An Inertial-Optical Tracking System for Quantitative, Freehand, 3D Ultrasound

Three dimensional (3D) ultrasound has become an increasingly popular medical imaging tool over the last decade. It offers significant advantages over Two Dimensional (2D) ultrasound, such as improved accuracy, the ability to display image planes that are physically impossible with 2D ultrasound, and reduced dependence on the skill of the sonographer. Among 3D medical imaging techniques, ultrasound is the only one portable enough to be used by first responders, on the battlefield, and in rural areas. There are three basic methods of acquiring 3D ultrasound images. In the first method, a 2D array transducer is used to capture a 3D volume directly, using electronic beam steering. This method is mainly used for echocardiography. In the second method, a linear array transducer is mechanically actuated, giving a slower and less expensive alternative to the 2D array. The third method uses a linear array transducer that is moved by hand. This method is known as freehand 3D ultrasound. Whether using a 2D array or a mechanically actuated linear array transducer, the position and orientation of each image is known ahead of time. This is not the case for freehand scanning. To reconstruct a 3D volume from a series of 2D ultrasound images, assumptions must be made about the position and orientation of each image, or a mechanism for detecting the position and orientation of each image must be employed. The most widely used method for freehand 3D imaging relies on the assumption that the probe moves along a straight path with constant orientation and speed. This method requires considerable skill on the part of the sonographer. Another technique uses features within the images themselves to form an estimate of each image\u27s relative location. However, these techniques are not well accepted for diagnostic use because they are not always reliable. The final method for acquiring position and orientation information is to use a six Degree-of-Freedom (6 DoF) tracking system. Commercially available 6 DoF tracking systems use magnetic fields, ultrasonic ranging, or optical tracking to measure the position and orientation of a target. Although accurate, all of these systems have fundamental limitations in that they are relatively expensive and they all require sensors or transmitters to be placed in fixed locations to provide a fixed frame of reference. The goal of the work presented here is to create a probe tracking system for freehand 3D ultrasound that does not rely on any fixed frame of reference. This system tracks the ultrasound probe using only sensors integrated into the probe itself. The advantages of such a system are that it requires no setup before it can be used, it is more portable because no extra equipment is required, it is immune from environmental interference, and it is less expensive than external tracking systems. An ideal tracking system for freehand 3D ultrasound would track in all 6 DoF. However, current sensor technology limits this system to five. Linear transducer motion along the skin surface is tracked optically and transducer orientation is tracked using MEMS gyroscopes. An optical tracking system was developed around an optical mouse sensor to provide linear position information by tracking the skin surface. Two versions were evaluated. One included an optical fiber bundle and the other did not. The purpose of the optical fiber is to allow the system to integrate more easily into existing probes by allowing the sensor and electronics to be mounted away from the scanning end of the probe. Each version was optimized to track features on the skin surface while providing adequate Depth Of Field (DOF) to accept variation in the height of the skin surface. Orientation information is acquired using a 3 axis MEMS gyroscope. The sensor was thoroughly characterized to quantify performance in terms of accuracy and drift. This data provided a basis for estimating the achievable 3D reconstruction accuracy of the complete system. Electrical and mechanical components were designed to attach the sensor to the ultrasound probe in such a way as to simulate its being embedded in the probe itself. An embedded system was developed to perform the processing necessary to translate the sensor data into probe position and orientation estimates in real time. The system utilizes a Microblaze soft core microprocessor and a set of peripheral devices implemented in a Xilinx Spartan 3E field programmable gate array. The Xilinx Microkernel real time operating system performs essential system management tasks and provides a stable software platform for implementation of the inertial tracking algorithm. Stradwin 3D ultrasound software was used to provide a user interface and perform the actual 3D volume reconstruction. Stradwin retrieves 2D ultrasound images from the Terason t3000 portable ultrasound system and communicates with the tracking system to gather position and orientation data. The 3D reconstruction is generated and displayed on the screen of the PC in real time. Stradwin also provides essential system features such as storage and retrieval of data, 3D data interaction, reslicing, manual 3D segmentation, and volume calculation for segmented regions. The 3D reconstruction performance of the system was evaluated by freehand scanning a cylindrical inclusion in a CIRS model 044 ultrasound phantom. Five different motion profiles were used and each profile was repeated 10 times. This entire test regimen was performed twice, once with the optical tracking system using the optical fiber bundle, and once with the optical tracking system without the optical fiber bundle. 3D reconstructions were performed with and without the position and orientation data to provide a basis for comparison. Volume error and surface error were used as the performance metrics. Volume error ranged from 1.3% to 5.3% with tracking information versus 15.6% to 21.9% without for the version of the system without the optical fiber bundle. Volume error ranged from 3.7% to 7.6% with tracking information versus 8.7% to 13.7% without for the version of the system with the optical fiber bundle. Surface error ranged from 0.319 mm RMS to 0.462 mm RMS with tracking information versus 0.678 mm RMS to 1.261 mm RMS without for the version of the system without the optical fiber bundle. Surface error ranged from 0.326 mm RMS to 0.774 mm RMS with tracking information versus 0.538 mm RMS to 1.657 mm RMS without for the version of the system with the optical fiber bundle. The prototype tracking system successfully demonstrated that accurate 3D ultrasound volumes can be generated from 2D freehand data using only sensors integrated into the ultrasound probe. One serious shortcoming of this system is that it only tracks 5 of the 6 degrees of freedom required to perform complete 3D reconstructions. The optical system provides information about linear movement but because it tracks a surface, it cannot measure vertical displacement. Overcoming this limitation is the most obvious candidate for future research using this system. The overall tracking platform, meaning the embedded tracking computer and the PC software, developed and integrated in this work, is ready to take advantage of vertical displacement data, should a method be developed for sensing it

Towards electron holography of working transistors

As semiconductor device dimensions are reduced to the deep sub-micron regime, minor departures from the designed distributions of electrostatic potentials can affect device performance dramatically. Parameter optimisation in device processing and modelling is crucial for achieving precise potential profiles. Such optimisation is not possible without comprehensive feedback from advanced characterisation techniques. The ability to acquire two- and three-dimensional measurements of potential distributions with high spatial resolution, high precision and under an applied electrical bias is therefore in great demand. The technique of off-axis electron holography in the transmission electron microscope (TEM) promises to fulfil these requirements in two dimensions and can be combined with electron tomography for three-dimensional measurements. In this dissertation, the practical challenges that are involved in the application of electron holography to the characterisation of electrostatic potentials in working MOSFETs are addressed. A novel method for the application of electrical contacts to a TEM specimen is developed and applied to a diode structure. Off-axis electron holography measurements are carried out on a pn junction using both this and an alternative geometry and compared with simulations. A semi-biased MOSFET is then characterised successfully using electron holography, suggesting that the examination of working transistors in the TEM is a realistic prospect. In order to investigate sources of error and practical challenges, the influence of diffraction contrast on electron holographic phase images is investigated. The effects of electron beam irradiation on the in-situ characterisation of electrical properties in semiconductor devices are then assessed using three complementary techniques: off-axis electron holography and measurements of electron beam induced current in the TEM and secondary electron dopant contrast in the scanning electron microscope

Doppler Encoded Excitation Patterning (DEEP) Microscopy

Traditional optical imaging systems rely on lenses and spatially-resolved detection to probe distinct locations on the object. We develop a novel computational approach to 2D and 3D imaging that instead measures the object\u27s spatial Fourier transform using a single-element detector and without requiring precision optics. This wide-field technique can be used to image biological and synthetic structures in fluoresced or scattered light using coherent or broadband illumination. It employs dynamic structured illumination, acousto-optics, RF electronics, and tomographic algorithms to circumvent several trade-offs in conventional imaging, such as the dependence of the optical transfer function on the imaging lenses and the coupling of resolution and depth of field. We use Fourier optics concepts to derive the dynamic optical transfer function, evaluate different Fourier sampling strategies, and investigate and compare tomographic algorithms for 2D and 3D image synthesis. We also develop conceptual and analytical models to describe imaging of fluorescent as well as amplitude and phase scattering objects, the effects of broadband and spatially-incoherent illumination, and nonlinear wide-field super-resolution imaging. We consider sources of noise, analyze and simulate SNR behavior for several types of noise and Fourier sampling strategies, and compare the sensitivity of the technique to conventional imaging. We describe several experimental proof-of-concept systems and present two-dimensional high-resolution tomographic image reconstructions in both scattered and fluoresced light demonstrating a thousandfold improvement in the depth of field compared to conventional lens-based microscopy. Finally, we explore approaches for high-speed Fourier sampling and propose several related sensing techniques, including wide-field fluorescence imaging in scattering media

A Method Of Moments Approach for the Design Of RF Coils for MRI

Magnetic Resonance Imaging (MRI) is a widely used soft-tissue imaging modality that has evolved over the past several years into a powerful and versatile medical diagnostic tool capable of providing in-vivo diagnostic images of human and animal anatomies. Current research efforts in MRI system design are driven by the need to obtain detailed high resolution images with improved image signal-to-noise ratio (SNR) at a given magnetic field strength. Invariably, this requirement demands the development of high performance MRI radio frequency (RF) coils. However, the complexities and stringent requirements of modern clinical MRI systems necessitate the development of new modeling methodologies for the design of high performance RF coils. This dissertation addresses this need by developing a distinct Method of Moments (MoM) modeling approach suitable for the simulation of RF coils loaded with biological tissues. The unique implementation utilizes two distinct basis functions in order to collectively describe the surface current density on the RF coil, and the sum of the volume current density and the displacement current density in the associated biological tissue. By selecting basis functions with similar properties to the actual physical quantities they describe, we avoided spurious solutions normally associated with MoM based implementations. The validity of our modeling method was confirmed by comparisons with analytical solutions as well as physical measurements, yielding good agreement. Furthermore, we applied the MoM based modeling method in the design and development of a novel 4-channel receive-only RF coil for breast imaging in a clinical 1.5T system. The new coil design was inspired by the multi-channel array concept, where multiple conducting strips were arranged in an anatomically conforming profile with the intention of improving sensitivity and SNR. In addition, the coil structure featured an open breast coil concept in order to facilitate MRI-guided biopsy and patient comfort. A comparison of simulation results and actual physical measurements from the prototype RF coil demonstrated good agreement with one another. Also, imaging tests were conducted on a pair of MRI phantoms as well as on a human patient after obtaining proper authorization. The tests revealed good magnetic field homogeneity and a high SNR in the region of interest. In addition, performance comparisons between the prototype 4-channel RF coil and existing high end clinical 4-channel RF breast coils indicated an achievement of superior SNR in conjunction with very good magnetic field homogeneity. Currently, the prototype 4-channel RF coil has outperformed all existing high end clinical 4-channel RF coils used in comparison studies

Sulphur Induced Degradation of Nickel-Based Solid Oxide Fuel Cell Anodes

Solid Oxide Fuel Cells (SOFCs) are high temperature solid-state electrochemical devices that convert fuel into electricity and heat with high efficiency. Many fuels suitable for SOFCs derive from hydrocarbon sources, such as natural gas or biogas; however, these contain significant impurities, most notably compounds containing sulphur, which can poison the nickel electrocatalyst in the anode of the fuel cell. Sulphur removal is usually carried out but it is complicated and expensive to achieve levels below 1 part per million (ppm). An enhanced scientific understanding of chemical interactions on the surface of SOFC electrodes is critical to the development of robust nickel-based anodes, but the mechanisms and effects of sulphur poisoning are not fully understood. The scope of this thesis is to advance the field of sulphur-poisoning research by studying the effect of current density on the sulphur-induced degradation, and focuses on intermediate-temperature (IT) conditions with nickel-gadolinia doped ceria (Ni-CGO), which is the most promising anode material for IT-SOFCs, operating between 600–800 °C. The work of this thesis is aimed at (i) investigating the kinetics of sulphur poisoning, and the effect of current density, by use of a specially built three-electrode electrochemical test rig; (ii) analysis of structural modifications to the anode microstructure as a result of exposure to fuel cell conditions and (iii) development and prototype testing of a miniature SOFC test rig with optical access for in situ Raman spectroscopy. Fuel cell operation at higher current density was found to partially mitigate the sulphur poisoning of up to 3 ppm H2S in H2 fuel, while microstructural analysis found that the presence of as little as 0.5 ppm H2S accelerated restructuring of nickel grain surfaces. Finally, preliminary proof-of-concept results were obtained for the in situ Raman rig, and suggestions for a future design are discussed

Atténuation des interactions électromagnétiques entre le module de détection LabPET II et l’IRM

Les scanners TEP/IRM simultanés offrent une occassion unique d'examiner en même temps les propriétés anatomiques et fonctionnelles des tissus malins, tout en évitant l'incertitude des systèmes séquentiels de TEP/IRM. Cependant, le couplage électromagnétique entre les deux modalités constitue un défi important à relever. Ces interférences électromagnétiques entravent les performances du scanner et altèrent la qualité d'image de chaque modalité. Bien que les métaux possèdent d'excellentes propriétés de blindage contre les fréquences radioélectriques, ils ne constituent pas nécessairement une option de blindage appropriée pour modifier les champs magnétiques induisant des courants de Foucault dans les couches métalliques. En conséquence, il existe une demande considérable pour un nouveau matériau de protection et une approche originale pour retirer les pièces métalliques du champ de vision IRM. L’objectif de ce projet était d’initier les études en vue de la réalisation d’un scanner TEP/IRM simultané basé sur des modules de détection LabPET II hautement pixélisés afin d’obtenir une résolution spatiale millimétrique pour le cerveau humain et le chien. L'électronique LabPET II comprend des circuits intégrés à application spécifique dans lesquels le signal est numérisé à proximité de la photodiode à avalanche et offre un environnement moins sensible aux interférences électromagnétiques. Pour atteindre l'objectif principal, premièrement, l'effet du matériau métallique des modules de détection LabPET II sur les performances de la TEP et de l'IRM est examiné théoriquement. Les résultats confirment que les composants métalliques du module de détection LabPET II altèrent le champ magnétique, génèrent des courants de Foucault ce qui augmente leur température. Ensuite, les performances électroniques des modules de détection LabPET II sous l’influence de bobines d’IRM faites sur mesure sont examinées. La résolution en énergie et la résolution temporelle se détériorent en présence de bobines RF et de bobines à gradient en raison des perturbations électromagnétiques. Subséquemment, un module de détection LabPET II blindé par une fine couche de composite cuivre-argent est étudié, prouvant que le blindage contre les interférences électromagnétiques avec le composite rétablit les performances en TEP, fournissant moins d'induction par courants de Foucault. En outre, une nouvelle configuration de blindage basée sur un composite de couche flexible de nanotubes de carbone a été fabriquée pour limiter les interférences électromagnétiques. Les composites de nanotubes de carbone créent une couche hautement conductrice avec des chemins conducteurs minimaux, ce qui permet de réduire les courants de Foucault. Le principal résultat scientifique de ce projet est que le blindage composite empêche les interférences de basses et hautes fréquences et réduit l'induction de courants de Foucault, offrant ainsi la flexibilité nécessaire pour acquérir une séquence rapide de commutation de gradients. D'un point de vue technique, le module de détection LabPET II ainsi blindé présente une excellente performance dans un environnement de type IRM, ce qui permet de concevoir un insert TEP basé sur la technologie LabPET II.Abstract: Simultaneous PET/ MRI scanners provide a unique opportunity to investigate anatomical and functional properties of malignant tissues at the same time while avoiding the uncertainty of a sequential PET/MRI systems. However, electromagnetic coupling between the two modalities is a significant challenge that needs to be addressed. These electromagnetic interferences (EMI) hinder the performance of both scanners and distort the image quality of each modality. Although metals have excellent radio-frequency shielding properties, they are not necessarily an appropriate shielding option for altering magnetic fields that induce eddy currents in any metallic layer. Thus, there is a considerable demand for a new shielding material and an original approach to remove metallic parts from the MRI field of view. The objective of this project was to initiate the realization of a simultaneous PET/MRI scanner based on highly pixelated LabPET II detection modules to achieve millimeter spatial resolution for the human brain and dogs. The LabPET II electronics include application specific integrated circuits where the signal is digitized near the avalanche photodiode and offers an environment less susceptible to EMI. To fulfill the main aim, for the first time, the effect of the metallic material of LabPET II on PET and MRI performance was theoretically examined. Results confirm that metallic components of the LabPET II detection modules distort the magnetic field, generate eddy currents, and increase temperature. Then, the LabPET II electronics performance under the influence of custom-made MRI coils was investigated. Its energy and timing resolutions deteriorate in the presence of both RF and gradient signals because of EMIs. Thus, a LabPET II detection module shielded by a thin layer of the copper-silver composite was investigated, proving that shielding EMIs with the composite restores the PET performance, with less eddy current induction. Besides, a new shielding configuration based on a flexible layer of carbon nanotube (CNT) composite was fabricated to limit the EMIs. The CNT composite creates a highly conductive layer with minimal conductive paths that allows eddy currents to be decreased. The primary scientific outcome of this project is that the novel composite shielding rejects both low and high-frequency interferences and reduces eddy current induction, offering the flexibility to acquire a fast gradient switching sequence. From a technical point of view, the shielded LabPET II detection module demonstrates an excellent performance in an MRI-like environment supporting the feasibility of designing a PET-insert based on LabPET II technology

Towards new generation of neuro-implantable devices : engineering neuron/carbon nanotubes integrated functional units

2008/2009Le nanotecnologie sono un campo delle scienze che utilizza materiali e dispositivi ingegnerizzati aventi la più piccola organizzazione funzionale a livello di dimensioni nanometriche. Questo implica che nanodispositivi e nanomateriali possano interagire con i sistemi biologici a livello molecolare con un elevato grado di specificità. É largamente accettato che l’applicazione delle nanotecnologie nell’ambito delle neuroscienze abbia un forte potenziale (Silva, 2006). In questo contesto, i nanotubi di carbonio (CNT), un’innovativa forma di carbonio composta da strutture tubulari di grafite dalle dimensioni nanometriche dotate di buone proprietà di conduzione elettrica, si sono dimostrati promettenti candidati per sviluppare la tecnologia di dispositivi impiantabili in ambito biomedico. Diversi studi hanno dimostrato la biocompatibilità dei substrati di CNT per i neuroni in termini di adesione, crescita e differenziamento cellulare (riassunti in Sucapane et al., 2009). Al fine di aumentare la nostra conoscenza riguardo alle interazioni presenti in sistemi ibridi formati da CNT e neuroni, abbiamo caratterizzato l’attività di reti neuronali cresciuti su supporti di CNT attraverso la tecnica del patch clamp. Il nostro gruppo ha riportato che circuti neuronali cresciuti in vitro su substrati di CNT presentano un’aumentata attività sinaptica spontanea rispetto al controllo a fronte di comparabili proprietà base (proprietà passive di membrana, morfologia e densità dei neuroni) delle colture nelle due condizioni di crescita (Lovat et al., 2005). Si è quindi ipotizzato che tale aumentata attività spontanea potesse originare da una modificazione nel modo in cui i singoli neuroni generano il segnale elettrico. A tal fine, si sono monitorate variazioni nelle proprietà elettrogeniche di singoli neuroni, utilizzando un protocollo standard per caratterizzare l’integrazione di potenziali d’azione retropropaganti nei dendriti (Larkum et al., 1999). In configurazione current clamp, attraverso brevi iniezioni di corrente nel soma della cellula, abbiamo indotto una serie di regolari potenziali d’azione (PA) a varie frequenze nel neurone sotto registrazione, quindi abbiamo studiato la presenza di un’addizionale depolarizzazione somatica dopo l’ultimo PA del treno. Abbiamo osservato che neuroni di controllo mostrano nella maggioranza dei casi una iperpolarizzazione (AHP) del potenziale di membrana dopo l’ultimo PA del treno, mentre una depolarizzazione (ADP) è presente solo in una piccola quota di casi. In presenza di CNT, invece, l’ADP risulta essere l’evento predominante. L’ADP è inoltre abolita dall’applicazione di CoCl2, un bloccante non specifico dei canali calcio voltaggio dipendenti. Per di più, l’area dell’ADP può essere diminuita dall’applicazione di nifedipina (10 μM) e l’ulteriore coapplicazione di NiCl2 (50 μM) elimina totalmente l’ADP, suggerendo che sia i canali calcio voltaggio dipendenti ad alta soglia di attivazione, sia quelli a bassa soglia, siano coinvolti in questo processo (Cellot et al., 2009). Attraverso la microscopia elettronica a trasmissione (TEM) e, più recentemente, mediante quella a scansione (SEM) è stata messa in evidenza la presenza di discontinui punti di stretto contatto tra CNT e membrane neuronali: la nostra ipotesi è che tali strutture ibride siano in grado di favorire la retropropagazione dei PA nei dendriti distali. La maggiore eccitabilità a livello del singolo neurone, inoltre, potrebbe essere responsabile dell’incremento di attività spontanea della rete neuronale. Abbiamo quindi ulteriormente caratterizzato l’attività della rete neuronale attraverso registrazioni da coppie di neuroni, dove il neurone presinaptico veniva stimolato ad avere treni di potenziali d’azione a 20 Hz in configurazione current clamp e simultaneamente il neurone postsinaptico era monitorato in configurazione voltage clamp per vedere la presenza o l’assenza di una risposta sinaptica. I nostri esperimenti indicano che la probabilità di trovare connessioni monosinaptiche gabaergiche tra neuroni è aumentata in presenza di CNT (56% vs 40% in controllo). Inoltre, è stato rilevato un ulteriore effetto dei CNT sulla plasticità a breve termine delle sinapsi: nelle condizioni di controllo, treni di potenziali d’azione nella cellula presinaptica evocano nella cellula postsinaptica nel 90% dei casi una chiara depressione nell’ampiezza di consecutivi ePSCs, mentre solo in meno del 10% è possibile rilevare una facilitazione. Al contrario, in presenza di CNT, nel 39% delle coppie, il neurone postsinaptico risponde in modo chiaramente facilitativo. Nelle più recenti serie di esperimenti, abbiamo voluto indagare più approfonditamente l’origine di questa modificazione in termini di plasticità sinaptica; a tal fine, abbiamo trattato neuroni in controllo e su CNT con tetrodotossina 1 µM per 5 giorni, al fine di bloccare completamente l’attività elettrica della rete neuronale, e abbiamo compiuto delle registrazioni da coppie di neuroni. Mentre la risposta prevalentemente di depressione dei controlli non è modificata da tale trattamento, neuroni cresciuti su substrati di cnt in condizioni di blocco dell’attività elettrica non presentano più sinapsi con caratteristiche di facilitazione, ma hanno un comportamento simile ai contolli. Questi risultati indicano che la facilitazione è una proprietà tipica di sinapsi attive sviluppatesi in presenza di CNT.XXII Ciclo198

Effect of curing conditions and harvesting stage of maturity on Ethiopian onion bulb drying properties

The study was conducted to investigate the impact of curing conditions and harvesting stageson the drying quality of onion bulbs. The onion bulbs (Bombay Red cultivar) were harvested at three harvesting stages (early, optimum, and late maturity) and cured at three different temperatures (30, 40 and 50 oC) and relative humidity (30, 50 and 70%). The results revealed that curing temperature, RH, and maturity stage had significant effects on all measuredattributesexcept total soluble solids