3D Wavelet-based Fusion Techniques for Biomedical Imaging

Hoy en día las técnicas de adquisición de imágenes tridimensionales son comunes en diversas áreas, pero cabe destacar la relevancia que han adquirido en el ámbito de la imagen biomédica, dentro del cual encontramos una amplia gama de técnicas como la microscopía confocal, microscopía de dos fotones, microscopía de fluorescencia mediante lámina de luz, resonancia magnética nuclear, tomografía por emisión de positrones, tomografía de coherencia óptica, ecografía 3D y un largo etcétera. Un denominador común de todas esas aplicaciones es la constante necesidad por aumentar la resolución y la calidad de las imágenes adquiridas. En algunas de dichas técnicas de imagen tridimensional se da una interesante situación: aunque que cada volumen adquirido no contiene información suficiente para representar el objeto bajo estudio dentro de los parámetros de calidad requeridos por algunas aplicaciones finales, el esquema de adquisición permite la obtención de varios volúmenes que representan diferentes vistas de dicho objeto, de tal forma que cada una de las vistas proporciona información complementaria acerca del mismo. En este tipo de situación es posible, mediante la combinación de varias de esas vistas, obtener una mejor comprensión del objeto que a partir de cada una de ellas por separado. En el contexto de esta Tesis Doctoral se ha propuesto, desarrollado y validado una nueva metodología de proceso de imágenes basada en la transformada wavelet disc¬reta para la combinación, o fusión, de varias vistas con información complementaria de un mismo objeto. El método de fusión propuesto aprovecha la capacidad de descom¬posición en escalas y orientaciones de la transformada wavelet discreta para integrar en un solo volumen toda la información distribuida entre el conjunto de vistas adquiridas. El trabajo se centra en dos modalidades diferentes de imagen biomédica que per¬miten obtener tales adquisiciones multi-vista. La primera es una variante de la micro¬scopía de fluorescencia, la microscopía de fluorescencia mediante lámina de luz, que se utiliza para el estudio del desarrollo temprano de embriones vivos en diferentes modelos animales, como el pez cebra o el erizo de mar. La segunda modalidad es la resonancia magnética nuclear con realce tardío, que constituye una valiosa herramienta para evaluar la viabilidad del tejido miocárdico en pacientes con diversas miocardiopatías. Como parte de este trabajo, el método propuesto ha sido aplicado y validado en am¬bas modalidades de imagen. En el caso de la aplicación a microscopía de fluorescencia, los resultados de la fusión muestran un mejor contraste y nivel de detalle en comparación con cualquiera de las vistas individuales y el método no requiere de conocimiento previo acerca la función de dispersión puntual del sistema de imagen. Además, los resultados se han comparado con otros métodos existentes. Con respecto a la aplicación a imagen de resonancia magnética con realce tardío, los volúmenes fusionados resultantes pre-sentan una mejora cuantitativa en la nitidez de las estructuras relevantes y permiten una interpretación más sencilla y completa de la compleja estructura tridimensional del tejido miocárdico en pacientes con cardiopatía isquémica. Para ambas aplicaciones los resultados de esta tesis se encuentran actualmente en uso en los centros clínicos y de investigación con los que el autor ha colaborado durante este trabajo. Además se ha puesto a libre disposición de la comunidad científica la implementación del método de fusión propuesto. Por último, se ha tramitado también una solicitud de patente internacional que cubre el método de visualización desarrollado para la aplicación de Resonancia Magnética Nuclear. Abstract Nowadays three dimensional imaging techniques are common in several fields, but es-pecially in biomedical imaging, where we can find a wide range of techniques including: Laser Scanning Confocal Microscopy, Laser Scanning Two Photon Microscopy, Light Sheet Fluorescence Microscopy, Magnetic Resonance Imaging, Positron Emission To-mography, Optical Coherence Tomography, 3D Ultrasound Imaging, etc. A common denominator of all those applications being the constant need for further increasing resolution and quality of the acquired images. Interestingly, in some of the mentioned three-dimensional imaging techniques a remarkable situation arises: while a single volume does not contain enough information to represent the object being imaged within the quality parameters required by the final application, the acquisition scheme allows recording several volumes which represent different views of a given object, with each of the views providing complementary information. In this kind of situation one can get a better understanding of the object by combining several views instead of looking at each of them separately. Within such context, in this PhD Thesis we propose, develop and test new image processing methodologies based on the discrete wavelet transform for the combination, or fusion, of several views containing complementary information of a given object. The proposed fusion method exploits the scale and orientation decomposition capabil¬ities of the discrete wavelet transform to integrate in a single volume all the available information distributed among the set of acquired views. The work focuses in two different biomedical imaging modalities which provide such multi-view datasets. The first one is a particular fluorescence microscopy technique, Light-Sheet Fluorescence Microscopy, used for imaging and gaining understanding of the early development of live embryos from different animal models (like zebrafish or sea urchin). The second is Delayed Enhancement Magnetic Resonance Imaging, which is a valuable tool for assessing the viability of myocardial tissue on patients suffering from different cardiomyopathies. As part of this work, the proposed method was implemented and then validated on both imaging modalities. For the fluorescence microscopy application, the fusion results show improved contrast and detail discrimination when compared to any of the individual views and the method does not rely on prior knowledge of the system’s point spread function (PSF). Moreover, the results have shown improved performance with respect to previous PSF independent methods. With respect to its application to Delayed Enhancement Magnetic Resonance Imaging, the resulting fused volumes show a quantitative sharpness improvement and enable an easier and more complete interpretation of complex three-dimensional scar and heterogeneous tissue information in ischemic cardiomyopathy patients. In both applications, the results of this thesis are currently in use in the clinical and research centers with which the author collaborated during his work. An imple¬mentation of the fusion method has also been made freely available to the scientific community. Finally, an international patent application has been filed covering the visualization method developed for the Magnetic Resonance Imaging application.

Criteria for Positioning Active Multilateration Stations Located Close to Distance Measuring Equipment

The need for the use of another surveillance system when radar cannot be used is the reason for the development of the Multilateration (MLT) Systems. However, there are many systems that operate in the L-Band (960-1215MHz) that could produce interference between systems. At airports, some interference has been detected between transmissions of MLT systems (1030MHz and 1090MHz) and Distance Measuring Equipment (DME) (960-1215MHz).

Rapid prototyping for biomedical engineering: current capabilities and Challenges

A new set of manufacturing technologies has emerged in the past decades to address market requirements in a customized way and to provide support for research tasks that require prototypes. These new techniques and technologies are usually referred to as rapid prototyping and manufacturing technologies, and they allow prototypes to be produced in a wide range of materials with remarkable precision in a couple of hours. Although they have been rapidly incorporated into product development methodologies, they are still under development, and their applications in bioengineering are continuously evolving. Rapid prototyping and manufacturing technologies can be of assistance in every stage of the development process of novel biodevices, to address various problems that can arise in the devices' interactions with biological systems and the fact that the design decisions must be tested carefully. This review focuses on the main fields of application for rapid prototyping in biomedical engineering and health sciences, as well as on the most remarkable challenges and research trends.

CDAPubMed: a browser extension to retrieve EHR-based biomedical literature

Over the last few decades, the ever-increasing output of scientific publications has led to new challenges to keep up to date with the literature. In the biomedical area, this growth has introduced new requirements for professionals, e.g., physicians, who have to locate the exact papers that they need for their clinical and research work amongst a huge number of publications. Against this backdrop, novel information retrieval methods are even more necessary. While web search engines are widespread in many areas, facilitating access to all kinds of information, additional tools are required to automatically link information retrieved from these engines to specific biomedical applications. In the case of clinical environments, this also means considering aspects such as patient data security and confidentiality or structured contents, e.g., electronic health records (EHRs). In this scenario, we have developed a new tool to facilitate query building to retrieve scientific literature related to EHRs. Results: We have developed CDAPubMed, an open-source web browser extension to integrate EHR features in biomedical literature retrieval approaches. Clinical users can use CDAPubMed to: (i) load patient clinical documents, i.e., EHRs based on the Health Level 7-Clinical Document Architecture Standard (HL7-CDA), (ii) identify relevant terms for scientific literature search in these documents, i.e., Medical Subject Headings (MeSH), automatically driven by the CDAPubMed configuration, which advanced users can optimize to adapt to each specific situation, and (iii) generate and launch literature search queries to a major search engine, i.e., PubMed, to retrieve citations related to the EHR under examination. Conclusions: CDAPubMed is a platform-independent tool designed to facilitate literature searching using keywords contained in specific EHRs. CDAPubMed is visually integrated, as an extension of a widespread web browser, within the standard PubMed interface. It has been tested on a public dataset of HL7-CDA documents, returning significantly fewer citations since queries are focused on characteristics identified within the EHR. For instance, compared with more than 200,000 citations retrieved by breast neoplasm, fewer than ten citations were retrieved when ten patient features were added using CDAPubMed. This is an open source tool that can be freely used for non-profit purposes and integrated with other existing systems.

On a meaningful integration of web services in data-intensive biomedical environments: The DICODE approach

This paper reports on an innovative approach that aims to reduce information management costs in data-intensive and cognitively-complex biomedical environments. Recognizing the importance of prominent high-performance computing paradigms and large data processing technologies as well as collaboration support systems to remedy data-intensive issues, it adopts a hybrid approach by building on the synergy of these technologies. The proposed approach provides innovative Web-based workbenches that integrate and orchestrate a set of interoperable services that reduce the data-intensiveness and complexity overload at critical decision points to a manageable level, thus permitting stakeholders to be more productive and concentrate on creative activities.

Development of FEM/BEM and SEA models from experimental results for structural elements with attached equipment

This work focuses on the analysis of a structural element of MetOP-A satellite. Given the special interest in the influence of equipment installed on structural elements, the paper studies one of the lateral faces on which the Advanced SCATterometer (ASCAT) is installed. The work is oriented towards the modal characterization of the specimen, describing the experimental set-up and the application of results to the development of a Finite Element Method (FEM) model to study the vibro-acoustic response. For the high frequency range, characterized by a high modal density, a Statistical Energy Analysis (SEA) model is considered, and the FEM model is used when modal density is low. The methodology for developing the SEA model and a compound FEM and Boundary Element Method (BEM) model to provide continuity in the medium frequency range is presented, as well as the necessary updating, characterization and coupling between models required to achieve numerical models that match experimental results.

Testing equipment for the improvement of mechanical devices to minimize damage to fruit in commercial packing lines.

Damages -reduced in fruit packing lines is a major cause of grace reduction and quality loos in fresh marks: fruit. Fruit must be treated gently during in sir handling to improve their qualityin order to get a good price in a competitive market. The correct post-hardvest handling in fruit packing lines is a prerequisite to cut down the heavy post-harvest losses. Fruit packing lines must be evaluated, studying their design, the impacts applied to the fruits, the characteristics of the materials, etc. This study establishes the possibility of carrying out modifications and tests in a packing line during a long period of time. For this purpose, an experimental fruit packing line has been designed and located in the Agricultural Engineering Department of the Polythecnic University of Madrid with the aim of improving mechanical devices and fruit handling conditions to minimize damage to fruit. The experimental line consists of several transporting belts, one rollers transporter, one sizer, one elevator, one singularizer, and three trays to receive the calibrated fruit. The line has a length of 6.15 m and a width cf 1.9 m. Movement of the different components is regulated by electric motors with variable velocity electronically controlled. The height of the transfer points is variable and can be easily modified. The experimental line has been calibrated using two instrumented spheres IS 100 (8.8 cm Ø and6.2cm Ø). Average acceleration values obtained in all the transfers of the experimental line lay under 80 g's, although there is big variation for some of them being some values above 100 g's.

INFOBIOMED: European Network of Excellence on Biomedical Informatics to support individualised healthcare

INFOBIOMED is an European Network of Excellence (NoE) funded by the Information Society Directorate-General of the European Commission (EC). A consortium of European organizations from ten different countries is involved within the network. Four pilots, all related to linking clinical and genomic information, are being carried out. From an informatics perspective, various challenges, related to data integration and mining, are included.

A novel scanning lens instrument for evaluating Fresnel lens performance: equipment development and initial results

A system dedicated to the optical transmittance characterization of Fresnel lenses has been developed at NREL, in collaboration with the UPM. The system quantifies the optical efficiency of the lens by generating a performance map. The shape of the focused spot may also be analyzed to understand change in the lens performance. The primary instrument components (lasers and CCD detector) have been characterized to confirm their capability for performing optical transmittance measurements. Measurements performed on SoG and PMMA lenses subject to a variety of indoor conditions (e.g., UV and damp heat) identified differences in the optical efficiency of the evaluated lenses, demonstrating the ability of the Scanning Lens Instrument (SLI) to distinguish between the aged lenses.

Signal analysis and feature generation for pattern identification of partial discharges in high-voltage equipment

This paper proposes a method for the identification of different partial discharges (PDs) sources through the analysis of a collection of PD signals acquired with a PD measurement system. This method, robust and sensitive enough to cope with noisy data and external interferences, combines the characterization of each signal from the collection, with a clustering procedure, the CLARA algorithm. Several features are proposed for the characterization of the signals, being the wavelet variances, the frequency estimated with the Prony method, and the energy, the most relevant for the performance of the clustering procedure. The result of the unsupervised classification is a set of clusters each containing those signals which are more similar to each other than to those in other clusters. The analysis of the classification results permits both the identification of different PD sources and the discrimination between original PD signals, reflections, noise and external interferences. The methods and graphical tools detailed in this paper have been coded and published as a contributed package of the R environment under a GNU/GPL license.

Uncertainty Estimation for Performance Evaluation of a Confocal Microscope as Metrology Equipment

Both in industry and research, the quality control of micrometric manufactured parts is based on the measurement of parameters whose traceability is sometimes difficult to guarantee. In some of these parts, the confocal microscopy shows great aptitudes to characterize a measurand qualitatively and quantitatively. The confocal microscopy allows the acquisition of 2D and 3D images that are easily manipulated. Nowadays, this equipment is manufactured by many different brands, each of them claiming a resolution probably not in accord to their real performance. The Laser Center (Technical University of Madrid) has a confocal microscope to verify the dimensions of the micro mechanizing in their own research projects. The present study pretends to confirm that the magnitudes obtained are true and reliable. To achieve this, a methodology for confocal microscope calibration is proposed, as well as an experimental phase for dimensionally valuing the equipment by 4 different standard positions, with its seven magnifications and the six objective lenses that the equipment currently has, in the x–y and z axis. From the results the uncertainty will be estimated along with an effect analysis of the different magnifications in each of the objective lenses.

Rapid prototyping of multi-scale biomedical microdevices by combining additive manufacturing technologies

The possibility of designing and manufacturing biomedical microdevices with multiple length-scale geometries can help to promote special interactions both with their environment and with surrounding biological systems. These interactions aim to enhance biocompatibility and overall performance by using biomimetic approaches. In this paper, we present a design and manufacturing procedure for obtaining multi-scale biomedical microsystems based on the combination of two additive manufacturing processes: a conventional laser writer to manufacture the overall device structure, and a direct-laser writer based on two-photon polymerization to yield finer details. The process excels for its versatility, accuracy and manufacturing speed and allows for the manufacture of microsystems and implants with overall sizes up to several millimeters and with details down to sub-micrometric structures. As an application example we have focused on manufacturing a biomedical microsystem to analyze the impact of microtextured surfaces on cell motility. This process yielded a relevant increase in precision and manufacturing speed when compared with more conventional rapid prototyping procedures.

Permanent deformation estimates of dynamic equipment foundations: Application to a gas turbine in granular soils

Permanent displacements of a gas turbine founded on a fine, poorly graded, and medium density sand are studied. The amplitudes and modes of vibration are computed using Barkan´s formulation, and the “High-Cycle Accumulation” (HCA) model is employed to account for accumulated deformations due to the high number of cycles. The methodology is simple: it can be easily incorporated into standard mathematical software, and HCA model parameters can be estimated based on granulometry and index properties. Special attention is devoted to ‘transient’ situations at equipment´s start-up, during which a range of frequencies – including frequencies that could be similar to the natural frequencies of the ground – is traversed. Results show that such transient situations could be more restrictive than stationary situations corresponding to normal operation. Therefore, checking the stationary situation only might not be enough, and studying the influence of transient situations on computed permanent displacements is needed to produce a proper foundation design

Equipment and procedures for ON-SITE testing of PV plants and BIPV

Actual system performance of a PV system can differ from its expected behaviour.. This is the main reason why the performance of PV systems should be monitored, analyzed and, if needed, improved on. Some of the current testing procedures relating to the electrical behaviour of PV systems are appropriated for detecting electrical performance losses, but they are not well-suited to reveal hidden defects in the modules of PV plants and BIPV, which can lead to future losses. This paper reports on the tests and procedures used to evaluate the performance of PV systems, and especially on a novel procedure for quick on-site measurements and defect recognition caused by overheating in PV modules located in operating PV installations.

Thermoelectric assessment of laser peening induced effects on a metallic biomedical Ti6Al4V

Laser peening has recently emerged as a useful technique to overcome detrimental effects associated to another well-known surface modification processes such as shot peening or grit blasting used in the biomedical field. It is worth to notice that besides the primary residual stress effect, thermally induced effects might also cause subtle surface and subsurface microstructural changes that might influence corrosion resistance. Moreover, since maximum loads use to occur at the surface, they could also play a critical role in the fatigue strength. In this work, plates of Ti-6Al-4V alloy of 7 mm in thickness were modified by laser peening without using a sacrificial outer layer. Irradiation by a Q-switched Nd-YAG laser (9.4 ns pulse length) working in fundamental harmonic at 2.8 J/pulse and with water as confining medium was used. Laser pulses with a 1.5 mm diameter at an equivalent overlapping density (EOD) of 5000 cm-2 were applied. Attempts to analyze the global induced effects after laser peening were addressed by using the contacting and non-contacting thermoelectric power (TEP) techniques. It was demonstrated that the thermoelectric method is entirely insensitive to surface topography while it is uniquely sensitive to subtle variations in thermoelectric properties, which are associated with the different material effects induced by different surface modification treatments. These results indicate that the stress-dependence of the thermoelectric power in metals produces sufficient contrast to detect and quantitatively characterize regions under compressive residual stress based on their thermoelectric power contrast with respect to the surrounding intact material. However, further research is needed to better separate residual stress effects from secondary material effects, especially in the case of low-conductivity engineering materials like titanium alloys.