Intraoperative Navigation Systems for Image-Guided Surgery

Recent technological advancements in medical imaging equipment have resulted in a dramatic improvement of image accuracy, now capable of providing useful information previously not available to clinicians. In the surgical context, intraoperative imaging provides a crucial value for the success of the operation. Many nontrivial scientific and technical problems need to be addressed in order to efficiently exploit the different information sources nowadays available in advanced operating rooms. In particular, it is necessary to provide: (i) accurate tracking of surgical instruments, (ii) real-time matching of images from different modalities, and (iii) reliable guidance toward the surgical target. Satisfying all of these requisites is needed to realize effective intraoperative navigation systems for image-guided surgery. Various solutions have been proposed and successfully tested in the field of image navigation systems in the last ten years; nevertheless several problems still arise in most of the applications regarding precision, usability and capabilities of the existing systems. Identifying and solving these issues represents an urgent scientific challenge. This thesis investigates the current state of the art in the field of intraoperative navigation systems, focusing in particular on the challenges related to efficient and effective usage of ultrasound imaging during surgery. The main contribution of this thesis to the state of the art are related to: Techniques for automatic motion compensation and therapy monitoring applied to a novel ultrasound-guided surgical robotic platform in the context of abdominal tumor thermoablation. Novel image-fusion based navigation systems for ultrasound-guided neurosurgery in the context of brain tumor resection, highlighting their applicability as off-line surgical training instruments. The proposed systems, which were designed and developed in the framework of two international research projects, have been tested in real or simulated surgical scenarios, showing promising results toward their application in clinical practice

Detail Enhancing Denoising of Digitized 3D Models from a Mobile Scanning System

The acquisition process of digitizing a large-scale environment produces an enormous amount of raw geometry data. This data is corrupted by system noise, which leads to 3D surfaces that are not smooth and details that are distorted. Any scanning system has noise associate with the scanning hardware, both digital quantization errors and measurement inaccuracies, but a mobile scanning system has additional system noise introduced by the pose estimation of the hardware during data acquisition. The combined system noise generates data that is not handled well by existing noise reduction and smoothing techniques. This research is focused on enhancing the 3D models acquired by mobile scanning systems used to digitize large-scale environments. These digitization systems combine a variety of sensors – including laser range scanners, video cameras, and pose estimation hardware – on a mobile platform for the quick acquisition of 3D models of real world environments. The data acquired by such systems are extremely noisy, often with significant details being on the same order of magnitude as the system noise. By utilizing a unique 3D signal analysis tool, a denoising algorithm was developed that identifies regions of detail and enhances their geometry, while removing the effects of noise on the overall model. The developed algorithm can be useful for a variety of digitized 3D models, not just those involving mobile scanning systems. The challenges faced in this study were the automatic processing needs of the enhancement algorithm, and the need to fill a hole in the area of 3D model analysis in order to reduce the effect of system noise on the 3D models. In this context, our main contributions are the automation and integration of a data enhancement method not well known to the computer vision community, and the development of a novel 3D signal decomposition and analysis tool. The new technologies featured in this document are intuitive extensions of existing methods to new dimensionality and applications. The totality of the research has been applied towards detail enhancing denoising of scanned data from a mobile range scanning system, and results from both synthetic and real models are presented

Scanning angle Raman spectroscopy: Investigation of Raman scatter enhancement techniques for chemical analysis

Over the past 25 years Raman spectroscopy has transitioned from a technically challenging and time consuming research technique to a valuable and practical method of chemical analysis. During this time span, coined the `Raman renaissance\u27 by Dr. Richard McCreery, enhancement techniques and improvements to near-infrared detectors have played a significant role in extending the utility of this analytical technique. This thesis outlines advancements in Raman scatter enhancement techniques by applying evanescent fields, standing-waves (waveguides) and surface enhancements to increase the generated mean square electric field, which is directly related to the intensity of Raman scattering. These techniques are accomplished by employing scanning angle Raman spectroscopy (Chapter 2-4) and surface enhanced Raman spectroscopy (Chapter 5). In Chapter 6, a 1064 nm multichannel Raman spectrometer is discussed for chemical analysis of lignin. Extending dispersive multichannel Raman spectroscopy to 1064 nm reduces the fluorescence interference that can mask the weaker Raman scattering. Overall, these techniques help address the major obstacles in Raman spectroscopy for chemical analysis, which include the inherently weak Raman cross section and susceptibility to fluorescence interference. Chapter 1 is a general introduction to total internal reflection (TIR) Raman spectroscopy and scanning angle (SA) Raman spectroscopy. Brief introductions to surface enhanced Raman spectroscopy and 1064 nm multichannel Raman spectroscopy are provided in their respective Chapters, 5 and 6. In Chapters 2-4, the utility of scanning angle Raman spectroscopy is put into practice for compositional and thickness measurements of thin polymer films. SA-Raman spectroscopy can be classified as an enhancement technique that can be used for measuring interfacial phenomena with chemical specificity. With improvements to modern technology, scanning angle Raman spectroscopy can provide a practical and adaptable technique for applications where surface enhanced Raman spectroscopy (SERS) is impractical. In Chapters 3-4, the total internal reflection Raman spectroscopy configuration is expanded to include surface plasmon resonance and plasmon waveguide resonance Raman spectroscopy. Chapters 2-6 contain published manuscripts. This work develops a foundation of applied chemical measurements for numerous devices, including thin polymer films and photovoltaic devices. Chapter 7 provides general conclusions to the preceding chapters as well as the future prospects of SA-Raman spectroscopy measurements. The appendix describes recent developments in SERS substrates with a primary focus on applications for single cell analysis. It is a section published in a review paper entitled Single Cell Optical Imaging and Spectroscopy in Chemical Reviews

Controlling the multipolar interference of nanoantennas

The emission and detection of light is a main pillar of both fundamental research and the advancement of modern technologies. From digital communications and quantum computing to novel cancer treatments and faded jeans, light-matter interactions are at the core of each of these things, and the fundamental building block of nearly every one of these interactions is the electric dipole. The emission and absorption from every molecule, atom, quantum dot and semiconductor is predominantly electric dipole by nature. While it is the most efficient, fastest, brightest, and easiest to understand process, it is not the only process by which light can be emitted and absorbed; magnetic dipoles, electric quadrupoles, and more, all exist in nature. Optical nanoantennas are the basic element for efficient interfacing between photons and single photon emitters, as they address the inherent size mismatch between the physical size of the emitters and the much larger wavelength of light with which they interact. Optical nanoantennas are also generally electric dipole in nature, as their fundamental resonance is that of an oscillating positive and negative charge. However, unlike nature, these antennas can be engineered to promote higher order modes so that non-electric dipole resonances are not the only contributor. The topic of this Thesis is the control of light emission through modes beyond the electric dipole, both from single emitters coupled to optical nanoantennas and from the emission of light directly from the antennas themselves. In the Introduction, we provide an overview of basic antenna theory, and in Chapter 1, we describe the experimental and theoretical methods used throughout this Thesis. In Chapter 2, we direct light emission from a quantum dot coupled to a two-dimensional antenna excited at a higher-order mode, and represent its emission pattern with a multipole expansion. To demonstrate the importance of a characteristic of light unavailable to spontaneous emission, its phase, we measure the angular emission patterns of second harmonic generation directly from single nanoantennas in Chapter 3, and once more model its patterns with the multipole model. In Chapter 4, we delve into the second harmonic generation from a crystalline semiconductor, and detect competing second order nonlinear processes that were not present in the previous chapter. Finally, in Chapter 5 we combine the previous three chapters and design an optical nanoantenna, which through two nonlinear processes that coexist when driven in a higher-order mode, radiates its second harmonic unidirectionally, with a switchable emission direction. The results in this Thesis demonstrate that not only can optical nanoantennas control light emission from single emitters, but that when they are also the emitters themselves we can actively switch the direction in which light is emitted. With this change in paradigm, we now have a new lever with which to tailor the emission of light at the nanoscale. This coherent control of light emission has potential applications in any technology that benefits from higher light-matter interaction efficiencies, and particularly those that require coherenceL'emissió i detecció de la llum és un pilar principal tant de la investigació fonamental com de l'avanç de les noves tecnologies. Des de les comunicacions digitals i la computació quàntica fins als nous tractaments del càncer i els texans degradats, les interaccions llum-matèria són el nucli de cadascuna d'aquestes qüestions, i el component fonamental de gairebé totes aquestes interaccions és el dipol elèctric. L'emissió i l'absorció de totes les molècules, àtoms, punts quàntics i semiconductors és predominantment de dipol elèctric per naturalesa. Si bé és el procés més eficient, ràpid, brillant i fàcil d'entendre, no és l'únic procés pel qual la llum pot ser emesa i absorbida; dipols magnètics, quadrupols elèctrics i molts més existeixen a la natura. Les nanoantenes òptiques són l'element bàsic per a una interfície eficient entre fotons i emissors de fotons individuals, ja que s'ocupen de la disparitat inherent entre la mida física dels emissors i la major longitud d'ona amb la qual interactuen. Les nanoantenes òptiques generalment són també un dipol elèctric, ja que la seva ressonància fonamental és la d'una càrrega positiva i negativa oscil·lant. Tanmateix, a diferència de la naturalesa, aquestes antenes es poden dissenyar per promoure modes d'ordre superior, de manera que les ressonàncies dipolars no elèctriques no siguin l'únic contribuent. El tema d'aquesta tesi és el control de l'emissió de llum a través de modes que no siguin de tipus dipol elèctric, tant d’emissors individuals acoblats a nanoantenes òptiques com de l'emissió de llum directament des de les pròpies antenes. A la Introducció, oferim una descripció general de la teoria bàsica de nanoantenes, i al Capítol 1 descrivim els mètodes experimentals i teòrics utilitzats al llarg d'aquesta tesi. En el Capítol 2, dirigim l'emissió de llum a partir d'un punt quàntic acoblat a una antena bidimensional excitada a un mode d'ordre superior, i representem el seu patró d'emissió amb una expansió multipolar. Per demostrar l'importància d'una característica de la llum no disponible a l'emissió espontània, la seva fase, mesurem els patrons angulars d'emissió de la generació de segon harmònic directament des de nanoantenes individuals en el Capítol 3. En el Capítol 4, aprofundim en la generació de segon harmònic a partir d'un semiconductor cristal·lí, i detectem processos no lineals de segon ordre competidors que no estaven presents al capítol anterior. Finalment, al Capítol 5, combinem els tres capítols anteriors i dissenyem una nanoantena òptica, que a través de dos processos no lineals que coexisteixen quan s'excita en un ordre d'ordre superior, emet el seu segon harmònic de forma unidireccional, amb aquesta direcció d'emissió sent invertible. Els resultats d'aquesta Tesi demostren que no només les nanoantenes òptiques controlen l'emissió de llum d'emissors individuals, sinó que quan elles mateixes són els emissors, podem canviar activament la direcció en què s'emet la llum. Amb aquest canvi de paradigma, tenim una eina nova per controlar l'emissió de llum a la nanoescala. Aquest control coherent de l'emissió de llum té aplicacions potencials en qualsevol tecnologia que es vulgui beneficiar d'una major eficiència en la interacció de la llum-matèria, i en particular d'aquelles que requereixen coherència.Postprint (published version

2D photonic crystals to enhance up-conversion emission for silicon photovoltaics

This thesis investigates the application of 2D photonic crystals to enhance the emission of up-conversion layers to improve the efficiency of silicon photovoltaics. Two up-conversion material compositions are of particular interest in this work: erbium doped titanium dioxide (TiO2:Er) and erbium doped yttrium fluoride (YF3:Er). The 2D photonic crystals under investigation are composed of TiO2:Er and air; and YF3:Er and silicon. These nano-structures are investigated using both simulation and experimental methods. Further work in this thesis analyses the properties of the highly conductive polymer poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) for use as a transparent electrode and thin film electrically conductive adhesive for the application of silicon photovoltaics. The design and geometrical parameters for the 2D photonic crystals were optimised through simulations (plane wave expansion and finite-difference time-domain), before the structures were experimentally fabricated and optically characterised. The novel analysis of the refractive index of the prepared up-conversion materials using ellipsometry was a key step in the design of the photonic crystal structures. A maximum photoluminescence enhancement of 3.79 times was observed for the 980 nm emission profile, however this could not be successfully attributed to a photonic crystal effect. The optical, mechanical and electronic properties of PEDOT:PSS were characterised for thin film samples, using novel ellipsometry analysis

Magnetic field directed self-assembly of gold Pickering emulsion for preparing patterned film.

Patterning plays a vital in role in sensor-based devices like surface-enhanced Raman spectroscopy (SERS), surface-enhanced infrared absorption (SEIRA), radio frequency (RF) antennas and many others. The linear array spacing and width of gold strips has been shown to increase the local intensity through near-field coupling with diffracted electromagnetic waves. This rise in local charge boosts vibrational energies of molecules in close-surface contact or proximity, resulting in increased IR absorption. The strip-like or any other types of patterns are efficiently achieved through top-down nanofabrication processes like atomic-force-deposition, nanoimprinting, UV-Lithography etc., which involve high capital cost, complex processing and occasionally low throughput. This research was therefore undertaken with the aim of reducing the process complexities and improving scalability, by applying a magnetic and spin coating directed self-assembly (MSCDS) to prepare optically sensitive dipole-dipole chain-like ordered arrays of the gold nanoparticle Pickering ferrofluid in polyvinyl alcohol (PVA) emulsion, in the form of a thin film on glass and silicon substrate. Previously-conducted MSCDS processes lacked the control over the dimensions of the prepared patterns. Here, the static magnetic field approach was taken to modify the MSCDS process to overcome the limitation of pattern dimension control, providing tuneability for optical applications. Quantitative image analysis of the patterned thin film allowed for the measurement of pattern geometrical dimension (chain length-CL, chain gap-CG and chain thickness-CT), which was then correlated with processing parameters such as magnetic field configurations (single, compound and concentric), spinning speeds and viscosities of Pickering emulsion. Upon optimization, spectroscopical characterisation was performed on prepared patterned thin film to demonstrate the capability of the modified MSDS process in enhancing the molecular detection at low concentrations. The UV-vis spectra of the patterns demonstrated the impact of CT and CG on the degree of gold-iron oxide nanoscale interactions leading to tuneability of absorption bands between 390-700nm. The coupling of the increased optical sensitivity through enhanced charge transfer dynamics with the mid-infra-red range grating order (CT+CG) resulted in an amplification in vibrational band excitation of molecular bonds. For example, SEIRA measurements of thin film patterns showed a vibrational signal enhancement in asymmetric vibration of -CH2 (2920cm-1) bonds of PVA by 40%, as CT increased by 178% from 1.2μm at probing 45 degree grazing angle. Furthermore, the magneto-optical SERS phenomenon - involving local polarization of gold nanoparticles through the neighbouring magnetised iron oxide nanoparticle in the presence of external magnetic field - was exploited to reveal the varying degree of enhancement in peaks related to Rhodamine 6G (R6G) coated on thin film nanostructure, which was dependent on magnetized CT/CG morphology; especially the C-C-C ring (671 cm-1), for which the Raman peak increased by 12,000% when magnetized by a 43mT field. In summary, the modified MSCDC process is cheap with an expandable throughput rate ( > 0.1 m2/h) and flexible designs, offering both nanoscale and microscale tuneability of pattern dimensions. Even with higher defectivity (~14%) in comparison to the nanoimprinting method, this method can potentially be used to create repetitive array-like structure. Furthermore, the use of iron oxide reduces the cost without sacrificing the optical performance and thus contributes to the optical tuneability of the thin film nanostructure, thereby making the entire product a potential absorbing antenna and microfluidics thin film for biomolecule detection

Controlling the multipolar interference of nanoantennas

The emission and detection of light is a main pillar of both fundamental research and the advancement of modern technologies. From digital communications and quantum computing to novel cancer treatments and faded jeans, light-matter interactions are at the core of each of these things, and the fundamental building block of nearly every one of these interactions is the electric dipole. The emission and absorption from every molecule, atom, quantum dot and semiconductor is predominantly electric dipole by nature. While it is the most efficient, fastest, brightest, and easiest to understand process, it is not the only process by which light can be emitted and absorbed; magnetic dipoles, electric quadrupoles, and more, all exist in nature. Optical nanoantennas are the basic element for efficient interfacing between photons and single photon emitters, as they address the inherent size mismatch between the physical size of the emitters and the much larger wavelength of light with which they interact. Optical nanoantennas are also generally electric dipole in nature, as their fundamental resonance is that of an oscillating positive and negative charge. However, unlike nature, these antennas can be engineered to promote higher order modes so that non-electric dipole resonances are not the only contributor. The topic of this Thesis is the control of light emission through modes beyond the electric dipole, both from single emitters coupled to optical nanoantennas and from the emission of light directly from the antennas themselves. In the Introduction, we provide an overview of basic antenna theory, and in Chapter 1, we describe the experimental and theoretical methods used throughout this Thesis. In Chapter 2, we direct light emission from a quantum dot coupled to a two-dimensional antenna excited at a higher-order mode, and represent its emission pattern with a multipole expansion. To demonstrate the importance of a characteristic of light unavailable to spontaneous emission, its phase, we measure the angular emission patterns of second harmonic generation directly from single nanoantennas in Chapter 3, and once more model its patterns with the multipole model. In Chapter 4, we delve into the second harmonic generation from a crystalline semiconductor, and detect competing second order nonlinear processes that were not present in the previous chapter. Finally, in Chapter 5 we combine the previous three chapters and design an optical nanoantenna, which through two nonlinear processes that coexist when driven in a higher-order mode, radiates its second harmonic unidirectionally, with a switchable emission direction. The results in this Thesis demonstrate that not only can optical nanoantennas control light emission from single emitters, but that when they are also the emitters themselves we can actively switch the direction in which light is emitted. With this change in paradigm, we now have a new lever with which to tailor the emission of light at the nanoscale. This coherent control of light emission has potential applications in any technology that benefits from higher light-matter interaction efficiencies, and particularly those that require coherenceL'emissió i detecció de la llum és un pilar principal tant de la investigació fonamental com de l'avanç de les noves tecnologies. Des de les comunicacions digitals i la computació quàntica fins als nous tractaments del càncer i els texans degradats, les interaccions llum-matèria són el nucli de cadascuna d'aquestes qüestions, i el component fonamental de gairebé totes aquestes interaccions és el dipol elèctric. L'emissió i l'absorció de totes les molècules, àtoms, punts quàntics i semiconductors és predominantment de dipol elèctric per naturalesa. Si bé és el procés més eficient, ràpid, brillant i fàcil d'entendre, no és l'únic procés pel qual la llum pot ser emesa i absorbida; dipols magnètics, quadrupols elèctrics i molts més existeixen a la natura. Les nanoantenes òptiques són l'element bàsic per a una interfície eficient entre fotons i emissors de fotons individuals, ja que s'ocupen de la disparitat inherent entre la mida física dels emissors i la major longitud d'ona amb la qual interactuen. Les nanoantenes òptiques generalment són també un dipol elèctric, ja que la seva ressonància fonamental és la d'una càrrega positiva i negativa oscil·lant. Tanmateix, a diferència de la naturalesa, aquestes antenes es poden dissenyar per promoure modes d'ordre superior, de manera que les ressonàncies dipolars no elèctriques no siguin l'únic contribuent. El tema d'aquesta tesi és el control de l'emissió de llum a través de modes que no siguin de tipus dipol elèctric, tant d’emissors individuals acoblats a nanoantenes òptiques com de l'emissió de llum directament des de les pròpies antenes. A la Introducció, oferim una descripció general de la teoria bàsica de nanoantenes, i al Capítol 1 descrivim els mètodes experimentals i teòrics utilitzats al llarg d'aquesta tesi. En el Capítol 2, dirigim l'emissió de llum a partir d'un punt quàntic acoblat a una antena bidimensional excitada a un mode d'ordre superior, i representem el seu patró d'emissió amb una expansió multipolar. Per demostrar l'importància d'una característica de la llum no disponible a l'emissió espontània, la seva fase, mesurem els patrons angulars d'emissió de la generació de segon harmònic directament des de nanoantenes individuals en el Capítol 3. En el Capítol 4, aprofundim en la generació de segon harmònic a partir d'un semiconductor cristal·lí, i detectem processos no lineals de segon ordre competidors que no estaven presents al capítol anterior. Finalment, al Capítol 5, combinem els tres capítols anteriors i dissenyem una nanoantena òptica, que a través de dos processos no lineals que coexisteixen quan s'excita en un ordre d'ordre superior, emet el seu segon harmònic de forma unidireccional, amb aquesta direcció d'emissió sent invertible. Els resultats d'aquesta Tesi demostren que no només les nanoantenes òptiques controlen l'emissió de llum d'emissors individuals, sinó que quan elles mateixes són els emissors, podem canviar activament la direcció en què s'emet la llum. Amb aquest canvi de paradigma, tenim una eina nova per controlar l'emissió de llum a la nanoescala. Aquest control coherent de l'emissió de llum té aplicacions potencials en qualsevol tecnologia que es vulgui beneficiar d'una major eficiència en la interacció de la llum-matèria, i en particular d'aquelles que requereixen coherència