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Theses

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Antennes zijn alom tegenwoordig in ons dagelijkse leven. Ze zitten in onze gsm's, radio's, Wi-Fi-routers en op nog veel meer, goed verborgen, plaatsen. Men zou zelfs kunnen stellen dat telkens als er een draadloos signaal moet worden verstuurd, er een antenne aan te pas komt. De omschrijving van een draadloos signaal kan nu zeer breed worden opgenomen. Geluid dat van een radio komt, is bijvoorbeeld zo'n draadloos signaal dat door een antenne wordt uitgezonden. De antenne is dan de luidspreker, waar een elektrisch signaal wordt omgezet in een draadloos signaal, het geluid. De interessante vraag is nu, van waar komt het elektrische signaal dat het geluid produceert? Wel, dit signaal werd door een tweede antenne uit de lucht gepikt. Een eenvoudige radio bestaat dus al uit twee antennes, een die de overal aanwezige radiogolven kan lezen, en een tweede die het signaal van de eerste antenne omzet in geluid. Om samen te vatten hebben we dus dat een antenne een draadloos signaal kan ontvangen, of uitzenden. Wat nu met zichtbaar licht? Dit is ook een draadloos signaal, dus moeten er antennes voor kunnen worden ontworpen. Het probleem met zo'n antennes voor zichtbaar licht is echter dat ze enorm klein moeten worden gemaakt, zo klein als een tiende van de dikte van een haarpijl. Dit maakt dat deze antennes niet meer met het blote oog zichtbaar zijn, maar toch nog zichtbaar licht kunnen uitzenden en ontvangen. Fijn, zou men nu kunnen denken, schaal elk antenne ontwerp dat we kennen tot de dimensies miniem worden en dan hebben we antennes voor zichtbaar licht. Dit is echter niet zo eenvoudig, omdat de fysica in deze omstandigheden manifest verschilt van de fysica van bijvoorbeeld radioantennes. Om zo'n minuscule antennes te kunnen begrijpen is er, voor elk ontwerp, nieuw onderzoek nodig, en zo'n onderzoek gebeurd er in deze thesis. Hierin wordt een specifiek ontwerp onderzocht, waar we vooral geïnteresseerd zijn in een bepaald aspect van de antenne. We onderzoeken namelijk of dit ontwerp licht directioneel kan verstrooien. Dit betekent voor deze antenne dan dat het verticaal invallend licht enkel terug wordt uitgezonden naar links, of enkel terug wordt uitgezonden naar rechts. Dit ontwerp kan dan vergeleken worden met een radio, die afhankelijk van het signaal dat hij detecteert, enkel geluid produceert uit de linker of de rechter luidspreker. Zo'n soort radio, is echter vreemd, storend en heeft totaal geen interessante toepassingen. Voor de gelijkaardige zichtbare licht antenne is dit niet het geval. De toepassingen van deze antenne zijn interessant, nuttig en direct toepasbaar in hoog technologische apparaten. Toch, is dit niet het doel van deze thesis, wat hier in wordt bedreven is fysica, en fysica interesseert zich niet in de toepassingen. Voor ons is aantonen dat we licht kunnen controleren en sturen op een nanometer schaal, al wat telt.

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Fluorescence microscopy is an important tool for every biologist, and in recent years huge progress was made in increasing the resolution and image quality. This progress comes at the cost of bulky equipment, expensive optical setups and the requirement of highly skilled operators. In the IROCSIM project at imec, a world leading research center for nanotechnology, a new type of microscopy is proposed. By using photonic integrated circuits, combined with a monolithic integrated CMOS imager all free-space optics are eliminated and a fluorescence microscope can be fully integrated on a chip, making it affordable, portable and easy to use. The resolution is maintained by using dedicated structured illumination patterns based on interference of light from different waveguides. The excitation of the sample is based on total internal reflection (TIRF), providing high axial resolution and leading to high signal-to-background ratios. In this thesis a system model for integrated photonics-based microscopy is developed to guide the design optimization process of the microscopy chips. The system model helps in understanding the combination of on-chip waveguide-based excitation of the sample and lens-free imaging with an on-chip integrated imager. In the model, all parts of the on-chip microscope are included, starting with the photonic integrated circuit, the generation of illumination patterns, the TIRF-based sample excitation, the optical filter and the monolithic integrated CMOS imager. The process of excitation and emission of the fluorophores is modeled, and a simulation is included to determine the radiation pattern of a fluorophore close to a planar interface. Fluorophores close to the interface were found to have a highly structured radiation pattern strongly affecting spatial distribution of light on the image sensor. The model developed in this thesis provides deep insight in the important design parameters and speeds up the prototyping of a microscopy technique that will revolutionize the field of fluorescence microscopy. Furthermore it provides a flexible framework that can be used to characterize other waveguide-based microscopy techniques.

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High-resolution fluorescence microscopy systems are inevitable for modern life science research. However, these devices are bulky and expensive. Ongoing effort is being made to go to compact and cost-effective systems through the development of on-chip microscopy techniques. On-chip approaches employ the evanescent field at the surface of waveguides for sample illumination. However, the implementation of microscopes on photonic chips raises the need for new test sample preparation and imaging protocols. The traditional microscopy system is inherently flexible in sample preparation. From glass microscope slides to cell cultures in microwell plates, samples can simply be inserted in the light path of the microscopy system. In addition, assessment of the attainable lateral resolution of (new) fluorescence microscopy techniques can be done using commercial, ready-to-use and standardized microscopy slides. In on-chip microscopy devices, samples need to be brought directly on chip. Therefore, sample preparation needs to be redefined. Working protocols are developed for two commonly used test samples: fixed and stained adhesive cells and sub-resolution fluorescent beads. Test sample quality is evaluated in light of application for lateral resolution assessment in on-chip microscopy devices. Assessment parameters include the sample density and position with respect to the waveguide surface. The potential of these test samples for practical lateral resolution assessment is demonstrated using widefield images. Three methods are employed: practical implementation of the Rayleigh criterion, the full width at half maximum method and Fourier spectrum analysis. The results underline that theoretical resolution limits are not always experimentally obtained due to both limitations of the test samples and of the assessment technique. Finally, DNA origami nanorulers are shown to be successfully immobilized on chip, and are therefore very promising as a biological calibration standard for on-chip microscopy techniques. If the test sample quality and suitability for lateral resolution assessment can be verified by on-chip fluorescence microscopy techniques in the future, the developed working protocols could be routinely applied for demonstration and assessment of newly developed microscopy systems.

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Fluorescence microscopy is a key technique for research in biology, medicine etc. Certain molecules, called fluorophores, emit light in a specific colour when they are illuminated. The miniaturisation of a fluorescence microscope onto a chip would make the technique more widely accessible. It would also make it suitable for applications that need fast and parallel analysis, like DNA sequencing. The functioning of a chip for fluorescence microscopy contains several interesting elements. Light from a laser is transported on the chip by waveguides, and these waveguides send light beams from different directions into a central region where an interference pattern forms. The fluorophores within the sample placed on top of the central region feel this light. They start to emit their own light that can be captured with a CMOS sensor, a chip similar to a normal camera. However, the captured light creates blurry pictures, because it is not focused like with normal lenses. Only illuminating specific spots instead of the full sample makes it possible to calculate the origin of the captured light, since we know which part was illuminated. These light spots can then be moved to scan over the entire sample and create a detailed image. The goal is now to design a chip with these abilities. Crossing waves create interference patterns, and interference patterns with bright spots at regular locations are called optical lattices. Not any optical lattice is suitable for structured illumination, it is important that the spots are bright enough and that there is enough distance between them. The integer lattice method, developed by D. Kouznetsov, provides a systematic way of investigating possible lattices, and it also defines how they can be created and translated. This led to the currently existing design of an optical lattice-generating chip. It is 5.6 mm x 5.6 mm, but a lattice is only in the central region of 100 μm x 100 μm generated. This is not efficient and therefore, an alternative way to design a compact chip is desired. A computer can simulate the pattern generated for a device and optimise this for a lattice. This process is called inverse design and produces compact, but irregular devices. Now, the optical lattice can not be translated any more to scan the sample. In this thesis, explainable AI is used to extract design concepts for a compact, regular optical lattice-generating chip. Shapley values, a form of explainable AI, originate from game theory and can indicate the regions in an image most relevant for a neural network. A neural network is a layered structure of mathematical calculations with tunable parameters able to perform very complex tasks. With inverse design, a large database of two classes of optical lattice-generating devices was created, and the neural network was trained on this database to distinguish devices generating different optical lattices. The Shapley values of the dataset with respect to this network were computed and analysed. Specific features similar to the elements of the integer lattice method were recognized. The Shapley values provided guidance towards a new design. This design is defined by mathematics rather than the seemingly random shapes of inverse design, and it is slightly more compact than inverse designs. Unfortunately, it has similar difficulties in fabrication and translating the optical lattice as inverse design, and further research is needed.