Mabaso, Matsilele Aubrey
29 May 2014
M.Ing. (Electrical and Electronic Engineering) / Advances in bio-imaging have triggered the development of a highly sophisticated imaging tool known as fluorescence microscopy. Fluorescence microscopy is used in many biological applications to visualize sub-cellular processes and gives the ability to image three-dimensional (3D) structures in living cells. The use of fluorescence microscopy and specific staining methods make biological molecules appear as bright spots in image data. The analysis of fluorescence microscopy images requires the detection and tracking of hundreds spots in image data and is of great importance for biologists to better understand cell functions. However, the analysis of these data is still performed manually in most biological laboratories worldwide. The manual analysis of these data is both time consuming, laborious and susceptible to human errors. Several computer-based algorithms have been proposed for the detection and tracking of spots in microscopy images. Most of these methods were validated on limited image data and relatively few studies have been performed for the comparison of these methods in real applications. This study quantitatively compared the performance of four detection and two tracking methods applied in microscopy images for the analysis of bright spots. The performance of the algorithms was validated on both synthetic and real images. The synthetic images offered a better way of validating algorithms against ground truth reference results. Results indicate that there are major differences in algorithm performance for both detection and tracking. In the detection results the Isotropic Undecimated Wavelet Transform (IUWT) and the Laplacian of Gaussian (LoG) achieved better results than the other methods in comparison when values are considered. The tracking results indicate that the Interacting Multiple Model (IMM) method achieved better results than the Feature Point Tracking (FPT) method when Jaccard Similarity Scores (JSC) are considered.
30 August 2017
The fact that optical force is very significant in the microscopic world and can be used to manipulate microparticles has triggered an evolution in micromanipulation, in particular, the manipulation of biological species and colloidal particles. The induced optical force can easily be more than 103 times of the particle's weight. The particle size that are accessible to optical forces ranges from tens of nanometers to hundreds of micrometers. One of the most well-known tools in optical manipulation is called optical tweezers, which is, in essence, performing optical trapping by a strongly focused light beam. The optical force induced by the incident light wave can be generally decomposed into two mathematically and physically distinct components, namely the conservative (gradient force) and non-conservative (scattering and absorption force) forces. Such a split helps in the study of optical forces and elucidates the underlying physics (e.g., the optical trapping). For example, in optical trapping, the conservative gradient force drives the particles toward the intensity maxima and traps the particles there, whereas the non-conservative scattering and absorption force tends to push the particles away and thus has some destabilizing effects. However, while a significant portion of paper dealing with optical trapping explicitly mentioned gradient and scattering forces, the true and exact force profiles of the decomposed optical forces have been mysteries for decades. Researchers still use these concepts, and to certain extent, they imagine the force profile according to their own convenience. This thesis is mainly devoted to the analytical and numerical studies of the decomposition of optical forces. The intrinsic nature of the decomposed optical forces will be discussed, and the approaches of generating a purely conservative force field are presented.. First, the analytical approaches for decomposing the optical force into the gradient force and the scattering and absorption force are described. These approaches can be applied to different particle sizes (smaller than 40% of the wavelength if the multipoles are only considered up to the electric octopole or much larger than the wavelength under the geometrical optics limit), but they still cannot describe the experimentally accessible particle size, which is on the order of micrometer. Second, within the dipole limit, the origin of scattering force is shown to be resulted from the radiation reaction, the polarizations, and the topological charges. In addition, it is found that the conservativeness of the force is closely related to the force constant matrix (the linear term in the Taylor expansion of the optical force) at every point, and certain symmetries in these force constant matrix can guarantee the force to be conservative.. A numerical method that utilizes the fast Fourier transform (FFT) was developed to decompose the conservative and non-conservative forces. This approach is valid when the total force field is spatially localized and decayed sufficiently fast as we move away from the beam center (e.g., optical tweezers or alike) or is spatially periodic (e.g. plane incident waves). We also considered spherical aberration due to the mismatch of the refractive indices between the oil and water media in a typical optical tweezers setup within the FFT method. Various particle sizes, materials, and numerical apertures were also considered. For the periodic force field generated by a collection of plane waves, it is demonstrated that an incident 2-dimensional standing wave could generate a purely conservative force field. The accuracy of this fast Fourier transform approach is analyzed in details and shown to be quite accurate. Moreover, an incident 3-dimensional standing wave could also induce a conservative force field for intermediately sized particles.. Finally, three counter-intuitive examples obtained with the fast Fourier transform approach are presented. These examples clearly demonstrated the need to calculate the gradient and scattering forces accurately, as not doing so would lead to qualitatively wrong results.
No description available.
High entropy alloys (HEAs) based on refractory elements have shown a great potential for high temperature structural applications. In particular, the ones containing Al, exhibits a microstructure similar to the γ-γ' in Ni-based superalloys. While these alloys exhibit impressive strengths at room temperature (RT) and at elevated temperatures, the continuous B2 matrix in these alloys is likely to be responsible for their brittle behavior at RT. Phase stability of five such alloys are studied by thermo-mechanical treatments and characterization techniques using scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Two of these alloys showed an inverted microstructure, where the disordered BCC phase becomes continuous, and therefore, they were characterized in detail using SEM, TEM, atom probe tomography (APT) and synchrotron x-ray diffraction experiments. The phenomenon of phase inversion lead to a better combination of strength and ductility as compared to the non-inverted microstructure.To enhance the stability of B2 intermetallic phase which provides the strength when present in a BCC matrix, multicomponent B2 phase compositions stable at 1000°C in some of the above studied alloys, were melted separately. The aim was to establish a single phase B2 at 1000°C and understand the mechanical behavior of these single-phase multicomponent B2 intermetallic alloys. These alloys exhibited a ductile behavior under compression and retained ~1 GPa yield strength at temperature up to 600°C. The ductile nature of these alloys is attributed to the change in bonding nature form directional to metallic bonding, possibly resulting from a significantly high configurational entropy compared to binary or ternary stoichiometric B2 compounds.
Tsang Min Ching, Jean-Marc
19 January 2021
Rapid development of genetically encoded fluorescent indicators has provided a diverse chemical toolkit to probe complex biological systems, leading to the expansion of fluorescence microscopy for biological research and applications. However, the inherent constraints on resolution, speed and field of view have hindered the development of high speed, three dimensional fluorescence imaging over large spatial scales for biological microscopy. This thesis describes two strategies based on confocal microscopy to provide single-shot volumetric fluorescence imaging over large scales. In the first part, we describe a multiplane line-scan imaging strategy, which uses a series of axially distributed reflecting slits to probe different depths within a sample volume. Our technique, called line-scan multi-z confocal microscopy, enables the simultaneous imaging of an optically sectioned image stack with a single camera at frame rates of hundreds of hertz, without the need for axial scanning. We demonstrate the applicability of our system to monitor fast dynamics in biological samples by performing calcium imaging of neuronal activity in mouse brains and voltage imaging of cardiomyocytes in cardiac samples. In the second part, we describe a fiber bundle-based endomicroscopy technique, which provides pseudo-volumetric imaging over large field of views, without the need for axial scanning. Our technique uses a gradient refractive index lens to achieve an axially extended illumination and a series of reflecting pinholes of different diameters to simultaneously probe different number of fiber cores. The fluorophores are localized from the series of acquired images using a convolution neural network. We validate our system by localizing fluorescent beads distributed in a volume sample.
Gareau, Daniel S.
Thesis (Ph.D.) OGI School of Science & Engineering at OHSU, December 2006. / Abstract: leaves xvii-xviii. Includes bibliographical references (leaves 197-204).
Wu, Kui, Downer, Michael Coffin,
(has links) (PDF)
Thesis (Ph. D.)--University of Texas at Austin, 2004. / Supervisor: Michael C. Downer. Vita. Includes bibliographical references.
Exploring Atomic Force Microscopy To Probe Charge Transport Through Molecular Films And For The Development Of Combinatorial Force MicroscopyChisholm, Roderick A. Unknown Date
No description available.
Computational modeling of stimulated emission depletion microscopy in biological cells under one- and two-photon excitationMark, Andrew Evan 03 February 2015 (has links)
The finite-difference time-domain method is used to simulate the propagation of focused beams used for stimulated emission depletion (STED) microscopy as they scatter through layers of biological cells. Depletion beams that facilitate axial and lateral confinement of the fluorescence emission are modeled, and the effective point spread function of the system as a function of focal depth is assessed under one- and two-photon excitation. Results show that the lateral depletion beam retains a well-defined minimum up to the maximum simulation depth of 42 µm. In addition, the relative spatial shift between excitation and de-excitation beam foci is less than 44 nm for all simulated depths. PSF calculations suggest that sub-diffraction imaging is possible beyond the maximum simulated depth, as long as the fluorescence emission is detectable. However, strong attenuation of the fluorescence emission by the axial confinement beam may make this beam unsuitable for sub-diffraction imaging in scattering samples. / text
28 August 2008
Not available / text
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