally by reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. Equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines.Comment: 18 pages, 6 figure

A single slice approach for simulating two-beam electron diffraction of nanocrystals

[EN] A simple computational method that can be used to simulate TEM image contrast of an electron beam diffracted by a crystal under two-beam dynamical scattering conditions is presented. The approach based on slicing the shape factor is valid for a general crystal morphology, with and without crystalline defects, avoids the column approximation, and provides the complex exit wave at the focal and the image planes also under weak-beam conditions. The approach is particularly efficient for large crystals and the 3D model required for the calculations can be measured experimentally using electron tomography. The method is applied to show that the shape of a diffracted spot can be affected by shifts, broadening and secondary maxima of appreciable intensity, even for a perfect crystal. The methodology is extended for the case of electron precession diffraction, and to show how can be used to improve nanometrology from diffraction patterns. The method is used also to perform simulations of simple models of crystalline defects. The accuracy of the method is demonstrated through examples of experimental and simulated dark-field images of MgO and ZrO2 nanocrystals and thin layers of CeO2

Analysis of Granular Packing Structure by Scattering of THz Radiation

Scattering methods are widespread used to characterize the structure and constituents of matter on small length scales. This motivates this introductory text on identifying prospective approaches to scattering-based methods for granular media. A survey to light scattering by particles and particle ensembles is given. It is elaborated why the established scattering methods using X-rays and visible light cannot in general be transferred to granular media. Spectroscopic measurements using Terahertz radiation are highlighted as they to probe the scattering properties of granular media, which are sensitive to the packing structure. Experimental details to optimize spectrometer for measurements on granular media are discussed. We perform transmission measurements on static and agitated granular media using Fourier-transform spectroscopy at the THz beamline of the BessyII storage ring. The measurements demonstrate the potential to evaluate degrees of order in the media and to track transient structural states in agitated bulk granular media.Comment: 12 Pages, 9 Figures, 56 Reference

Cristais fotónico plasmónicos autoensamblados para o control da luz na nanoescala

This thesis is the result of more than ve years of research on the study of several kind of photonic and plasmonic systems. Main body of this research has been performed in the Photonics Crystals Group at the Material Science Institute of Madrid (ICMM - center belonging to the national research council of Spain-CSIC) under the supervision of Prof. Ceferino L opez Fernandez and Dr. Juan F. Galisteo Lopez

Analysing the lattice transition of thin filaments in striated muscle

Thin filaments, through interaction with thick filaments, form the contractile apparatus of striated muscle. Therefore, the length and arrangement of the thin filaments are of key importance to the function of the muscle. The thin filaments from adjacent sarcomeres are anchored at the Z-disc. In 1968 Pringle predicted that thin filament are organised in the Z-disc in a rhomboid lattice rather than a square lattice. Previous experimental evidence has been insufficient to verify Pringle’s suggestion. In the A-band the thin filaments interdigitate with the thick filaments on a hexagonal lattice, hence from the Z-disc to the A-band, there is a transition of the lattice from square to hexagonal. In this project, I have firstly used Fourier analysis and electron tomography to investigate the thin filament lattice in the Z-disc. I have used electron tomography to determine how the lattice transition occurs between the Z-disc and the A-band. Electron tomography of these samples also allowed me to determine the lengths of thin filaments, showing unequivocally that they are of variable lengths in cardiac muscle

Structure of isolated Z-disks from honeybee flight muscle

The Z-disk is a complex structure comprising some 40 proteins that are involved in the transmission of force developed during muscle contraction and in important signalling pathways that govern muscle homeostasis. In the Z-disk the ends of antiparallel thin filaments from adjacent sarcomeres are crosslinked by α-actinin. The structure of the Z-disk lattice varies greatly throughout the animal kingdom. In vertebrates the thin filaments form a tetragonal lattice, whereas invertebrate flight muscle has a hexagonal lattice. The width of the Z-disk varies considerably and correlates with the number of α-actinin bridges. A detailed description at a high resolution of the Z-disk lattice is needed in order to better understand muscle function and disease. The molecular architecture of the Z-disk lattice in honeybee (Apis mellifera) is known from plastic embedded thin sections to a resolution of 7 nm, which is not sufficient to dock component protein crystal structures. It has been shown that sectioning is a damaging process that leads to the loss of finer details present in biological specimens. However, the Apis Z-disk is a thin structure (120 nm) suitable for cryo EM. We have isolated intact honeybee Z-disks from indirect flight muscle, thus obviating the need of plastic sectioning. We have employed cryo electron tomography and image processing to investigate the arrangement of proteins within the hexagonal lattice of the Apis Z-disk. The resolution obtained, ~6 nm, was probably limited by damage caused by the harshness of the conditions used to extract the myofibrils and isolate the Z-disks