Optimal and fast rotational alignment of volumes with missing data in Fourier space

AbstractElectron tomography of intact cells has the potential to reveal the entire cellular content at a resolution corresponding to individual macromolecular complexes. Characterization of macromolecular complexes in tomograms is nevertheless an extremely challenging task due to the high level of noise, and due to the limited tilt angle that results in missing data in Fourier space. By identifying particles of the same type and averaging their 3D volumes, it is possible to obtain a structure at a more useful resolution for biological interpretation. Currently, classification and averaging of sub-tomograms is limited by the speed of computational methods that optimize alignment between two sub-tomographic volumes. The alignment optimization is hampered by the fact that the missing data in Fourier space has to be taken into account during the rotational search. A similar problem appears in single particle electron microscopy where the random conical tilt procedure may require averaging of volumes with a missing cone in Fourier space. We present a fast implementation of a method guaranteed to find an optimal rotational alignment that maximizes the constrained cross-correlation function (cCCF) computed over the actual overlap of data in Fourier space

Nanometer-scale Tomographic Reconstruction of 3D Electrostatic Potentials in GaAs/AlGaAs Core-Shell Nanowires

We report on the development of Electron Holographic Tomography towards a versatile potential measurement technique, overcoming several limitations, such as a limited tilt range, previously hampering a reproducible and accurate electrostatic potential reconstruction in three dimensions. Most notably, tomographic reconstruction is performed on optimally sampled polar grids taking into account symmetry and other spatial constraints of the nanostructure. Furthermore, holographic tilt series acquisition and alignment have been automated and adapted to three dimensions. We demonstrate 6 nm spatial and 0.2 V signal resolution by reconstructing various, previously hidden, potential details of a GaAs/AlGaAs core-shell nanowire. The improved tomographic reconstruction opens pathways towards the detection of minute potentials in nanostructures and an increase in speed and accuracy in related techniques such as X-ray tomography

Electron tomography at 2.4 {\AA} resolution

Transmission electron microscopy (TEM) is a powerful imaging tool that has found broad application in materials science, nanoscience and biology(1-3). With the introduction of aberration-corrected electron lenses, both the spatial resolution and image quality in TEM have been significantly improved(4,5) and resolution below 0.5 {\AA} has been demonstrated(6). To reveal the 3D structure of thin samples, electron tomography is the method of choice(7-11), with resolutions of ~1 nm^3 currently achievable(10,11). Recently, discrete tomography has been used to generate a 3D atomic reconstruction of a silver nanoparticle 2-3 nm in diameter(12), but this statistical method assumes prior knowledge of the particle's lattice structure and requires that the atoms fit rigidly on that lattice. Here we report the experimental demonstration of a general electron tomography method that achieves atomic scale resolution without initial assumptions about the sample structure. By combining a novel projection alignment and tomographic reconstruction method with scanning transmission electron microscopy, we have determined the 3D structure of a ~10 nm gold nanoparticle at 2.4 {\AA} resolution. While we cannot definitively locate all of the atoms inside the nanoparticle, individual atoms are observed in some regions of the particle and several grains are identified at three dimensions. The 3D surface morphology and internal lattice structure revealed are consistent with a distorted icosahedral multiply-twinned particle. We anticipate that this general method can be applied not only to determine the 3D structure of nanomaterials at atomic scale resolution(13-15), but also to improve the spatial resolution and image quality in other tomography fields(7,9,16-20).Comment: 27 pages, 17 figure

SOPHIE velocimetry of Kepler transit candidates XVI. Tomographic measurement of the low obliquity of KOI-12b, a warm Jupiter transiting a fast rotator

We present the detection and characterization of the transiting warm Jupiter KOI-12b, first identified with Kepler with an orbital period of 17.86 days. We combine the analysis of Kepler photometry with Doppler spectroscopy and line-profile tomography of time-series spectra obtained with the SOPHIE spectrograph to establish its planetary nature and derive its properties. To derive reliable estimates for the uncertainties on the tomographic model parameters, we devised an empirical method to calculate statistically independent error bars on the time-series spectra. KOI-12b has a radius of 1.43$\pm$0.13$R_\mathrm{Jup}$ and a 3$\sigma$ upper mass limit of 10$M_\mathrm{Jup}$. It orbits a fast-rotating star ($v$sin$i_{\star}$ = 60.0$\pm$0.9 km s$^{-1}$) with mass and radius of 1.45$\pm$0.09 $M_\mathrm{Sun}$ and 1.63$\pm$0.15 $R_\mathrm{Sun}$, located at 426$\pm$40 pc from the Earth. Doppler tomography allowed a higher precision on the obliquity to be reached by comparison with the analysis of the Rossiter-McLaughlin radial velocity anomaly, and we found that KOI-12b lies on a prograde, slightly misaligned orbit with a low sky-projected obliquity $\lambda$ = 12.6$\stackrel{+3.0}{_{-2.9}}^\circ$. The properties of this planetary system, with a 11.4 magnitude host-star, make of KOI-12b a precious target for future atmospheric characterization.Comment: 19 pages, 10 figure

Inherited crustal deformation along the East Gondwana margin revealed by seismic anisotropy tomography

Acknowledgments We thank Mallory Young for providing phase velocity measurements in mainland Australia and Tasmania. Robert Musgrave is thanked for making available his tilt-filtered magnetic intensity map. In the short term, data may be made available by contacting the authors (S.P. or N.R.). A new database of passive seismic data recorded in Australia is planned as part of a national geophysics data facility for easy access download. Details on the status of this database may be obtained from the authors (S.P., N.R., or A.M.R.). There are no restrictions on access for noncommercial use. Commercial users should seek written permission from the authors (S.P. or N.R.). Ross Cayley publishes with the permission of the Director of the Geological Survey of Victoria.Peer reviewedPublisher PD

High-speed in vitro intensity diffraction tomography

We demonstrate a label-free, scan-free intensity diffraction tomography technique utilizing annular illumination (aIDT) to rapidly characterize large-volume three-dimensional (3-D) refractive index distributions in vitro. By optimally matching the illumination geometry to the microscope pupil, our technique reduces the data requirement by 60 times to achieve high-speed 10-Hz volume rates. Using eight intensity images, we recover volumes of ∼350 μm  ×  100 μm  ×  20  μm, with near diffraction-limited lateral resolution of   ∼  487  nm and axial resolution of   ∼  3.4  μm. The attained large volume rate and high-resolution enable 3-D quantitative phase imaging of complex living biological samples across multiple length scales. We demonstrate aIDT’s capabilities on unicellular diatom microalgae, epithelial buccal cell clusters with native bacteria, and live Caenorhabditis elegans specimens. Within these samples, we recover macroscale cellular structures, subcellular organelles, and dynamic micro-organism tissues with minimal motion artifacts. Quantifying such features has significant utility in oncology, immunology, and cellular pathophysiology, where these morphological features are evaluated for changes in the presence of disease, parasites, and new drug treatments. Finally, we simulate the aIDT system to highlight the accuracy and sensitivity of the proposed technique. aIDT shows promise as a powerful high-speed, label-free computational microscopy approach for applications where natural imaging is required to evaluate environmental effects on a sample in real time.https://arxiv.org/abs/1904.06004Accepted manuscrip

Synergy between the Large Synoptic Survey Telescope and the Square Kilometre Array

We provide an overview of the science benefits of combining information from the Square Kilometre Array (SKA) and the Large Synoptic Survey Telescope (LSST). We first summarise the capabilities and timeline of the LSST and overview its science goals. We then discuss the science questions in common between the two projects, and how they can be best addressed by combining the data from both telescopes. We describe how weak gravitational lensing and galaxy clustering studies with LSST and SKA can provide improved constraints on the causes of the cosmological acceleration. We summarise the benefits to galaxy evolution studies of combining deep optical multi-band imaging with radio observations. Finally, we discuss the excellent match between one of the most unique features of the LSST, its temporal cadence in the optical waveband, and the time resolution of the SKA.Comment: SKA Synergies Chapter, Advancing Astrophysics with the SKA (AASKA14) Conference, Giardini Naxos (Italy), June 9th-13th 201