Next-generation optical microscopy

A new breed of microscopy techniques is coming to the forefront of optical imaging. They enhance the attainable 3D resolution of imaging in live and ``fixed'' cells' (with minimal structural perturbation) by greater than tenfold, bringing subcellular structures in sharp focus Along with long-term imaging, deep tissue and high throughput capablities, new insights in various fields of biology are being generated. The main set of these next-generation optical microscopy techniques along with select applications is described in this article.

Characterization and Space-Time Downscaling of the Inundation Extent over the Inner Niger Delta Using GIEMS and MODIS Data

The objective in this work is to develop downscaling methodologies to obtain a long time record of inundation extent at high spatial resolution based on the existing low spatial resolution results of the Global Inundation Extent from Multi-Satellites (GIEMS) dataset. In semiarid regions, high-spatial-resolution a priori information can be provided by visible and infrared observations from the Moderate Resolution Imaging Spectroradiometer (MODIS). The study concentrates on the Inner Niger Delta where MODIS-derived inundation extent has been estimated at a 500-m resolution. The space-time variability is first analyzed using a principal component analysis (PCA). This is particularly effective to understand the inundation variability, interpolate in time, or fill in missing values. Two innovative methods are developed (linear regression and matrix inversion) both based on the PCA representation. These GIEMS downscaling techniques have been calibrated using the 500-m MODIS data. The downscaled fields show the expected space-time behaviors from MODIS. A 20-yr dataset of the inundation extent at 500 m is derived from this analysis for the Inner Niger Delta. The methods are very general and may be applied to many basins and to other variables than inundation, provided enough a priori high-spatial-resolution information is available. The derived high-spatial-resolution dataset will be used in the framework of the Surface Water Ocean Topography (SWOT) mission to develop and test the instrument simulator as well as to select the calibration validation sites (with high space-time inundation variability). In addition, once SWOT observations are available, the downscaled methodology will be calibrated on them in order to downscale the GIEMS datasets and to extend the SWOT benefits back in time to 1993.

Real-time maximum a-posteriori image reconstruction for fluorescence microscopy

Rapid reconstruction of multidimensional image is crucial for enabling real-time 3D fluorescence imaging. This becomes a key factor for imaging rapidly occurring events in the cellular environment. To facilitate real-time imaging, we have developed a graphics processing unit (GPU) based real-time maximum a-posteriori (MAP) image reconstruction system. The parallel processing capability of GPU device that consists of a large number of tiny processing cores and the adaptability of image reconstruction algorithm to parallel processing (that employ multiple independent computing modules called threads) results in high temporal resolution. Moreover, the proposed quadratic potential based MAP algorithm effectively deconvolves the images as well as suppresses the noise. The multi-node multi-threaded GPU and the Compute Unified Device Architecture (CUDA) efficiently execute the iterative image reconstruction algorithm that is similar to 200-fold faster (for large dataset) when compared to existing CPU based systems. (C) 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.

Disaggregation of LST over India: comparative analysis of different vegetation indices

The non-availability of high-spatial-resolution thermal data from satellites on a consistent basis led to the development of different models for sharpening coarse-spatial-resolution thermal data. Thermal sharpening models that are based on the relationship between land-surface temperature (LST) and a vegetation index (VI) such as the normalized difference vegetation index (NDVI) or fraction vegetation cover (FVC) have gained much attention due to their simplicity, physical basis, and operational capability. However, there are hardly any studies in the literature examining comprehensively various VIs apart from NDVI and FVC, which may be better suited for thermal sharpening over agricultural and natural landscapes. The aim of this study is to compare the relative performance of five different VIs, namely NDVI, FVC, the normalized difference water index (NDWI), soil adjusted vegetation index (SAVI), and modified soil adjusted vegetation index (MSAVI), for thermal sharpening using the DisTrad thermal sharpening model over agricultural and natural landscapes in India. Multi-temporal LST data from Landsat-7 Enhanced Thematic Mapper Plus (ETM+) and Moderate Resolution Imaging Spectroradiometer (MODIS) sensors obtained over two different agro-climatic grids in India were disaggregated from 960 m to 120 m spatial resolution. The sharpened LST was compared with the reference LST estimated from the Landsat data at 120 m spatial resolution. In addition to this, MODIS LST was disaggregated from 960 m to 480 m and compared with ground measurements at five sites in India. It was found that NDVI and FVC performed better only under wet conditions, whereas under drier conditions, the performance of NDWI was superior to other indices and produced accurate results. SAVI and MSAVI always produced poorer results compared with NDVI/FVC and NDWI for wet and dry cases, respectively.

Understanding planet formation through high precision photometry and spectroscopy

From studies of protoplanetary disks to extrasolar planets and planetary debris, we aim to understand the full evolution of a planetary system. Observational constraints from ground- and space-based instrumentation allows us to measure the properties of objects near and far and are central to developing this understanding. We present here three observational campaigns that, when combined with theoretical models, reveal characteristics of different stages and remnants of planet formation. The Kuiper Belt provides evidence of chemical and dynamical activity that reveals clues to its primordial environment and subsequent evolution. Large samples of this population can only be assembled at optical wavelengths, with thermal measurements at infrared and sub-mm wavelengths currently available for only the largest and closest bodies. We measure the size and shape of one particular object precisely here, in hopes of better understanding its unique dynamical history and layered composition.

Molecular organic chemistry is one of the most fundamental and widespread facets of the universe, and plays a key role in planet formation. A host of carbon-containing molecules vibrationally emit in the near-infrared when excited by warm gas, T~1000 K. The NIRSPEC instrument at the W.M. Keck Observatory is uniquely configured to study large ranges of this wavelength region at high spectral resolution. Using this facility we present studies of warm CO gas in protoplanetary disks, with a new code for precise excitation modeling. A parameterized suite of models demonstrates the abilities of the code and matches observational constraints such as line strength and shape. We use the models to probe various disk parameters as well, which are easily extensible to others with known disk emission spectra such as water, carbon dioxide, acetylene, and hydrogen cyanide.

Lastly, the existence of molecules in extrasolar planets can also be studied with NIRSPEC and reveals a great deal about the evolution of the protoplanetary gas. The species we observe in protoplanetary disks are also often present in exoplanet atmospheres, and are abundant in Earth's atmosphere as well. Thus, a sophisticated telluric removal code is necessary to analyze these high dynamic range, high-resolution spectra. We present observations of a hot Jupiter, revealing water in its atmosphere and demonstrating a new technique for exoplanet mass determination and atmospheric characterization. We will also be applying this atmospheric removal code to the aforementioned disk observations, to improve our data analysis and probe less abundant species. Guiding models using observations is the only way to develop an accurate understanding of the timescales and processes involved. The futures of the modeling and of the observations are bright, and the end goal of realizing a unified model of planet formation will require both theory and data, from a diverse collection of sources.

From molecules to organs : Microscopy and multi-scale nature of development

Morphogenesis is a phenomenon of intricate balance and dynamic interplay between processes occurring at a wide range of scales (spatial, temporal and energetic). During development, a variety of physical mechanisms are employed by tissues to simultaneously pattern, move, and differentiate based on information exchange between constituent cells, perhaps more than at any other time during an organism's life. To fully understand such events, a combined theoretical and experimental framework is required to assist in deciphering the correlations at both structural and functional levels at scales that include the intracellular and tissue levels as well as organs and organ systems. Microscopy, especially diffraction-limited light microscopy, has emerged as a central tool to capture the spatio-temporal context of life processes. Imaging has the unique advantage of watching biological events as they unfold over time at single-cell resolution in the intact animal. In this work I present a range of problems in morphogenesis, each unique in its requirements for novel quantitative imaging both in terms of the technique and analysis. Understanding the molecular basis for a developmental process involves investigating how genes and their products- mRNA and proteins-function in the context of a cell. Structural information holds the key to insights into mechanisms and imaging fixed specimens paves the first step towards deciphering gene function. The work presented in this thesis starts with the demonstration that the fluorescent signal from the challenging environment of whole-mount imaging, obtained by in situ hybridization chain reaction (HCR), scales linearly with the number of copies of target mRNA to provide quantitative sub-cellular mapping of mRNA expression within intact vertebrate embryos. The work then progresses to address aspects of imaging live embryonic development in a number of species. While processes such as avian cartilage growth require high spatial resolution and lower time resolution, dynamic events during zebrafish somitogenesis require higher time resolution to capture the protein localization as the somites mature. The requirements on imaging are even more stringent in case of the embryonic zebrafish heart that beats with a frequency of ~ 2-2.5 Hz, thereby requiring very fast imaging techniques based on two-photon light sheet microscope to capture its dynamics. In each of the hitherto-mentioned cases, ranging from the level of molecules to organs, an imaging framework is developed, both in terms of technique and analysis to allow quantitative assessment of the process in vivo. Overall the work presented in this thesis combines new quantitative tools with novel microscopy for the precise understanding of processes in embryonic development.

CFD modeling of single-phase flow in a packed bed with MRI validation

Computational fluid dynamics (CFD) simulations are becoming increasingly widespread with the advent of more powerful computers and more sophisticated software. The aim of these developments is to facilitate more accurate reactor design and optimization methods compared to traditional lumped-parameter models. However, in order for CFD to be a trusted method, it must be validated using experimental data acquired at sufficiently high spatial resolution. This article validates an in-house CFD code by comparison with flow-field data obtained using magnetic resonance imaging (MRI) for a packed bed with a particle-to-column diameter ratio of 2. Flows characterized by inlet Reynolds numbers, based on particle diameter, of 27, 55, 111, and 216 are considered. The code used employs preconditioning to directly solve for pressure in low-velocity flow regimes. Excellent agreement was found between the MRI and CFD data with relative error between the experimentally determined and numerically predicted flow-fields being in the range of 3-9%. © 2012 American Institute of Chemical Engineers (AIChE).

Cathodoluminescence study of GaN-based film structures

GaN films grown on sapphire substrate with an emphasis on epitaxial lateral overgrown (ELOG) layers with an array of rhombic shaped mask area as well as InGaN/GaN MQW laser diode layer structures were investigated by cathodoluminescence (CL) spectroscopy and CL imaging at room and low temperatures. The microscopic imaging with a high-spatial resolution clearly reveals the distribution of threading dislocations and point defects in ELOG GaN films. The secondary electron and CL data measured on cleaved faces of laser diodes are analyzed in consideration with luminescence mechanisms in semiconductor heterostructures and around the p - n junction, providing important information on the defects and carrier dynamics in laser diode devices.

Optical analysis of dislocation-related physical processes in GaN-based epilayers

In this paper, recent progresses in optical analysis of dislocation-related physical properties in GaN-based epilayers are surveyed with a brief review. The influence of dislocations on both near-band edge emission and yellow luminescence (YL) is examined either in a statistical way as a function of dislocation density or focused on individual dislocation lines with a high spatial resolution. Threading dislocations may introduce non-radiative recombination centers and enhance YL, but their effects are affected by the structural and chemical environment. The minority carrier diffusion length may be dependent on either dislocation density or impurity doping as confirmed by the result of photovoltaic spectra. The in situ optical monitoring of the strain evolution process is employed during GaN heteroepitaxy using an AIN interlayer. A typical transition of strain from compression to tension is observed and its correlation with the reduction and inclination of threading dislocation lines is revealed. (c) 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High-spin isomeric structures in exotic odd-odd nuclei: Exploration of the proton drip line and beyond

We investigate the role of two-quasiparticle isomeric states along the proton drip line, using configuration-constrained potential-energy-surface calculations. In contrast to even-even nuclei, odd-odd nuclei can have coexisting low-lying two-quasiparticle states. The low excitation energy and high angular momentum can lead to long-lived isomers. Also, because of the hindrance by spin selection, the probabilities of beta and proton decays from high-spin isomers can be reduced significantly. The present calculations reproduce reasonably well the available data for observed isomers in such nuclei. Unobserved high-spin isomers are predicted, which could be useful for future experimental studies of exotic nuclei at and beyond the proton drip line.

Competing fusion and quasifission reaction mechanisms in the production of superheavy nuclei

Within the framework of a dinuclear system model, a new master equation is constructed and solved, which includes the relative distance of nuclei as a new dynamical variable in addition to the mass asymmetry variable so that the nucleon transfer, which leads to fusion and the evolution of the relative distance, which leads to quasifission (QF) are treated simultaneously in a consistent way. The QF mass yields and evaporation residual cross sections to produce superheavy nuclei are systematically investigated under this framework. The results fit the experimental data well. It is shown that the Kramers formula gives results of QF, which agree with those by our diffusion treatment, only if the QF barrier is high enough. Otherwise some large discrepancies occur.

Structural analysis of monoterpene glycosides extracted from Paeonia lactiflora Pall. using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and high-performance liquid chromatography/electrospray ionization tandem mass spectrometry

Paeoniflorin standard was first investigated by electrospray ionization Fourier transform ion cyclotron resonance tandem mass spectrometry (ESI-FTICR-MS/MS) using a sustained off-resonance irradiation (SORI) collision-induced dissociation (CID) method at high mass resolution. The experimental results demonstrated that the unambiguous elemental composition of product ions can be obtained at high mass resolution. Comparing MS/MS spectra and the experimental methods of hydrogen and deuterium exchange, the logical fragmentation pathways of paeoniflorin have been proposed. Then, the extracts of the traditional Chinese medicine Paeonia lactiflora Pall. were analyzed by high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC/ESI-MS/MS). By comparison with the ESI-FTICR-MS/MS data of paeoniflorin, the isomers paeoniflorin and albiflorin in Paeonia lactiflora Pall. have been identified using HPLC/MS with CID in an ion trap and in-source CID. Furthermore, using the characteristic fragmentation pathways, the retention times (t(R)) in HPLC and MS/MS spectra, the structures of three other kinds of monoterpene glycoside compounds have been identified on-line without time-consuming isolation.

改进叠前深度偏移的计算效率＆叠前高分辨率成像

An high-resolution prestack imaging technique of seismic data is developed in this thesis. By using this technique, the reflected coefficients of sheet sands can be gained in order to understand and identify thin oil reservoirs. One-way wave equation based migration methods can more accurately model seismic wave propagation effect such as multi-arrivals and obtain almost correct reflected energy in the presence of complex inhomogeneous media, and therefore, achieve more superiorities in imaging complex structure. So it is a good choice to apply the proposed high-resolution imaging to the presatck depth migration gathers. But one of the main shorting of one-way wave equation based migration methods is the low computational efficiency, thus the improvement on computational efficiency is first carried out. The method to improve the computational efficiency of prestack depth migration is first presented in this thesis, that is frequency-dependent varying-step depth exploration scheme plus a table-driven, one-point wavefield interpolation technology for wave equation based migration methods; The frequency-dependent varying-step depth exploration scheme reduces the computational cost of wavefield depth extrapolation, and the a table-driven, one-point wavefield interpolation technology reconstructs the extrapolated wavefield with an equal, desired vertical step with high computational efficiency. The proposed varying-step depth extrapolation plus one-point interpolation scheme results in 2/3 reduction in computational cost when compared to the equal-step depth extrapolation of wavefield, but gives the almost same imaging. The frequency-dependent varying-step depth exploration scheme is presented in theory by using the optimum split-step Fourier. But the proposed scheme can also be used by other wave equation based migration methods of the frequency domain. The proposed method is demonstrated by using impulse response, 2-D Marmousi dataset, 3-D salt dataset and the 3-D field dataset. A method of high-resolution prestack imaging is presented in the 2nd part of this thesis. The seismic interference method to solve the relative reflected coefficients is presented. The high-resolution imaging is obtained by introducing a sparseness- constrained least-square inversion into the reflected coefficient imaging. Gaussian regularization is first imposed and a smoothed solution is obtained by solving equation derived from the least-square inversion. Then the Cauchy regularization is introducing to the least-square inversion , the sparse solution of relative reflected coefficients can be obtained, that is high-resolution solution. The proposed scheme can be used together with other prestack imaging if the higher resolution is needed in a target zone. The seismic interference method in theory and the solution to sparseness-constrained least-square inversion are presented. The proposed method is demonstrated by synthetic examples and filed data.

New phosphorescence based probes and techniques for the analysis of cellular oxygen and respiration

Real time monitoring of oxygenation and respiration is on the cutting edge of bioanalysis, including studies of cell metabolism, bioenergetics, mitochondrial function and drug toxicity. This thesis presents the development and evaluation of new luminescent probes and techniques for intracellular O2 sensing and imaging. A new oxygen consumption rate (OCR) platform based on the commercial microfluidic perfusion channel μ-slides compatible with extra- and intracellular O2 sensitive probes, different cell lines and measurement conditions was developed. The design of semi-closed channels allowed cell treatments, multiplexing with other assays and two-fold higher sensitivity to compare with microtiter plate. We compared three common OCR platforms: hermetically sealed quartz cuvettes for absolute OCRs, partially sealed with mineral oil 96-WPs for relative OCRs, and open 96-WPs for local cell oxygenation. Both 96-WP platforms were calibrated against absolute OCR platform with MEF cell line, phosphorescent O2 probe MitoXpress-Intra and time-resolved fluorescence reader. Found correlations allow tracing of cell respiration over time in a high throughput format with the possibility of cell stimulation and of changing measurement conditions. A new multimodal intracellular O2 probe, based on the phosphorescent reporter dye PtTFPP, fluorescent FRET donor and two-photon antennae PFO and cationic nanoparticles RL-100 was described. This probe, called MM2, possesses high brightness, photo- and chemical stability, low toxicity, efficient cell staining and high-resolution intracellular O2 imaging with 2D and 3D cell cultures in intensity, ratiometric and lifetime-based modalities with luminescence readers and FLIM microscopes. Extended range of O2 sensitive probes was designed and studied in order to optimize their spectral characteristics and intracellular targeting, using different NPs materials, delivery vectors, ratiometric pairs and IR dyes. The presented improvements provide useful tool for high sensitive monitoring and imaging of intracellular O2 in different measurement formats with wide range of physiological applications.

Spectrotemporal CT data acquisition and reconstruction at low dose.

PURPOSE: X-ray computed tomography (CT) is widely used, both clinically and preclinically, for fast, high-resolution anatomic imaging; however, compelling opportunities exist to expand its use in functional imaging applications. For instance, spectral information combined with nanoparticle contrast agents enables quantification of tissue perfusion levels, while temporal information details cardiac and respiratory dynamics. The authors propose and demonstrate a projection acquisition and reconstruction strategy for 5D CT (3D+dual energy+time) which recovers spectral and temporal information without substantially increasing radiation dose or sampling time relative to anatomic imaging protocols. METHODS: The authors approach the 5D reconstruction problem within the framework of low-rank and sparse matrix decomposition. Unlike previous work on rank-sparsity constrained CT reconstruction, the authors establish an explicit rank-sparse signal model to describe the spectral and temporal dimensions. The spectral dimension is represented as a well-sampled time and energy averaged image plus regularly undersampled principal components describing the spectral contrast. The temporal dimension is represented as the same time and energy averaged reconstruction plus contiguous, spatially sparse, and irregularly sampled temporal contrast images. Using a nonlinear, image domain filtration approach, the authors refer to as rank-sparse kernel regression, the authors transfer image structure from the well-sampled time and energy averaged reconstruction to the spectral and temporal contrast images. This regularization strategy strictly constrains the reconstruction problem while approximately separating the temporal and spectral dimensions. Separability results in a highly compressed representation for the 5D data in which projections are shared between the temporal and spectral reconstruction subproblems, enabling substantial undersampling. The authors solved the 5D reconstruction problem using the split Bregman method and GPU-based implementations of backprojection, reprojection, and kernel regression. Using a preclinical mouse model, the authors apply the proposed algorithm to study myocardial injury following radiation treatment of breast cancer. RESULTS: Quantitative 5D simulations are performed using the MOBY mouse phantom. Twenty data sets (ten cardiac phases, two energies) are reconstructed with 88 μm, isotropic voxels from 450 total projections acquired over a single 360° rotation. In vivo 5D myocardial injury data sets acquired in two mice injected with gold and iodine nanoparticles are also reconstructed with 20 data sets per mouse using the same acquisition parameters (dose: ∼60 mGy). For both the simulations and the in vivo data, the reconstruction quality is sufficient to perform material decomposition into gold and iodine maps to localize the extent of myocardial injury (gold accumulation) and to measure cardiac functional metrics (vascular iodine). Their 5D CT imaging protocol represents a 95% reduction in radiation dose per cardiac phase and energy and a 40-fold decrease in projection sampling time relative to their standard imaging protocol. CONCLUSIONS: Their 5D CT data acquisition and reconstruction protocol efficiently exploits the rank-sparse nature of spectral and temporal CT data to provide high-fidelity reconstruction results without increased radiation dose or sampling time.