Fourier ptychographic microscopy for high-resolution, large field of view imaging
| dc.contributor.advisor | Neethling, Pieter H. | en_ZA |
| dc.contributor.advisor | Bosman, Gurthwin W. | en_ZA |
| dc.contributor.author | Fouche, Eugene Egbert | en_ZA |
| dc.contributor.other | Stellenbosch University. Faculty of Science. Dept. of Physics. | en_ZA |
| dc.date.accessioned | 2023-11-28T08:24:01Z | |
| dc.date.accessioned | 2024-01-08T16:41:27Z | |
| dc.date.available | 2023-11-28T08:24:01Z | |
| dc.date.available | 2024-01-08T16:41:27Z | |
| dc.date.issued | 2023-12 | |
| dc.description | Thesis (MSc)--Stellenbosch University, 2023. | en_ZA |
| dc.description.abstract | 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. | en_ZA |
| dc.description.abstract | AFRIKAANSE OPSOMMING: Fourier tigografiese mikroskopie (FPM) is 'n afbeeldingstegniek wat die beperkinge van konvensionele mikroskopie oorkom om hoë-resolusie, groot gesigsveld beelde van 'n monster te verkry. Gewoonlik is daar 'n kompromis tussen resolusie en gesigsveld, maar met FPM kan monsters teen 'n hoë resolusie bekyk word, terwyl 'n groot gesigsveld gehandhaaf word. In FPM word verskeie lae-resolusie beelde van 'n monster gebruik om die monster teen 'n baie hoër resolusie te rekonstrueer. Die monster word vanuit verskeie hoeke belig, en vir elke beligtingshoek word 'n lae- resolusie beeld geneem deur 'n lens met 'n lae numeriese diafragma (NA) te gebruik. Die lae NA lens het 'n groot gesigsveld, en die verskillende beligtingshoeke laat 'n mens toe om inligting oor die kleiner monsterkenmerke te bekom. Dit laat 'n mens toe om 'n hoë-resolusie, groot gesigsveld beeld van die monster te skep deur 'n iteratiewe rekonstruksie-algoritme te gebruik. 'n LED matriks word tipies gebruik om die beligting uit verskillende hoeke te verskaf. Baie werklike monsters verander beide die amplitude en die fase van die lig wat deur hulle beweeg. Op ‘n kamera kan slegs die intensiteit gemeet word, en die fase-inligting gaan verlore. In FPM laat die verskillende beelde 'n mens toe om die fase van die monster te bekom, sowel as die amplitude. Die fase kan gebruik word om foute in die mikroskoopsisteem reg te stel, en verbeter ook die kontras waarmee daar na biologiese monsters gekyk kan word. In hierdie tesis word die teoretiese raamwerk agter FPM verduidelik, en simulasies word uitgevoer om die effek van die LED matriks grootte en die aantal iterasies van die rekonstruksie-algoritme op die kwaliteit van die gerekonstrueerde monster te ondersoek. Die foutkorreksie (defokus-aberrasie) word ook geïllustreer. Twee opstellings word gebou om FPM eksperimenteel te ondersoek. Die eerste opstelling gebruik 'n LED matriks as ligbron en word gebruik om bekende kalibrasieteikens sowel as biologiese monsters af te beeld. Hierdie opstelling word ook aangepas om polarisasie- sensitiewe FPM (pFPM) op dubbelbrekende mineraalmonsters uit te voer om die verskillende kristaldomeine in die monsters te identifiseer. Die tweede opstelling gebruik 'n laser as ligbron en 'n 2-dimensionele ruimtelike ligmodulator (2D-SLM) om die verskeie beligtingshoeke te skep. Hierdie opstelling word gebruik om 'n bekende kalibrasieteiken af te beeld. Beide opstellings word gekarakteriseer, en hulle vermoëns word vergelyk om hul geskiktheid vir verskillende afbeeldingscenario's te illustreer. | af_ZA |
| dc.description.version | Masters | en_ZA |
| dc.format.extent | xvii, 89 pages, 7 pages supplementary notes : illustrations | en_ZA |
| dc.identifier.uri | https://scholar.sun.ac.za/handle/10019.1/128943 | |
| dc.language.iso | en_ZA | en_ZA |
| dc.language.iso | en_ZA | en_ZA |
| dc.publisher | Stellenbosch : Stellenbosch University | en_ZA |
| dc.rights.holder | Stellenbosch University | en_ZA |
| dc.subject.lcsh | Fourier ptychographic microscopy -- Data processing | en_ZA |
| dc.subject.lcsh | Image processing -- Digital techniques | en_ZA |
| dc.subject.lcsh | Microscopy -- Technique | en_ZA |
| dc.subject.lcsh | High resolution imaging -- Mathematical models | en_ZA |
| dc.subject.lcsh | Imaging systems -- Image quality | en_ZA |
| dc.subject.lcsh | Fourier transform optics | en_ZA |
| dc.subject.name | UCTD | en_ZA |
| dc.title | Fourier ptychographic microscopy for high-resolution, large field of view imaging | en_ZA |
| dc.type | Thesis | en_ZA |