Innovations of wide-field optical-sectioning fluorescence microscopy : toward high-speed volumetric bio-imaging with simplicity

Optical microscopy has become an indispensable tool for biological researches since its invention, mostly owing to its sub-cellular spatial resolutions, non-invasiveness, instrumental simplicity, and the intuitive observations it provides. Nonetheless, obtaining reliable, quantitative spatial information from conventional wide-field optical microscopy is not always intuitive as it appears to be. This is because in the acquired images of optical microscopy the information about out-of-focus regions is spatially blurred and mixed with in-focus information. In other words, conventional wide-field optical microscopy transforms the three-dimensional spatial information, or volumetric information about the objects into a two-dimensional form in each acquired image, and therefore distorts the spatial information about the object. Several fluorescence holography-based methods have demonstrated the ability to obtain three-dimensional information about the objects, but these methods generally rely on decomposing stereoscopic visualizations to extract volumetric information and are unable to resolve complex 3-dimensional structures such as a multi-layer sphere.

The concept of optical-sectioning techniques, on the other hand, is to detect only two-dimensional information about an object at each acquisition. Specifically, each image obtained by optical-sectioning techniques contains mainly the information about an optically thin layer inside the object, as if only a thin histological section is being observed at a time. Using such a methodology, obtaining undistorted volumetric information about the object simply requires taking images of the object at sequential depths.

Among existing methods of obtaining volumetric information, the practicability of optical sectioning has made it the most commonly used and most powerful one in biological science. However, when applied to imaging living biological systems, conventional single-point-scanning optical-sectioning techniques often result in certain degrees of photo-damages because of the high focal intensity at the scanning point. In order to overcome such an issue, several wide-field optical-sectioning techniques have been proposed and demonstrated, although not without introducing new limitations and compromises such as low signal-to-background ratios and reduced axial resolutions. As a result, single-point-scanning optical-sectioning techniques remain the most widely used instrumentations for volumetric imaging of living biological systems to date.

In order to develop wide-field optical-sectioning techniques that has equivalent optical performance as single-point-scanning ones, this thesis first introduces the mechanisms and limitations of existing wide-field optical-sectioning techniques, and then brings in our innovations that aim to overcome these limitations. We demonstrate, theoretically and experimentally, that our proposed wide-field optical-sectioning techniques can achieve diffraction-limited optical sectioning, low out-of-focus excitation and high-frame-rate imaging in living biological systems. In addition to such imaging capabilities, our proposed techniques can be instrumentally simple and economic, and are straightforward for implementation on conventional wide-field microscopes. These advantages together show the potential of our innovations to be widely used for high-speed, volumetric fluorescence imaging of living biological systems.

The role of molybdenum oxide as anode interfacial modification in the improvement of efficiency and stability in organic light-emitting diodes

It has been experimentally found that molybdenum oxide (MoO3) as the interfacial modification layer on indium-tin-oxide (ITO) in organic light-emitting diodes (OLEDs) significantly improves the efficiency and lifetime. In this paper, the role of MoO3 and MoO3 doped N,N '-di(naphthalene-1-yl)-N,N '-diphenyl-benzidine (NPB) as the interface modification layer on ITO in improvement of the efficiency and stability of OLEDs is investigated in detail by atomic force microscopy (AFM), polarized optical microscopy, transmission spectra, ultraviolet photoemission spectroscopy (UPS) and X-ray photoemission spectroscopy (XPS).

Focusing of light by a nanohole array

The authors demonstrate a mechanism for focusing at optical frequencies based on the use of nanohole quasiperiodic arrays in metal screens. Using coherent illumination at 660 nm and scanning aperture optical microscopy, similar to 290 nm "hot spots" were observed at a distance of similar to 12.5 mu m from the array. Even smaller hot spots of about similar to 200 nm in waist were observed closer to the plane of the array.(c) 2007 American Institute of Physics.

A study of the scutellum in eight Chagas disease vector species from genus Triatoma (Hemiptera, Reduviidae) using optical and scanning electron microscopy

The aim of this study was to analyze the external morphology of the scutellum through optical microscopy and scanning electron microscopy (SEM) in male specimens of Triatoma costalimai, T. delpontei, T. eratyrusiformis, T. matogrossensis, T. infestans melanosoma, T. sherlocki, T. tibiamaculata, and T. vandae. A total of 30 photographs of the scutellum were made. Magnification varied from 50X to 750X. Regarding depth and forms of the central depression, the heart-shaped form was predominant, with some exceptions, so that this shape appears to be a common characteristic for species of genus Triatoma Laporte, 1832. In T. eratyrusiformis, a kind of sensillum with important taxonomic value was observed. The different sizes and shapes of the designs found on the posterior process of the scutellum were also of important taxonomic interest. The study of the scutellum based on SEM showed valuable characteristics, allowing the use of this structure to aid the diagnosis of triatomine species. Thus, more specimens in subsequent studies and analyses of morphometric parameters should contribute to agreement on phylogenetic aspects in this genus. A Key to eight species of Triatoma based on male scutellar morphology is presented.

Correlative light-electron fractography for fatigue striations characterization in metallic alloys

The correlative light-electron fractography technique combines correlative microscopy concepts to the extended depth-from-focus reconstruction method, associating the reliable topographic information of 3-D maps from light microscopy ordered Z-stacks to the finest lateral resolution and large focus depth from scanning electron microscopy. Fatigue striations spacing analysis can be precisely measured, by correcting the mean surface tilting with the knowledge of local elevation data from elevation maps. This new technique aims to improve the accuracy of quantitative fractography in fatigue fracture investigations. Microsc. Res. Tech. 76:909-913, 2013. © 2013 Wiley Periodicals, Inc.

Micrinite in Southern Hemisphere sub-bituminous and bituminous coals : redefined as fine grained kaolinite

A range of complementary analytical techniques including SEM/EDS, TEM/EDS and conventional optical microscopy has been rigorously applied to precisely defined areas of micrinite in polished coal samples from Australia and New Zealand. Elemental analyses of micrinite regions showed a high abundance of Al, Si and O and high resolution images of micrinite revealed a grain size < 1μm. Electron diffraction and elemental analyses from individual grains within the optically and electron-optically correlated micrinite regions are consistent with the occurence of fine-grained kaolinite. The optical properties of "dark clay" and "micrinite" (i.e. fine-grained kaolinite) can be understood in terms of the diffuse scattering of visible light from the surfaces of materials with different grain sizes in single-phase or multi-phase mixtures.

Synthesis, structural analysis and solvatochromic behaviour of 4,6-bis (4-butoxyphenyl)-2-methoxynicotinonitrile mesogen

In this communication, we report the synthesis and characterisation of a new luminescent liquid crystalline material, 4,6-bis (4-butoxyphenyl)-2-methoxynicotinonitrile (3). We have confirmed its structure by Fourier transform infrared and 1H nuclear magnetic resonance spectroscopy, elemental analysis and X-ray single crystal diffraction studies. The newly synthesised compound crystallises in a monoclinic system with the space group C2/c and its cell parameters are found to be a?=?25.181(4) angstrom, b?=?15.651(4)angstrom, c?=?12.703(19) angstrom, V?=?4880.4 (16) angstrom, Z?=?8. The results indicate that the presence of weak CH center dot center dot center dot O and CH center dot center dot center dot N hydrogen bonding as short-range intermolecular interactions are responsible for the formation of its crystal assembly. The measured torsion angle shows the existence of a distorted structure for the molecule wherein 4-butoxyphenylene ring substituent at the fourth position of the central pyridine ring forms a torsion angle chiC(4), C(3), C(10), C(19)] of 40.55 degrees. Its liquid crystalline behaviour was investigated with the aid of polarised optical microscopy and differential scanning calorimetry. The study reveals that the compound displays a broad nematic phase in the range of 78112 degrees C. Further, solution phase optical studies indicate that it is a blue light emitter in different non-polar and polar organic solvents at a concentration of 10-5M.

Effect of ultrasonic treatment on surface crystallization of calcium bismuth borate glasses

Transparent glasses in CaO-Bi2O3-B2O3 system were fabricated via the conventional melt-quenching technique. X-ray powder diffraction (XRD) and differential thermal analysis (DTA) carried out on the as-quenched samples confirmed their amorphous and glassy nature respectively. The surface crystallization behaviour of these glasses with and without ultrasonic surface treatment (UST) was monitored using XRD, optical microscopy and scanning electron microscopy (SEM). The volume fraction, depth of crystallization and the (001) orientation factor for the heat treated samples with and without UST were compared. The ultrasonically-treated samples on subsequent heat treatment were found to crystallize at lower temperatures associated with the highest degree of orientation factor (0.95) in contrast with those of non-UST samples. These surface crystallized glasses were found to exhibit nonlinear optical behaviour emitting green light (532 nm) when they were exposed to the infrared radiation (1064 nm) using Nd:YAG laser.

Anomalous structural relaxations in PVDF rich blends with PMMA in the presence of surface functionalized CNTs

The structural relaxations in PVDF rich blends with PMMA can be quite interesting in understanding the origin of the different molecular relaxations associated with the crystalline and amorphous phases, crystal-amorphous interphase and the segmental motions. In light of our recent findings, we understood that the origin of these molecular relaxations were strongly contingent on the concentration of PMMA in the blend, crystalline morphology and the surface functional moieties on multiwall carbon nanotubes (CNTs). In addition, for the blends with concentration of PMMA >= 25 wt%, the structural relaxations often merge and are dielectrically indistinguishable. In this study, we attempted to determine the critical width in composition where the structural relaxations can be distinctly realized both in the control as well as blends with amine functionalized CNTs (NH2-CNTs). Intriguingly, we observed that in a narrow zone in composition (with PMMA concentration >= 10 wt% and <= 25 wt%), the molecular relaxations can be dielectrically distinguished and they often merge for all other compositions. Furthermore, we attempted to understand how this critical width in composition is related to the crystalline morphology using small angle X-ray scattering and polarizing optical microscopy and the crystal structure using FTIR and Raman spectroscopy. We now understand that although the formation of beta crystals in the blends has no direct correlation with the observed molecular relaxations, the amorphous miscibility and the interphase regions seem to be dictating the origin of different molecular relaxations in the blends. The latter was observed to be strongly contingent on the concentration of PMMA in the blends.

Efficient generation of diffraction-limited multi-sheet pattern for biological imaging

We demonstrate a new technique to generate multiple light-sheets for fluorescence microscopy. This is possible by illuminating the cylindrical lens using multiple copies of Gaussian beams. A diffraction grating placed just before the cylindrical lens splits the incident Gaussian beam into multiple beams traveling at different angles. Subsequently, this gives rise to diffraction-limited light-sheets after the Gaussian beams pass through the combined cylindrical lens-objective sub-system. Direct measurement of field at and around the focus of objective lens shows multi-sheet pattern with an average thickness of 7.5 mu m and inter-sheet separation of 380 mu m. Employing an independent orthogonal detection sub-system, we successfully imaged fluorescently-coated yeast cells (approximate to 4 mu m) encaged in agarose gel-matrix. Such a diffraction-limited sheet-pattern equipped with dedicated detection system may find immediate applications in the field of optical microscopy and fluorescence imaging. (C) 2015 Optical Society of America

3D Macroporous Solids from Chemically Cross-linked Carbon Nanotubes

We demonstrate a new technique to generate multiple light-sheets for fluorescence microscopy. This is possible by illuminating the cylindrical lens using multiple copies of Gaussian beams. A diffraction grating placed just before the cylindrical lens splits the incident Gaussian beam into multiple beams traveling at different angles. Subsequently, this gives rise to diffraction-limited light-sheets after the Gaussian beams pass through the combined cylindrical lens-objective sub-system. Direct measurement of field at and around the focus of objective lens shows multi-sheet pattern with an average thickness of 7.5 μm and inter-sheet separation of 380 μm. Employing an independent orthogonal detection sub-system, we successfully imaged fluorescently-coated yeast cells (≈4 μm) encaged in agarose gel-matrix. Such a diffraction-limited sheet-pattern equipped with dedicated detection system may find immediate applications in the field of optical microscopy and fluorescence imaging. © 2015 Optical Society of America

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

超分辨远场生物荧光成像——突破光学衍射极限

长期以来,远场光学荧光显微镜凭借其非接触、无损伤、可探测样品内部等优点,一直是生命科学中最常用的观测工具。但由于衍射极限的存在,使传统的宽场光学显微镜横向和纵向的分辨率分别仅约为230 nm和1000 nm。为了揭示细胞内分子尺度的动态和结构特征,提高光学显微镜分辨率成为生命科学发展的迫切要求,在远场荧光显微镜的基础上,科学家们已经发展出许多实用的提高分辨率甚至超越分辨率极限的成像技术。例如,采用横向结构光照明提高横向分辨率到约100 nm,利用纵向驻波干涉效应将纵向分辨率提高5~10倍。然而,直到在光学荧光显微镜中引入非线性效应后,衍射极限才被真正突破,如受激荧光损耗显微镜利用非线性效应实现了30~50 nm的三维分辨率。另外应用荧光分子之间能量转移共振原理以及单荧光分子定位技术也可以突破衍射极限,甚至可以将分子定位精度提高到几个纳米的量级。

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.

Investigation on the static recording characteristic of super-resolution near-field structure with antimony mask layer

Static recording characteristic of super-resolution near-field structure with antimony (Sb) is investigated in this paper. The recording marks are observed by a scanning electron microscopy (SEM), a high-resolution optical microscopy with a CCD camera and an atomic force microscopy (AFM). The super-resolution mechanism is also analyzed based on these static recording marks. Results show that the light reaching on recording layer is composed of two parts, one is the linear transmissive light (propagating field) and the other is the nonlinear evanescent light in the optical near field. The evanescent light may be greatly enhanced in the center of the spot because Sb will transit from a semiconductor to a metal when it is melted under the high laser power irradiation. This local melted area in the spot center may be like a metal tip in the optical near field that can collect and enhance the information that is far beyond the diffraction limit, which leads to the super-resolution recording and readout. (c) 2005 Elsevier Ltd. All rights reserved.