INTEGRATION OF INSTRUMENTATION AND PROCESSING SOFTWARE OF A LASER SPECKLE CONTRAST IMAGING SYSTEM

Laser speckle contrast imaging (LSCI) has the potential to be a powerful tool in medicine, but more research in the field is required so it can be used properly. To help in the progression of Michigan Tech's research in the field, a graphical user interface (GUI) was designed in Matlab to control the instrumentation of the experiments as well as process the raw speckle images into contrast images while they are being acquired. The design of the system was successful and is currently being used by Michigan Tech's Biomedical Engineering department. This thesis describes the development of the LSCI GUI as well as offering a full introduction into the history, theory and applications of LSCI.

DEVELOPMENT OF CONFOCAL IMAGING TECHNIQUES FOR PROBING INTERFACIAL DYNAMICS IN MICROSCALE, GAS-LIQUID, TWO-PHASE FLOW

Micro-scale, two-phase flow is found in a variety of devices such as Lab-on-a-chip, bio-chips, micro-heat exchangers, and fuel cells. Knowledge of the fluid behavior near the dynamic gas-liquid interface is required for developing accurate predictive models. Light is distorted near a curved gas-liquid interface preventing accurate measurement of interfacial shape and internal liquid velocities. This research focused on the development of experimental methods designed to isolate and probe dynamic liquid films and measure velocity fields near a moving gas-liquid interface. A high-speed, reflectance, swept-field confocal (RSFC) imaging system was developed for imaging near curved surfaces. Experimental studies of dynamic gas-liquid interface of micro-scale, two-phase flow were conducted in three phases. Dynamic liquid film thicknesses of segmented, two-phase flow were measured using the RSFC and compared to a classic film thickness deposition model. Flow fields near a steadily moving meniscus were measured using RSFC and particle tracking velocimetry. The RSFC provided high speed imaging near the menisci without distortion caused the gas-liquid interface. Finally, interfacial morphology for internal two-phase flow and droplet evaporation were measured using interferograms produced by the RSFC imaging technique. Each technique can be used independently or simultaneously when.

Plenoptic camera : theory and experimental results

The purpose of this research was to develop a working physical model of the focused plenoptic camera and develop software that can process the measured image intensity, reconstruct this into a full resolution image, and to develop a depth map from its corresponding rendered image. The plenoptic camera is a specialized imaging system designed to acquire spatial, angular, and depth information in a single intensity measurement. This camera can also computationally refocus an image by adjusting the patch size used to reconstruct the image. The published methods have been vague and conflicting, so the motivation behind this research is to decipher the work that has been done in order to develop a working proof-of-concept model. This thesis outlines the theory behind the plenoptic camera operation and shows how the measured intensity from the image sensor can be turned into a full resolution rendered image with its corresponding depth map. The depth map can be created by a cross-correlation of adjacent sub-images created by the microlenslet array (MLA.) The full resolution image reconstruction can be done by taking a patch from each MLA sub-image and piecing them together like a puzzle. The patch size determines what object plane will be in-focus. This thesis also goes through a very rigorous explanation of the design constraints involved with building a plenoptic camera. Plenoptic camera data from Adobe © was used to help with the development of the algorithms written to create a rendered image and its depth map. Finally, using the algorithms developed from these tests and the knowledge for developing the plenoptic camera, a working experimental system was built, which successfully generated a rendered image and its corresponding depth map.

CHARACTERIZATION OF THE ATMOSPHERIC EFFECTS ON THE TRANSMISSION OF THERMAL RADIATION

Atmospheric scattering plays a crucial rule in degrading the performance of electro optical imaging systems operating in the visible and infra-red spectral bands, and hence limits the quality of the acquired images, either through reduction of contrast or increase of image blur. The exact nature of light scattering by atmospheric media is highly complex and depends on the types, orientations, sizes and distributions of particles constituting these media, as well as wavelengths, polarization states and directions of the propagating radiation. Here we follow the common approach for solving imaging and propagation problems by treating the propagating light through atmospheric media as composed of two main components: a direct (unscattered), and a scattered component. In this work we developed a detailed model of the effects of absorption and scattering by haze and fog atmospheric aerosols on the optical radiation propagating from the object plane to an imaging system, based on the classical theory of EM scattering. This detailed model is then used to compute the average point spread function (PSF) of an imaging system which properly accounts for the effects of the diffraction, scattering, and the appropriate optical power level of both the direct and the scattered radiation arriving at the pupil of the imaging system. Also, the calculated PSF, properly weighted for the energy contributions of the direct and scattered components is used, in combination with a radiometric model, to estimate the average number of the direct and scattered photons detected at the sensor plane, which are then used to calculate the image spectrum signal to- noise ratio (SNR) in the visible near infra-red (NIR) and mid infra-red (MIR) spectral wavelength bands. Reconstruction of images degraded by atmospheric scattering and measurement noise is then performed, up to the limit imposed by the noise effective cutoff spatial frequency of the image spectrum SNR. Key results of this research are as follows: A mathematical model based on Mie scattering theory for how scattering from aerosols affects the overall point spread function (PSF) of an imaging system was developed, coded in MATLAB, and demonstrated. This model along with radiometric theory was used to predict the limiting resolution of an imaging system as a function of the optics, scattering environment, and measurement noise. Finally, image reconstruction algorithms were developed and demonstrated which mitigate the effects of scattering-induced blurring to within the limits imposed by noise.

Robustness of speckle imaging techniques applied to horizontal imaging scenarios

Atmospheric turbulence near the ground severely limits the quality of imagery acquired over long horizontal paths. In defense, surveillance, and border security applications, there is interest in deploying man-portable, embedded systems incorporating image reconstruction methods to compensate turbulence effects. While many image reconstruction methods have been proposed, their suitability for use in man-portable embedded systems is uncertain. To be effective, these systems must operate over significant variations in turbulence conditions while subject to other variations due to operation by novice users. Systems that meet these requirements and are otherwise designed to be immune to the factors that cause variation in performance are considered robust. In addition robustness in design, the portable nature of these systems implies a preference for systems with a minimum level of computational complexity. Speckle imaging methods have recently been proposed as being well suited for use in man-portable horizontal imagers. In this work, the robustness of speckle imaging methods is established by identifying a subset of design parameters that provide immunity to the expected variations in operating conditions while minimizing the computation time necessary for image recovery. Design parameters are selected by parametric evaluation of system performance as factors external to the system are varied. The precise control necessary for such an evaluation is made possible using image sets of turbulence degraded imagery developed using a novel technique for simulating anisoplanatic image formation over long horizontal paths. System performance is statistically evaluated over multiple reconstruction using the Mean Squared Error (MSE) to evaluate reconstruction quality. In addition to more general design parameters, the relative performance the bispectrum and the Knox-Thompson phase recovery methods is also compared. As an outcome of this work it can be concluded that speckle-imaging techniques are robust to the variation in turbulence conditions and user controlled parameters expected when operating during the day over long horizontal paths. Speckle imaging systems that incorporate 15 or more image frames and 4 estimates of the object phase per reconstruction provide up to 45% reduction in MSE and 68% reduction in the deviation. In addition, Knox-Thompson phase recover method is shown to produce images in half the time required by the bispectrum. The quality of images reconstructed using Knox-Thompson and bispectrum methods are also found to be nearly identical. Finally, it is shown that certain blind image quality metrics can be used in place of the MSE to evaluate quality in field scenarios. Using blind metrics rather depending on user estimates allows for reconstruction quality that differs from the minimum MSE by as little as 1%, significantly reducing the deviation in performance due to user action.

Quantum dot / optical protein bio-nano hybrid system biosensing

The integration of novel nanomaterials with highly-functional biological molecules has advanced multiple fields including electronics, sensing, imaging, and energy harvesting. This work focuses on the creation of a new type of bio-nano hybrid substrate for military biosensing applications. Specifically it is shown that the nano-scale interactions of the optical protein bacteriorhodopsin and colloidal semiconductor quantum dots can be utilized as a generic sensing substrate. This work spans from the basic creation of the protein to its application in a novel biosensing system. The functionality of this sensor design originates from the unique interactions between the quantum dot and bacteriorhodopsin molecule when in nanoscale proximity. A direct energy transfer relationship has been established between coreshell quantum dots and the optical protein bacteriorhodopsin that substantially enhances the protein’s native photovoltaic capabilities. This energy transfer phenomena is largely distance dependent, in the sub-10nm realm, and is characterized experimentally at multiple separation distances. Experimental results on the energy transfer efficiency in this hybrid system correlate closely to theoretical predictions. Deposition of the hybrid system with nano-scale control has allowed for the utilization of this energy transfer phenomena as a modulation point for a functional biosensor prototype. This work reveals that quantum dots have the ability to activate the bacteriorhodopsin photocycle through both photonic and non-photonic energy transfer mechanisms. By altering the energy transferred to the bacteriorhodopsin molecule from the quantum dot, the electrical output of the protein can be modulated. A biosensing prototype was created in which the energy transfer relationship is altered upon target binding, demonstrating the applicability of a quantum dot/bacteriorhodopsin hybrid system for sensor applications. The electrical nature of this sensing substrate will allow for its efficient integration into a nanoelectronics array form, potentially leading to a small-low power sensing platform for remote toxin detection applications.

Non-invasive method to predict viscosity and size using total internal reflection fluorescence microscopy (TIRFM) system

This study develops an automated analysis tool by combining total internal reflection fluorescence microscopy (TIRFM), an evanescent wave microscopic imaging technique to capture time-sequential images and the corresponding image processing Matlab code to identify movements of single individual particles. The developed code will enable us to examine two dimensional hindered tangential Brownian motion of nanoparticles with a sub-pixel resolution (nanoscale). The measured mean square displacements of nanoparticles are compared with theoretical predictions to estimate particle diameters and fluid viscosity using a nonlinear regression technique. These estimated values will be confirmed by the diameters and viscosities given by manufacturers to validate this analysis tool. Nano-particles used in these experiments are yellow-green polystyrene fluorescent nanospheres (200 nm, 500 nm and 1000 nm in diameter (nominal); 505 nm excitation and 515 nm emission wavelengths). Solutions used in this experiment are de-ionized (DI) water, 10% d-glucose and 10% glycerol. Mean square displacements obtained near the surface shows significant deviation from theoretical predictions which are attributed to DLVO forces in the region but it conforms to theoretical predictions after ~125 nm onwards. The proposed automation analysis tool will be powerfully employed in the bio-application fields needed for examination of single protein (DNA and/or vesicle) tracking, drug delivery, and cyto-toxicity unlike the traditional measurement techniques that require fixing the cells. Furthermore, this tool can be also usefully applied for the microfluidic areas of non-invasive thermometry, particle tracking velocimetry (PTV), and non-invasive viscometry.

Pupil phase apodization for achromatic imaging of extra-solar planets

Direct imaging of extra-solar planets in the visible and infrared region has generated great interest among scientists and the general public as well. However, this is a challenging problem. Diffculties of detecting a planet (faint source) are caused, mostly, by two factors: sidelobes caused by starlight diffraction from the edge of the pupil and the randomly scattered starlight caused by the phase errors from the imperfections in the optical system. While the latter diffculty can be corrected by high density active deformable mirrors with advanced phase sensing and control technology, the optimized strategy for suppressing the diffraction sidelobes is still an open question. In this thesis, I present a new approach to the sidelobe reduction problem: pupil phase apodization. It is based on a discovery that an anti-symmetric spatial phase modulation pattern imposed over a pupil or a relay plane causes diffracted starlight suppression sufficient for imaging of extra-solar planets. Numerical simulations with specific square pupil (side D) phase functions, such as ... demonstrate annulling in at least one quadrant of the diffraction plane to the contrast level of better than 10^12 with an inner working angle down to 3.5L/D (with a = 3 and e = 10^3). Furthermore, our computer experiments show that phase apodization remains effective throughout a broad spectrum (60% of the central wavelength) covering the entire visible light range. In addition to the specific phase functions that can yield deep sidelobe reduction on one quadrant, we also found that a modified Gerchberg-Saxton algorithm can help to find small sized (101 x 101 element) discrete phase functions if regional sidelobe reduction is desired. Our simulation shows that a 101x101 segmented but gapless active mirror can also generate a dark region with Inner Working Distance about 2.8L/D in one quadrant. Phase-only modulation has the additional appeal of potential implementation via active segmented or deformable mirrors, thereby combining compensation of random phase aberrations and diffraction halo removal in a single optical element.