FeatureMatch: A General ANNF Estimation Technique and its Applications

In this paper, we propose FeatureMatch, a generalised approximate nearest-neighbour field (ANNF) computation framework, between a source and target image. The proposed algorithm can estimate ANNF maps between any image pairs, not necessarily related. This generalisation is achieved through appropriate spatial-range transforms. To compute ANNF maps, global colour adaptation is applied as a range transform on the source image. Image patches from the pair of images are approximated using low-dimensional features, which are used along with KD-tree to estimate the ANNF map. This ANNF map is further improved based on image coherency and spatial transforms. The proposed generalisation, enables us to handle a wider range of vision applications, which have not been tackled using the ANNF framework. We illustrate two such applications namely: 1) optic disk detection and 2) super resolution. The first application deals with medical imaging, where we locate optic disks in retinal images using a healthy optic disk image as common target image. The second application deals with super resolution of synthetic images using a common source image as dictionary. We make use of ANNF mappings in both these applications and show experimentally that our proposed approaches are faster and accurate, compared with the state-of-the-art techniques.

B-Spline potential function for maximum a-posteriori image reconstruction in fluorescence microscopy

An iterative image reconstruction technique employing B-Spline potential function in a Bayesian framework is proposed for fluorescence microscopy images. B-splines are piecewise polynomials with smooth transition, compact support and are the shortest polynomial splines. Incorporation of the B-spline potential function in the maximum-a-posteriori reconstruction technique resulted in improved contrast, enhanced resolution and substantial background reduction. The proposed technique is validated on simulated data as well as on the images acquired from fluorescence microscopes (widefield, confocal laser scanning fluorescence and super-resolution 4Pi microscopy). A comparative study of the proposed technique with the state-of-art maximum likelihood (ML) and maximum-a-posteriori (MAP) with quadratic potential function shows its superiority over the others. B-Spline MAP technique can find applications in several imaging modalities of fluorescence microscopy like selective plane illumination microscopy, localization microscopy and STED. (C) 2015 Author(s).

Structured illumination microscopy

Illumination plays an important role in optical microscopy. Kohler illumination, introduced more than a century ago, has been the backbone of optical microscopes. The last few decades have seen the evolution of new illumination techniques meant to improve certain imaging capabilities of the microscope. Most of them are, however, not amenable for wide-field observation and hence have restricted use in microscopy applications such as cell biology and microscale profile measurements. The method of structured illumination microscopy has been developed as a wide-field technique for achieving higher performance. Additionally, it is also compatible with existing microscopes. This method consists of modifying the illumination by superposing a well-defined pattern on either the sample itself or its image. Computational techniques are applied on the resultant images to remove the effect of the structure and to obtain the desired performance enhancement. This method has evolved over the last two decades and has emerged as a key illumination technique for optical sectioning, super-resolution imaging, surface profiling, and quantitative phase imaging of microscale objects in cell biology and engineering. In this review, we describe various structured illumination methods in optical microscopy and explain the principles and technologies involved therein. (C) 2015 Optical Society of America

Inter-comparison and performance evaluation of chemistry transport models over Indian region

Aerosol loading over the South Asian region has the potential to affect the monsoon rainfall, Himalayan glaciers and regional air-quality, with implications for the billions in this region. While field campaigns and network observations provide primary data, they tend to be location/season specific. Numerical models are useful to regionalize such location-specific data. Studies have shown that numerical models underestimate the aerosol scenario over the Indian region, mainly due to shortcomings related to meteorology and the emission inventories used. In this context, we have evaluated the performance of two such chemistry-transport models: WRF-Chem and SPRINTARS over an India-centric domain. The models differ in many aspects including physical domain, horizontal resolution, meteorological forcing and so on etc. Despite these differences, both the models simulated similar spatial patterns of Black Carbon (BC) mass concentration, (with a spatial correlation of 0.9 with each other), and a reasonable estimates of its concentration, though both of them under-estimated vis-a-vis the observations. While the emissions are lower (higher) in SPRINTARS (WRF-Chem), overestimation of wind parameters in WRF-Chem caused the concentration to be similar in both models. Additionally, we quantified the under-estimations of anthropogenic BC emissions in the inventories used these two models and three other widely used emission inventories. Our analysis indicates that all these emission inventories underestimate the emissions of BC over India by a factor that ranges from 1.5 to 2.9. We have also studied the model simulations of aerosol optical depth over the Indian region. The models differ significantly in simulations of AOD, with WRF-Chem having a better agreement with satellite observations of AOD as far as the spatial pattern is concerned. It is important to note that in addition to BC, dust can also contribute significantly to AOD. The models differ in simulations of the spatial pattern of mineral dust over the Indian region. We find that both meteorological forcing and emission formulation contribute to these differences. Since AOD is column integrated parameter, description of vertical profiles in both models, especially since elevated aerosol layers are often observed over Indian region, could be also a contributing factor. Additionally, differences in the prescription of the optical properties of BC between the models appear to affect the AOD simulations. We also compared simulation of sea-salt concentration in the two models and found that WRF-Chem underestimated its concentration vis-a-vis SPRINTARS. The differences in near-surface oceanic wind speeds appear to be the main source of this difference. In-spite of these differences, we note that there are similarities in their simulation of spatial patterns of various aerosol species (with each other and with observations) and hence models could be valuable tools for aerosol-related studies over the Indian region. Better estimation of emission inventories could improve aerosol-related simulations. (C) 2015 Elsevier Ltd. All rights reserved.

Bright-field and fluorescence chip-scale microscopy for biological imaging

Optical microscopy is an essential tool in biological science and one of the gold standards for medical examinations. Miniaturization of microscopes can be a crucial stepping stone towards realizing compact, cost-effective and portable platforms for biomedical research and healthcare. This thesis reports on implementations of bright-field and fluorescence chip-scale microscopes for a variety of biological imaging applications. The term “chip-scale microscopy” refers to lensless imaging techniques realized in the form of mass-producible semiconductor devices, which transforms the fundamental design of optical microscopes.

Our strategy for chip-scale microscopy involves utilization of low-cost Complementary metal Oxide Semiconductor (CMOS) image sensors, computational image processing and micro-fabricated structural components. First, the sub-pixel resolving optofluidic microscope (SROFM), will be presented, which combines microfluidics and pixel super-resolution image reconstruction to perform high-throughput imaging of fluidic samples, such as blood cells. We discuss design parameters and construction of the device, as well as the resulting images and the resolution of the device, which was 0.66 µm at the highest acuity. The potential applications of SROFM for clinical diagnosis of malaria in the resource-limited settings is discussed.

Next, the implementations of ePetri, a self-imaging Petri dish platform with microscopy resolution, are presented. Here, we simply place the sample of interest on the surface of the image sensor and capture the direct shadow images under the illumination. By taking advantage of the inherent motion of the microorganisms, we achieve high resolution (~1 µm) imaging and long term culture of motile microorganisms over ultra large field-of-view (5.7 mm × 4.4 mm) in a specialized ePetri platform. We apply the pixel super-resolution reconstruction to a set of low-resolution shadow images of the microorganisms as they move across the sensing area of an image sensor chip and render an improved resolution image. We perform longitudinal study of Euglena gracilis cultured in an ePetri platform and image based analysis on the motion and morphology of the cells. The ePetri device for imaging non-motile cells are also demonstrated, by using the sweeping illumination of a light emitting diode (LED) matrix for pixel super-resolution reconstruction of sub-pixel shifted shadow images. Using this prototype device, we demonstrate the detection of waterborne parasites for the effective diagnosis of enteric parasite infection in resource-limited settings.

Then, we demonstrate the adaptation of a smartphone’s camera to function as a compact lensless microscope, which uses ambient illumination as its light source and does not require the incorporation of a dedicated light source. The method is also based on the image reconstruction with sweeping illumination technique, where the sequence of images are captured while the user is manually tilting the device around any ambient light source, such as the sun or a lamp. Image acquisition and reconstruction is performed on the device using a custom-built android application, constructing a stand-alone imaging device for field applications. We discuss the construction of the device using a commercial smartphone and demonstrate the imaging capabilities of our system.

Finally, we report on the implementation of fluorescence chip-scale microscope, based on a silo-filter structure fabricated on the pixel array of a CMOS image sensor. The extruded pixel design with metal walls between neighboring pixels successfully guides fluorescence emission through the thick absorptive filter to the photodiode layer of a pixel. Our silo-filter CMOS image sensor prototype achieves 13-µm resolution for fluorescence imaging over a wide field-of-view (4.8 mm × 4.4 mm). Here, we demonstrate bright-field and fluorescence longitudinal imaging of living cells in a compact, low-cost configuration.

Volatiles in Protoplanetary Disks

Planets are assembled from the gas, dust, and ice in the accretion disks that encircle young stars. Ices of chemical compounds with low condensation temperatures (<200 K), the so-called volatiles, dominate the solid mass reservoir from which planetesimals are formed and are thus available to build the protoplanetary cores of gas/ice giant planets. It has long been thought that the regions near the condensation fronts of volatiles are preferential birth sites of planets. Moreover, the main volatiles in disks are also the main C-and O-containing species in (exo)planetary atmospheres. Understanding the distribution of volatiles in disks and their role in planet-formation processes is therefore of great interest.

This thesis addresses two fundamental questions concerning the nature of volatiles in planet-forming disks: (1) how are volatiles distributed throughout a disk, and (2) how can we use volatiles to probe planet-forming processes in disks? We tackle the first question in two complementary ways. We have developed a novel super-resolution method to constrain the radial distribution of volatiles throughout a disk by combining multi-wavelength spectra. Thanks to the ordered velocity and temperature profiles in disks, we find that detailed constraints can be derived even with spatially and spectrally unresolved data -- provided a wide range of energy levels are sampled. We also employ high-spatial resolution interferometric images at (sub)mm frequencies using the Atacama Large Millimeter Array (ALMA) to directly measure the radial distribution of volatiles.

For the second question, we combine volatile gas emission measurements with those of the dust continuum emission or extinction to understand dust growth mechanisms in disks and disk instabilities at planet-forming distances from the central star. Our observations and models support the idea that the water vapor can be concentrated in regions near its condensation front at certain evolutionary stages in the lifetime of protoplanetary disks, and that fast pebble growth is likely to occur near the condensation fronts of various volatile species.

孔径光阑限制下高斯光束的传输

对高斯光束在硬边孔径限制下的衍射进行了详细的理论研究，就不同口径的圆孔限制下高斯光束在菲涅耳衍射区和夫琅禾费衍射区的分布进行了理论分析，从而得到了孔径受限高斯光束的横向以及轴向的衍射公式，进而对高斯光束在不同衍射区域内衍射光场分布形状随孔径尺寸变化时的演化规律进行了数值计算，并对小口径光阑受限的高斯光束的衍射与平行光经同尺寸光阑的衍射进行了比较。结果表明在较小口径下，两者的分布基本一致。得到的孔径光阑限制下高斯光束的传输规律为高斯光束在自由空间光通信和光学超分辨中的应用提供了理论基础。

Towards in situ Single Cell Systems Biology

Systems-level studies of biological systems rely on observations taken at a resolution lower than the essential unit of biology, the cell. Recent technical advances in DNA sequencing have enabled measurements of the transcriptomes in single cells excised from their environment, but it remains a daunting technical problem to reconstruct in situ gene expression patterns from sequencing data. In this thesis I develop methods for the routine, quantitative in situ measurement of gene expression using fluorescence microscopy.

The number of molecular species that can be measured simultaneously by fluorescence microscopy is limited by the pallet of spectrally distinct fluorophores. Thus, fluorescence microscopy is traditionally limited to the simultaneous measurement of only five labeled biomolecules at a time. The two methods described in this thesis, super-resolution barcoding and temporal barcoding, represent strategies for overcoming this limitation to monitor expression of many genes in a single cell. Super-resolution barcoding employs optical super-resolution microscopy (SRM) and combinatorial labeling via-smFISH (single molecule fluorescence in situ hybridization) to uniquely label individual mRNA species with distinct barcodes resolvable at nanometer resolution. This method dramatically increases the optical space in a cell, allowing a large numbers of barcodes to be visualized simultaneously. As a proof of principle this technology was used to study the S. cerevisiae calcium stress response. The second method, sequential barcoding, reads out a temporal barcode through multiple rounds of oligonucleotide hybridization to the same mRNA. The multiplexing capacity of sequential barcoding increases exponentially with the number of rounds of hybridization, allowing over a hundred genes to be profiled in only a few rounds of hybridization.

The utility of sequential barcoding was further demonstrated by adapting this method to study gene expression in mammalian tissues. Mammalian tissues suffer both from a large amount of auto-fluorescence and light scattering, making detection of smFISH probes on mRNA difficult. An amplified single molecule detection technology, smHCR (single molecule hairpin chain reaction), was developed to allow for the quantification of mRNA in tissue. This technology is demonstrated in combination with light sheet microscopy and background reducing tissue clearing technology, enabling whole-organ sequential barcoding to monitor in situ gene expression directly in intact mammalian tissue.

The methods presented in this thesis, specifically sequential barcoding and smHCR, enable multiplexed transcriptional observations in any tissue of interest. These technologies will serve as a general platform for future transcriptomic studies of complex tissues.

散射中心型超分辨近场结构的非线性光学特性研究进展

超分辨近场结构(Super-RENS)技术是近年来发展起来的一种新型近场光存储技术，是目前最有实用化前景的纳米尺度近场超分辨技术之一。初步研究表明，其近场超分辨特性与非线性响应密切相关，研究其非线性光学特性对阐明物理机制、发展新的掩模材料和非线性光学应用都具有重要意义。对散射中心型超分辨近场结构非线性光学特性的最新研究进展进行了介绍和分析。

Analysis on the spin reorientation of GdFeCo/DyFeCo exchange-coupled double-layer films

In this paper, GdFeCo/DyFeCo exchange-coupled double-layer films used for center aperture type magnetically induced super resolution were investigated through experiments and theoretical calculation. The samples were prepared by magnetron sputtering method. The polar Kerr effect was measured to prove the spin reorientation of the readout layer. Theoretical study of magnetization profiles was performed on the basis of the mean-field theory and the continuum model. The theoretical results showed that the magnetization orientation of the readout layer changed gradually from in-plane to out-of-plane with the rise of the temperature. Theoretical analysis explained the experimental results successfully. (c) 2005 Elsevier B.V. All rights reserved.

GdFeCo／TbFeCo磁超分辨磁光记录薄膜研究

用磁控溅射法制备了GdFeCo／TbFeCo交换耦合两层薄膜，利用不同温度的克尔磁滞回线和VSM磁滞回线研究了读出层（GdFeCo）变温磁化方向变化过程．结果表明，随温度升高读出层从平面磁化转变为垂直磁化，交换耦合两层薄膜具有中心孔探测磁超分辨的基本性能．转变过程主要受饱和磁化强度（Ms）的影响，在GdFeCo的补偿温度附近，读出层的磁化强度较小，退磁场能也较小，在交换耦合的作用下，使读出层（GdFeCo）的磁化方向发生转变．磁化方向的转变在75℃～125℃的温度范围内变化较快．

Synthesis, optical and thermal characterization of novel thiazolyl heterocyclic azo dye

Thiazolyl heterocyclic azo dye and its metal (Ni2+, Co2+)-azo complexes were synthesized. Their structures were confirmed by elemental analysis, UV-VIS absorption spectra, FT-IR, H-1 NMR and MALDI-MS. The thermal properties of metal complexes were studied by DSC-TGA. The optical constants (complex refractive index N=n + ik) and thickness of the complex thin films on polished single-crystal silicon substrates were investigated on a scanning ellipsometer. Results indicate that thiazolyl metal-azo complexes possess good optical and thermal properties. They would be a promising recording medium candidate for NVD with the Super-resolution near field structure (Super-RENS) technology. (c) 2007 Elsevier B.V. All rights reserved.

2-氨基-6-乙氧基苯并噻唑类偶氮染料及其金属鏊合物的合成及光学热学性能研究

合成了2-（2-氨基-6-乙氧基苯并噻唑基偶氮）-5-（N,N-二乙基氨基）三氟甲基磺酰苯胺偶氮染料（EBTDATFS）及其与乙酸镍、乙酸钴、乙酸铜、乙酸锌等金属盐鏊合的金属鏊合物。通过红外光谱、紫外-可见吸收光谱和MALDI质谱等对染料及其金属鏊合物进行了结构表征;使用旋涂方法在K9玻璃和抛光的单晶硅基片上制备薄膜;研究了镍金属鏊合物的热学性能;使用椭偏仪研究了Ni和Zn鏊合物的光学常数。结果表明：4种金属鏊合物薄膜最大吸收光谱为621-629nm,且长波边吸收峰陡峭;TGA-DSC测试结果表明镍金属鏊

纳米光存储薄膜结构的光学性质

近场超分辨纳米薄膜结构可以突破衍射极限实现纳米尺寸信息存储,是下一代海量存储技术的重要方案之一,也是纳米光子学研究中的热点。纳米膜层结构基于激光作用下的非线性局域光学效应实现超分辨。分析了超分辨近场薄膜结构突破衍射极限的光学原理,对超分辨纳米薄膜结构的表面等离子体激发特性、非线性光学特性、近场光学特性和超透镜效应等重要光学性质的最新研究进展做了系统介绍。

超分辨近场功能薄膜的膜层结构及其机理研究进展

超分辨近场结构光盘是最有希望达到100 GB以上的存储容量方式之一,而其记录和读出机理是研究中的重点,在近年文献研究的基础上,阐述了超分辨近场功能薄膜的膜层结构及其机理的研究进展。