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dc.contributor.advisorAhluwalia, Balpreet Singh
dc.contributor.authorLahrberg, Marcel
dc.date.accessioned2020-01-14T13:41:36Z
dc.date.available2020-01-14T13:41:36Z
dc.date.embargoEndDate2020-12-11
dc.date.issued2019-12-11
dc.description.abstract<p>Minimally invasive technologies to characterize the structure and functionality of biological samples on the cellular and molecular scale are fundamental to life sciences. Optical fluorescence imaging at visible wavelengths is able to acquire to do so. Due to the wavelike nature of light the maximum achievable resolution in conventional microscopy is limited by diffraction, about half the wavelength of the considered light. Although this diffraction limit is fundamental, techniques have been developed to perform imaging at a resolution of two to a hundred times better than this. All these techniques come with their specific benefits and trade-offs and the presented thesis seeks to make a contribution in the filed of super-resolution microscopy. Structured illumination microscopy (SIM) is a technique that improves the image resolution by acquiring images under non-planar illumination and subsequent image reconstruction. This image reconstruction requires a prior parameter estimation of the illumination pattern from the acquired data. A contribution to improve this parameter estimation is presented and demonstrated using simulation frame work developed for this purpose. It can be shown, that the deviation of the pattern parameters from their actual value can be reduced by up to 80 percent as compared to a more conventional method. <p>A common way to generate sinusoidal illumination patterns in SIM is to interfere two coherent beams of light using the the imaging objective lens, the epifluorescence configuration. Two new methods to generate those interference patterns, namely transillumination structured illumination microscopy (tSIM), and chip structured illumination microscopy (cSIM) are presented. A pattern generation independent of the objective lens allows to improve the spacebandwidth product (SBP) of SIM by increasing the resolution without sacrificing the field of view (FoV). Imaging simulations are shown to demonstrate this effect when mirrors are used to generate the patterns in tSIM. A theoretical improvement of the SBP of almost five times the SBP of a conventional setup is discussed. Instead of using mirrors, optical waveguides may be used to generate those illumination patterns a presented in cSIM. Thesewaveguides are simulated using Comsol. Imaging is simulated according to expected pattern parameters and the improved imaging is illustrated. <p>The advantages of optical waveguides as discussion for cSIM are then examined regarding their implementation for light sheet fluorescence microscopy (LSFM). The image quality in wide-field imaging can be improved by limiting the sample illumination to the plane that is actually imaged. This is commonly done in LSFM and requires appropriate beam shaping. The implementation of different waveguide designs to perform beam shaping with waveguides are investigated performing a variety of simulations in Comsol. Chip based axicons with a total width of 20 micrometer and a wedge angle of six degree show to generate promising beam profiles with a propagation length of about 150 micrometer. A possible lattice light sheet generation using two counter propagation axicons is investigated as well as double axicon for the generation of bottle beams. The use of optical phased arrays to perform dynamic beam shaping using sets of 16 and 32 elements of 1 micrometer width is shown and the beam tilting and shifting capabilities a visible wavelength are presented.en_US
dc.description.doctoraltypeph.d.en_US
dc.description.popularabstractThe light microscope is a popular tool in life sciences to achieve insight in the structure and functionality of biological tissues and even cells, that helps to understand processes on the large scale. This has an impact on the investigation of diseases and the development of medical treatments. Modern microscopy in this area employs fluorescence imaging, a technique that enhances the contrast in microscopic imaging by marking structures of interest in a sample and highlights it in the image. The major advantage of light microscopy in this area is its minimally invasive nature. The sample can be imaged under conditions close to its natural environment, thus keeping its original structure and functionality to a certain extend. However, the resolution of optical microscopy is originally limited by the wavelike nature of light. Whether or not two close objects in a sample are spatially resolved, meaning that they are display as two distinct instead of a single object in the image, is governed by the diffraction limit. This diffraction limit is fundamental. This means, that when imaging with a wavelength of visible light of half a micron, the resolution is limited to a quarter of a micron. Since relevant structural changes sometimes happen on a smaller scale, techniques are developed to circumvent this limit, while maintaining the high specificity in and minimal sample degradation of fluorescence imaging. Among others, structured illumination microscopy can achieve this by illumination the sample in a non-planar way. Upon computational image reconstruction, an image with improved resolution is achieved. After the raw data image acquisition, the illumination pattern, depending on the implementation, must be characterized in order to perform the image reconstruction. A contribution to improve this process is presented, showing an effect on the precision of the reconstruction. A conventional way to generate the illumination patterns is the use of the microscope's objective lens. This puts an inherent limit to he achievable resolution, and field of view to the technique. Performing mirror based, as well as optical waveguide based pattern generation is investigated in order to improve the resolution and field of view, using simulations. Here a simulation framework is presented that demonstrates the potential of those techniques. Finally, the capability of optical waveguides to perform beam shaping in order to provide well defined illumination patterns is examined. Appropriate parameters for the fabrication of such waveguides are derived.en_US
dc.identifier.isbn978-82-8236-376-1 (trykt) 978-82-8236-377-8 (pdf)
dc.identifier.urihttps://hdl.handle.net/10037/17093
dc.language.isoengen_US
dc.publisherUiT Norges arktiske universiteten_US
dc.publisherUiT The Arctic University of Norwayen_US
dc.relation.haspart<p>Paper 1: Lahrberg, M., Singh, M., Khare, K. & Ahluwalia, B.S. (2018). Accurate estimation of the illumination pattern’s orientation and wavelength in sinusoidal structured illumination microscopy. <i>Applied Optics, 57</i>(5), 1019-1025. Also available in Munin at <a href=https://hdl.handle.net/10037/13294>https://hdl.handle.net/10037/13294</a>. <p>Paper 2: Joseph, J., Faiz, K.P., Lahrberg, M., Tinguely, J.-C. & Ahluwalia, B.S. Improving the space-bandwidth product of structured illumination microscopy using a transillumination configuration. Published version in <i>Journal of Physics D: Applied Physics, 53</i>(4), 044006. Available in Munin at <a href=https://hdl.handle.net/10037/16968>https://hdl.handle.net/10037/16968</a>. <p>Paper 3: Helle, Ø.I., Dullo, F.T., Lahrberg, M., Tinguely, J.-C. & Ahluwalia, B.S. Structured illumination microscopy using a photonic chip. (Manuscript). Available in the file “thesis_entire.pdf” and on arXiv at <a href= https://arxiv.org/abs/1903.05512v1>arXiv:1903.05512</a>. <p>Paper 4: Lahrberg, M., Dullo, F.T. & Ahluwalia, B.S. Photonic-chip based free space beam shaping and steering for advanced optical microscopy application. Accepted for publication in <i>OSA Continuum</i>. Available in the file “thesis_entire.pdf”.en_US
dc.relation.projectIDinfo:eu-repo/grantAgreement/EC/FP7/336716/EU/High-speed chip-based nanoscopy to discover real-time sub-cellular dynamics/NANOSCOPY/en_US
dc.rights.accessRightsembargoedAccessen_US
dc.rights.holderCopyright 2019 The Author(s)
dc.subject.courseIDDOKTOR-004
dc.subjectVDP::Mathematics and natural science: 400::Physics: 430::Electromagnetism, acoustics, optics: 434en_US
dc.subjectVDP::Matematikk og Naturvitenskap: 400::Fysikk: 430::Elektromagnetisme, akustikk, optikk: 434en_US
dc.titleNovel strategies for super-resolution fluorescence microscopyen_US
dc.typeDoctoral thesisen_US
dc.typeDoktorgradsavhandlingen_US


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