Fluorescence optofluidic microscopy and fluorescence microscopy based on the Talbot effect

Light microscopy has been one of the most common tools in biological research, because of its high resolution and non-invasive nature of the light. Due to its high sensitivity and specificity, fluorescence is one of the most important readout modes of light microscopy. This thesis presents two new fluorescence microscopic imaging techniques: fluorescence optofluidic microscopy and fluorescent Talbot microscopy. The designs of the two systems are fundamentally different from conventional microscopy, which makes compact and portable devices possible. The components of the devices are suitable for mass-production, making the microscopic imaging system more affordable for biological research and clinical diagnostics.

Fluorescence optofluidic microscopy (FOFM) is capable of imaging fluorescent samples in fluid media. The FOFM employs an array of Fresnel zone plates (FZP) to generate an array of focused light spots within a microfluidic channel. As a sample flows through the channel and across the array of focused light spots, a filter-coated CMOS sensor collects the fluorescence emissions. The collected data can then be processed to render a fluorescence microscopic image. The resolution, which is determined by the focused light spot size, is experimentally measured to be 0.65 μm.

Fluorescence Talbot microscopy (FTM) is a fluorescence chip-scale microscopy technique that enables large field-of-view (FOV) and high-resolution imaging. The FTM method utilizes the Talbot effect to project a grid of focused excitation light spots onto the sample. The sample is placed on a filter-coated CMOS sensor chip. The fluorescence emissions associated with each focal spot are collected by the sensor chip and are composed into a sparsely sampled fluorescence image. By raster scanning the Talbot focal spot grid across the sample and collecting a sequence of sparse images, a filled-in high-resolution fluorescence image can be reconstructed. In contrast to a conventional microscope, a collection efficiency, resolution, and FOV are not tied to each other for this technique. The FOV of FTM is directly scalable. Our FTM prototype has demonstrated a resolution of 1.2 μm, and the collection efficiency equivalent to a conventional microscope objective with a 0.70 N.A. The FOV is 3.9 mm × 3.5 mm, which is 100 times larger than that of a 20X/0.40 N.A. conventional microscope objective. Due to its large FOV, high collection efficiency, compactness, and its potential for integration with other on-chip devices, FTM is suitable for diverse applications, such as point-of-care diagnostics, large-scale functional screens, and long-term automated imaging.

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.

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.

Fluorescence microscopy of nicotinic acetylcholine receptors

Neuronal nicotinic acetylcholine receptors (nAChRs) are pentameric ligand gated ion channels abundantly expressed in the central nervous system. Changes in the assembly and trafficking of nAChRs are pertinent to disease states including nicotine dependence, autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE), and Parkinson’s disease (PD). Here we investigate the application of high resolution fluorescence techniques for the study of nAChR assembly and trafficking. We also describe the construction and validation of a fluorescent α5 subunit and subsequent experiments to elucidate the cellular mechanisms through which α5 subunits are expressed, assembled into mature receptors, and trafficked to the cell surface. The effects of a known single nucleotide polymorphism (D398N) in the intracellular loop of α5 are also examined.

Additionally, this report describes the development of a combined total internal reflection fluorescence (TIRF) and lifetime imaging (FLIM) technique and the first application of this methodology for elucidation of stochiometric composition of nAChRs. Many distinct subunit combinations can form functional receptors. Receptor composition and stoichiometry confers unique biophysical and pharmacological properties to each receptor sub-type. Understanding the nature of assembly and expression of each receptor subtype yields important information about the molecular processes that may underlie the mechanisms through which nAChR contribute to disease and addiction states.

Ferromagnetic Resonance Force Microscopy

A new approach to magnetic resonance was introduced in 1992 based upon detection of spin-induced forces by J. Sidles [1]. This technique, now called magnetic resonance force microscopy (MRFM), was first demonstrated that same year via electron paramagnetic resonance (EPR) by D. Rugar et al. [2]. This new method combines principles of magnetic resonance with those of scanned probe technology to detect spin resonance through mechanical, rather than inductive, means. In this thesis the development and use of ferromagnetic resonance force microscopy (FMRFM) is described. This variant of MRFM, which allows investigation of ferromagnetic samples, was first demonstrated in 1996 by Z. Zhang et al. [3]. FMRFM enables characterization of (a) the dynamic magnetic properties of microscale magnetic devices, and (b) the spatial dependence of ferromagnetic resonance within a sample. Both are impossible with conventional ferromagnetic resonance techniques.

Ferromagnetically coupled systems, however, pose unique challenges for force detection. In this thesis the attainable spatial resolution - and the underlying physical mechanisms that determine it - are established. We analyze the dependence of the magnetostatic modes upon sample dimensions using a series of microscale yttrium iron garnet (YIG) samples. Mapping of mode amplitudes within these sample is attained with an unprecedented spatial resolution of 15μm. The modes, never before analyzed on this scale, fit simple models developed in this thesis for samples of micron dimensions. The application of stronger gradient fields induces localized perturbation of the ferromagnetic resonance modes. The first demonstrations of this effect are presented in this study, and a simple theoretical model is developed to explain our observations. The results indicate that the characteristics of the locally-detected ferromagnetic modes are still largely determined by the external fields and dimensions of the entire sample, rather than by the localized interaction volume (i.e., the locale most strongly affected by the local gradient field). Establishing this is a crucial first step toward understanding FMRFM in the high gradient field limit where the dispersion relations become locally determined. In this high gradient field regime, FMRFM imaging becomes analogous with that of EPR MRFM.

FMRFM has also been employed to characterize magnetic multilayers, similar to those utilized in giant magnetoresistance (GMR) devices, on a lateral scale 40 x 40μm. This is orders of magnitude smaller than possible via conventional methods. Anisotropy energies, thickness, and interface qualities of individual layers have been resolved.

This initial work clearly demonstrates the immense and unique potential that FMRFM offers for characterizing advanced magnetic nanostructures and magnetic devices.

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.

Computational microscopy: turning megapixels into gigapixels

The layout of a typical optical microscope has remained effectively unchanged over the past century. Besides the widespread adoption of digital focal plane arrays, relatively few innovations have helped improve standard imaging with bright-field microscopes. This thesis presents a new microscope imaging method, termed Fourier ptychography, which uses an LED to provide variable sample illumination and post-processing algorithms to recover useful sample information. Examples include increasing the resolution of megapixel-scale images to one gigapixel, measuring quantitative phase, achieving oil-immersion quality resolution without an immersion medium, and recovering complex three dimensional sample structure.

I. Anisotropy and crystal structure of ferromagnetic thin films. II. Investigations into magnetic microstructure by Lorentz microscopy

The induced magnetic uniaxial anisotropy of Ni-Fe alloy films has been shown to be related to the crystal structure of the film. By use of electron diffraction, the crystal structure or vacuum-deposited films was determined over the composition range 5% to 85% Ni, with substrate temperature during deposition at various temperatures in the range 25° to 500° C. The phase diagram determined in this way has boundaries which are in fair agreement with the equilibrium boundaries for bulk material above 400°C. The (α+ ɤ) mixture phase disappears below 100°C.

The measurement of uniaxial anisotropy field for 25% Ni-Fe alloy films deposited at temperatures in the range -80°C to 375°C has been carried out. Comparison of the crystal structure phase diagram with the present data and those published by Wilts indicates that the anisotropy is strongly sensitive to crystal structure. Others have proposed pair ordering as an important source of anisotropy because of an apparent peak in the anisotropy energy at about 50% Ni composition. The present work shows no such peak, and leads to the conclusion that pair ordering cannot be a dominant contributor.

Width of the 180° domain wall in 76% Ni-Fe alloy films as a function of film thickness up to 1800 Å was measured using the defocused mode of Lorentz microscopy. For the thinner films, the measured wall widths are in good agreement with earlier data obtained by Fuchs. For films thicker than 800 Å, the wall width increases with film thickness to about 9000 Å at 1800 Å film thickness. Similar measurements for polycrystalline Co films with thickness from 200 to 1500 Å have been made. The wall width increases from 3000 Å at 400 Å film thickness to about 6000 Å at 1500 Å film thickness. The wall widths for Ni-Fe and Co films are much greater than predicted by present theories. The validity of the classical determination of wall width is discussed, and the comparison of the present data with theoretical results is given.

Finally, an experimental study of ripple by Lorentz microscopy in Ni-Fe alloy films has been carried out. The following should be noted: (1) the only practical way to determine experimentally a meaningful wavelength is to find a well-defined ripple periodicity by visual inspection of a photomicrograph. (2) The average wavelength is of the order of 1µ. This value is in reasonable agreement with the main wavelength predicted by the theories developed by others. The dependence of wavelength on substrate deposition temperature, alloy composition and the external magnetic field has been also studied and the results are compared with theoretical predictions. (3) The experimental fact that the ripple structure could not be observed in completely epitaxial films gives confirmation that the ripple results from the randomness of crystallite orientation. Furthermore, the experimental observation that the ripple disappeared in the range 71 and 75% Ni supports the theory that the ripple amplitude is directly dependent on the crystalline anisotropy. An attempt to experimentally determine the order of magnitude of the ripple angle was carried out. The measured angle was about 0.02 rad. The discrepancy between the experimental data and the theoretical prediction is serious. The accurate experimental determination of ripple angle is an unsolved problem.

I. Baryon-antibaryon phase transition at high temperature. II. Inclusive virtual photon-hadron reactions in the parton model

Part I

Present experimental data on nucleon-antinucleon scattering allow a study of the possibility of a phase transition in a nucleon-antinucleon gas at high temperature. Estimates can be made of the general behavior of the elastic phase shifts without resorting to theoretical derivation. A phase transition which separates nucleons from antinucleons is found at about 280 MeV in the approximation of the second virial coefficient to the free energy of the gas.

Part II

The parton model is used to derive scaling laws for the hadrons observed in deep inelastic electron-nucleon scattering which lie in the fragmentation region of the virtual photon. Scaling relations are obtained in the Bjorken and Regge regions. It is proposed that the distribution functions become independent of both q² and ν where the Bjorken and Regge regions overlap. The quark density functions are discussed in the limit x→1 for the nucleon octet and the pseudoscalar mesons. Under certain plausible assumptions it is found that only one or two quarks of the six types of quarks and antiquarks have an appreciable density function in the limit x→1. This has implications for the quark fragmentation functions near the large momentum boundary of their fragmentation region. These results are used to propose a method of measuring the proton and neutron quark density functions for all x by making measurements on inclusively produced hadrons in electroproduction only. Implications are also discussed for the hadrons produced in electron-positron annihilation.

Computational Microscopy: Breaking the Limit of Conventional Optics

Computational imaging is flourishing thanks to the recent advancement in array photodetectors and image processing algorithms. This thesis presents Fourier ptychography, which is a computational imaging technique implemented in microscopy to break the limit of conventional optics. With the implementation of Fourier ptychography, the resolution of the imaging system can surpass the diffraction limit of the objective lens's numerical aperture; the quantitative phase information of a sample can be reconstructed from intensity-only measurements; and the aberration of a microscope system can be characterized and computationally corrected. This computational microscopy technique enhances the performance of conventional optical systems and expands the scope of their applications.