Department of Physics

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Browsing Department of Physics by browse.metadata.advisor "Bosman, Gurthwin W."

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    Development of a multimodal nonlinear imaging system for biophotonic applications
    (Stellenbosch : Stellenbosch University., 2020-04) Dwapanyin, George Okyere; Rohwer, Erich G.; Neethling, Pieter H.; Bosman, Gurthwin W.; Stellenbosch University. Faculty of Science. Dept. of Physics.
    ENGLISH ABSTRACT: Multiphoton microscopy techniques have gained wide prominence in biophotonics imaging applications since their inventions. Compared to conventional optical imaging, these nonlinear optical microscopy (NLOM) techniques are intrinsically confocal, and thus enables three-dimensional imaging with submicron spatial resolution. Additional advantages include decreased photodamage to tissue, increased depth of penetration as well as the ability to perform label-free imaging. Signal response in NLOM techniques depend nonlinearly on the peak intensity, therefore requiring a high peak intensity laser as source. Control of ultrashort pulses enables the generation of high peak intensity pulses with lower excitation pulse energies. This dissertation focuses on the development of a nonlinear microscopy system for biological applications based on the control of the spectral phase of broadband supercontinuum pulses generated in a polarization maintaining all normal dispersion photonic crystal fibre. We further demonstrate, for the first time, the real world application of a time domain ptychographic phase measurement technique known as i2PIE which allows for phase correction at the object plane, in microscopy, and how this phase control contributes to image enhancement in two photon excitation fluorescence (TPEF) and second harmonic generation (SHG) imaging of biological tissue. By comparing this new technique to the commonly used multiphoton intrapulse interference phase scan (MIIPS) measurement technique, we show that i2PIE offers an improved spectral phase measurement which can be used to generate shorter temporal pulses and ultimately produce higher peak intensities, even at lower pulse energies. Our results also show that for the same input pulse energies, i2PIE provides a higher contrast image and an improved signal to noise ratio compared to MIIPS. The results obtained from this work projects i2PIE as a promising phase measurement technique for the coherent control of ultrashort pulses used in nonlinear microscopy.
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    Fourier ptychographic microscopy for high-resolution, large field of view imaging
    (Stellenbosch : Stellenbosch University, 2023-12) Fouche, Eugene Egbert; Neethling, Pieter H. ; Bosman, Gurthwin W. ; Stellenbosch University. Faculty of Science. Dept. of Physics.
    ENGLISH ABSTRACT: Fourier ptychographic microscopy (FPM) is an imaging technique which overcomes the limitations of conventional microscopy to construct high-resolution, large field of view (FOV) images of a sample. Usually, there is a trade-off between resolution and field of view, but FPM allows samples to be viewed at a high resolution, while maintaining a large FOV. FPM is a computational imaging technique, where multiple low-resolution images of a sample are used to reconstruct the sample at a much higher resolution. The sample is illuminated from various angles, and a low-resolution image is captured for each illumination angle using a lens with a low numerical aperture (NA). The low NA lens has a large FOV, and the various illumination angles allows one to obtain information about the smaller sample features. This allows one to reconstruct a high-resolution, large FOV image of the sample using an iterative reconstruction algorithm. An LED array is typically used to provide the angularly varying illumination. Many real-world samples alter both the amplitude and the phase of the light that is transmitted through them. However, only the intensity can be measured on a camera, and the phase information is lost. In FPM, the various sample images allows one to recover the phase of the sample, as well as the amplitude. This can be used to correct for errors in the imaging setup, and also enhances the contrast when viewing biological samples. In this thesis, the theoretical framework behind FPM is explained, and simulations are performed to investigate the effect of the LED array size and the number of iterations of the reconstruction algorithm on the quality of the reconstructed sample. The error correction (defocus aberration) is also investigated. Two setups are constructed to investigate FPM experimentally. The first setup uses an LED array, and is used to image known calibration targets and real-world biological samples. This setup is also adapted to perform polarization-sensitive FPM (pFPM) on birefringent mineral samples to image the different crystal domains in the samples. The second setup uses a continuous wave laser as the light source and a 2-dimensional spatial light modulator (2D-SLM) to provide the angularly varying illumination. This setup is used to image a known calibration target. Both setups are characterised, and their performance is compared to illustrate their suitability for different imaging scenarios.
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    Light sheet fluorescence microscopy
    (Stellenbosch : Stellenbosch University, 2021-03) Badrodien, Imraan; Bosman, Gurthwin W.; Neethling, Pieter H.; Stellenbosch University. Faculty of Science. Dept. of Physics.
    ENGLISH ABSTRACT: Light sheet fluorescence microscopy is a powerful tool within the in field of microscopy. The inherent advantages over other fluorescence microscopy techniques include high sectioning capabilities, reduced photo-damage in the sample and short data acquisition times. In this thesis, a light sheet microscope is developed which allows the users to tailor the parameters of the light sheet for various applications, by implementing the use of a spatial light modulator (SLM) to dynamically alter the shape of the light sheet. Three different techniques for light sheet generation are investigated, namely by the use of a cylindrical lens, using an SLM, and by digitally scanning a beam. Each of the techniques were characterised. Using the light sheets, three dimensional fluorescence images are obtained. These three dimensional images are analysed to determine the imaging capabilities of the system, and the deconvolution of these images are implemented for image restoration. The result is a multi-purpose light sheet microscope for use in biological imaging.
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    Optical tweezers for advanced microscopy
    (Stellenbosch : Stellenbosch University, 2018-03) Erasmus, Anneke; Rohwer, Erich G.; Neethling, Pieter H.; Bosman, Gurthwin W.; Stellenbosch University. Faculty of Science. Dept. of Physics.
    ENGLISH SUMMARY: The integration of lasers into microscopy has enabled new areas of research and expanded existing ones. Not only can one now image samples to resolutions and contrast unheard of before lasers became common, but one can now use lasers to exert minuscule forces on micron sized structures in your sample. This is achieved by creating a stable, single beam optical trap by tightly focusing a laser onto the sample containing micronsized particles submerged in a uid. Moving the trap position allows for the manipulation of micron-sized particles inside the sample. Such an optical trap is known as optical tweezers. In this work, optical tweezers are constructed and the trap is characterized by calibrating the picoNewton sized forces applied to micron-sized particles close to the trap centre. Applications of optical tweezers can be found in various aspects of biophotonics, some of which are discussed in this thesis. Using the constructed optical tweezers, the intracellular forces of molecular motors inside an onion cell were measured and the results are discussed. The optical tweezers setup can be expanded to include di erent imaging techniques. Two such imaging techniques, namely nonlinear microscopy and ptychography, a lensless imaging technique, are discussed in detail. Linear uorescence micrographs were taken with the setup to illustrate how such an integration would work. Ptychography was demonstrated in a separate imaging setup to illustrate the underlying principles. In this fashion, the individual components are investigated and evaluated separately, with the ultimate goal of incorporating all of these techniques in a truly multimodal microscopy platform.
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    Point spread function engineering for fluorescence microscopy
    (Stellenbosch : Stellenbosch University, 2018-03) Holinirina Dina Miora, Ratsimandresy; Bosman, Gurthwin W.; Rohwer, Erich G.; Stellenbosch University. Faculty of Science. Dept. of Physics.
    ENGLISH SUMMARY: A tool for biological imaging is developed within this work. It consists of engineering the point spread function (PSF) of a fluorescent molecule or a nanoparticle emitter by modulating the phase of the fluorescence emission. The engineered PSF developed in this current work is called the double helix point spread function (DH-PSF). Information about the three dimensional position of an emitter and its orientation can be extracted using this PSF with a very high precision and accuracy. Other modalities, such as the pyramidal PSF and the bisected PSF, are also simulated and compared theoretically with the efficiency of the DH-PSF.
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    Single molecule diffusion in polymeric systems
    (Stellenbosch : Stellenbosch University, 2019-04) Sibanda, Charmaine; Bosman, Gurthwin W.; Rohwer, Erich G.; Stellenbosch University. Faculty of Science. Dept. of Physics.
    ENGLISH ABSTRACT : The dynamics of thin polymeric systems were studied in this research work using the diffusion of single fluorescent molecules observed by single molecule fluorescence microscopy. A wide field single fluorescence microscopy setup was designed together with a custom-built heating stage to study the nano-environments of two different polymeric systems and how these systems are affected by a change in temperature. The designed optical setup achieved a localization precision of 20 nm which further enabled the tracking of single molecules embedded in polymeric systems. The position trajectories of the single molecules in the polymer matrices are used to calculate the motion of the single molecules from which the diffusion coefficient data is extracted. The distribution of the diffusion coefficients is a consequence of the microscopic dynamics of the polymeric systems coupled to the probe molecules. The fluorescence intensity pattern analysis of the single molecules is also used as reporters of the nano-environment of thin polymeric films.
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    Towards the development of a MIR NOPA for time-domain ptychography
    (Stellenbosch : Stellenbosch University, 2021-03) De Beer, Anthonie; Bosman, Gurthwin W.; Neethling, Pieter H.; Stellenbosch University. Faculty of Science. Dept. of Physics.
    ENGLISH ABSTRACT: This thesis discusses a noncollinear optical parametric amplifier as a source of ultrafast mid-infrared light for spectroscopic experiments and aims to provide a consistent method for the generation thereof. The underlining theory and fundamental principles of this device is outlined as well as various experimental considerations. A design for an experimental setup to generate suitable ultrafast mid-infrared light is proposed and preliminary optical devices are implemented. Generation of a 160 nm bandwidth, near-infrared supercontinuum centred at 1067 nm is shown to be inadequate for the generation of mid-infrared pulses. Parasitic second harmonic-, sum frequency and difference frequency generation processes are also shown to impede mid-infrared generation. These restricting experimental phenomena are highlighted and methods to bypass these limits are given. Finally, as a demonstration of usefulness of such a source of infrared pulses, the novel time-domain ptychographic measurement, HIPPY, of a material’s response to mid-infrared light is simulated.
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    Ultrafast photochromism in metal-organic complexes
    (Stellenbosch : Stellenbosch University, 2016-12) Von Stein, Xavier; Schwoerer, Heinrich P. H.; Bosman, Gurthwin W.; Steenkamp, Christine M.; Stellenbosch University. Faculty of Science. Dept. of Physics
    ENGLISH ABSTRACT : Dithizone (H2Dz), an analytical reagent typically used in colourimetric analysis, reacts with various transition metals to form metal dithizonate complexes. These complexes display strong absorption in the visible region of the spectrum and exhibit photochromism: a photo-induced reversible transformation of the reactant to a product form with a distinctly di erent absorption spectrum. The photo-isomerisation of a C=N bond in the dithizone's backbone is responsible for this behaviour. This mechanism was con rmed in 2011 by the rst ultra-fast study on dithizonatophenylmercury(II) (DPM), a singleliganded complex. To compliment this study, transient absorption spectroscopy was used to capture temporally and spectrally resolved spectra of the photo-induced reaction in the dithizone ligand and select two-liganded dithizontates following excitation at their absorption maxima. The ligand, as well as the two-liganded Hg(HDz)2, Pb(HDz)2 and Zn(HDz)2 complexes showed two reaction paths following photo-excitation. The rst path is associated with an evolution along the rotational isomerisation coordinate which leads to product formation and ground state recovery with a time constant of 1 ps. This is in accordance to what was found for DPM. The second reaction path leads to a re-population of the ground state with a time constant of 10 ps. A physical process could not de nitively be assigned to the second pathway, although it is speculated that it may be due to an unstable intermediate along the C=N inversion coordinate. As the 1 and 10 ps paths were found to be intrinsic to the ligand, it was concluded that the second ligand does not participate in the dynamics, at least not on times below 500 ps. The Ni(HDz)2 complex was not analysed in detail due to complexities that arise given the possibility of ligand-ligand interactions and possible metal to ligand or ligand to metal charge transfer processes.