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(2018) Multi-Aperture Fourier Ptychographic Microscopy: Development of a High-Speed Gigapixel Coherent Computational Microscope

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(2018) Multi-Aperture Fourier Ptychographic Microscopy: Development of a High-Speed Gigapixel Coherent Computational Microscope Konda, Pavan Chandra (2018) Multi-Aperture Fourier Ptychographic Microscopy: development of a high-speed gigapixel coherent computational microscope. PhD thesis. http://theses.gla.ac.uk/9015/ Copyright and moral rights for this work are retained by the author A copy can be downloaded for personal non-commercial research or study, without prior permission or charge This work cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given Enlighten:Theses http://theses.gla.ac.uk/ [email protected] Multi-Aperture Fourier Ptychographic Microscopy: Development of a high-speed gigapixel coherent computational microscope Pavan Chandra Konda Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy University of Glasgow School of Physics and Astronomy College of Science and Engineering October 2017 Abstract Medical research and clinical diagnostics require imaging of large sample areas with sub-cellular resolution. Conventional imaging techniques can provide either high-resolution or wide field-of-view (FoV) but not both. This compromise is conventionally defeated by using a high NA objective with a small FoV and then mechanically scan the sample in order to acquire separate images of its different regions. By stitching these images together, a larger effective FoV is then obtained. This procedure, however, requires precise and expensive scanning stages and prolongs the acquisition time, thus rendering the observation of fast processes/phenomena impossible. A novel imaging configuration termed Multi- Aperture Fourier Ptychographic Microscopy (MA-FPM) is proposed here based on Fourier ptychography (FP), a technique to achieve wide-FoV and high-resolution using time-sequential synthesis of a high-NA coherent illumination. MA-FPM configuration utilises an array of objective lenses coupled with detectors to increase the bandwidth of the object spatial-frequencies captured in a single snapshot. This provides high-speed data-acquisition with wide FoV, high- resolution, long working distance and extended depth-of-field. In this work, a new reconstruction method based on Fresnel diffraction forward model was developed to extend FP reconstruction to the proposed MA- FPM technique. MA-FPM was validated experimentally by synthesis of a 3x3 lens array system from a translating objective-detector system. Additionally, a calibration procedure was also developed to register dissimilar images from multiple cameras and successfully implemented on the experimental data. A nine- fold improvement in captured data-bandwidth was demonstrated. Another experimental configuration was proposed using the Scheimpflug condition to correct for the aberrations present in the off-axis imaging systems. An experimental setup was built for this new configuration using 3D printed parts to minimise the cost. The design of this setup is discussed along with robustness analysis of the low-cost detectors used in this setup. A reconstruction model for the Scheimpflug configuration FP was developed and applied to the experimental Abstract III data. Preliminary experimental results were found to be in agreement with this reconstruction model. Some artefacts were observed in these results due to the calibration errors in the experiment. These can be corrected by using the self- calibration algorithm proposed in the literature, which is left as a future work. Extensions to this work can include implementing multiplexed illumination for further increasing the data acquisition speed and diffraction tomography for imaging thick samples. Table of Contents Abstract ............................................................................... ii Table of Contents ................................................................... iv List of Figures ....................................................................... vii Acknowledgements ................................................................. xi Declaration .......................................................................... xii Abbreviations ...................................................................... xiii Publications ........................................................................ xiv Chapter 1 Introduction ........................................................... 1 1.1 Motivation .................................................................. 1 1.2 Conventional imaging techniques ....................................... 3 1.2.1 Motorized scanning ................................................... 3 1.2.2 Super-resolution techniques ........................................ 4 1.2.3 Mesolens ................................................................ 4 1.2.4 Flatbed scanner with CCTV lens .................................... 5 1.2.5 Pixel super-resolution ................................................ 6 1.2.6 Gigapixel monocentric multi-scale camera ....................... 7 1.2.7 Aperture-synthesis imaging .......................................... 7 1.2.8 Spatial ptychography ................................................. 9 1.2.9 Fourier ptychography................................................ 10 1.3 Objectives of the research ............................................. 11 1.4 Thesis layout .............................................................. 12 Chapter 2 Fourier ptychography review ..................................... 14 Table of Contents V 2.1 Theory ..................................................................... 14 2.1.1 Space-Bandwidth product .......................................... 18 2.2 FP reconstruction algorithms ........................................... 20 2.2.1 FP optimization problem ........................................... 20 2.2.2 FP reconstruction procedure ....................................... 21 2.2.3 FP optimization variations .......................................... 23 2.2.4 Information multiplexing ........................................... 27 2.2.5 System error estimation algorithms ............................... 28 2.3 FP robustness analysis ................................................... 30 2.3.1 Fourier space overlap requirement ............................... 31 2.3.2 Partial coherence limits ............................................ 32 2.3.3 Illumination intensity fluctuations ................................ 33 2.3.4 Noise tolerance ...................................................... 34 2.3.5 LED position tolerances ............................................. 35 2.3.6 Pupil errors ........................................................... 36 2.3.7 LED sampling pattern................................................ 38 2.4 FP experimental configurations ........................................ 39 2.4.1 LED multiplexing with quasi-dome array ......................... 39 2.4.2 Oil-immersion condenser ........................................... 40 2.4.3 Aperture scanning ................................................... 41 2.4.4 Liquid crystal display (LCD) setup ................................. 41 2.4.5 Laser scanning ........................................................ 42 2.4.6 Reflective FP setup .................................................. 43 2.4.7 3D FPM ................................................................. 44 2.4.8 Raspberry Pi FP setup ............................................... 44 2.4.9 Macroscopic FP with camera array ................................ 45 2.4.10 Single pixel FP ....................................................... 46 2.5 Summary ................................................................... 46 Chapter 3 Multi-Aperture FPM ................................................. 48 3.1 MA-FPM Theory ........................................................... 48 3.1.1 MA-FPM design parameters ......................................... 51 3.2 Fresnel propagations based FPM reconstruction ..................... 53 3.2.1 Fresnel propagation algorithm ..................................... 54 3.2.2 Field propagation using Fresnel diffraction integral ............ 56 3.2.3 Pupil shift calculations .............................................. 61 Table of Contents VI 3.2.4 Experimental validation ............................................ 67 3.2.5 Spatially varying frequency sampling ............................. 69 3.3 Summary ................................................................... 73 Chapter 4 Multi-Aperture FPM experimental validation .................. 74 4.1 Experimental setup ...................................................... 74 4.2 Calibration procedure ................................................... 77 4.2.1 Aberrations estimation .............................................. 79 4.2.2 Image registration ................................................... 81 4.2.3 Calibration results ................................................... 82 4.3 Reconstruction algorithm ............................................... 84 4.4 Experimental results ..................................................... 85 4.5 Summary ................................................................... 89 Chapter 5 Scheimpflug MA-FPM ............................................... 90 5.1 Curved lens array .......................................................
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