Dissertations / Theses on the topic 'Infrared Diagnosis'

Hypothesis: NIRS can be used as a reliable method for the detection of an acute compartment syndrome. Methods:  1) A prospective clinical trial of 102 patients at risk of an ACS. Continuous invasive pressure and NIRS measurements were recorded and compared. 2) A porcine model of 15 animals to investigate the influence of a subcutaneous and intra-muscular haematoma on the ability of NIRS to detect an ACS. 3) Two studies of volunteer subjects investigated the relationship between adipose thickness, measured by ultrasound, and the values of StO₂ provided by NIRS. Results: 1) Correlation was observed between StO₂ and compartment pressure. Calculating the StO₂ difference between the injured and un-injured limbs reduced the inter-patient variability. 2) The presence of a sub-cutaneous haematoma increased the StO₂ value. 3) The StO₂ value over the leg correlated with adipose thickness and total tissue haemoglobin. Conclusions: Inter-patient variations in StO₂ made interpretation of clinical data difficult. The presence of a subcutaneous haematoma could cause a false negative diagnosis of ACS by elevating the StO₂ value. The quantitative use of NIRS to measure StO₂ could be improved by calibrating for adipose thickness.

Carcinome hépatocellulaire (CHC) est le sixième cancer et la deuxième cause de mortalité par cancer dans le monde. Dans la majorité des cas, le CHC se développe sur une maladie chronique associée à des étiologies variées telles que l'infection par le virus de l'hépatite B ou l’hépatite C, la consommation excessive d'alcool et des maladies métaboliques. Le développement des maladies chroniques du foie qui conduisent à la cirrhose puis au cancer induisent des modifications de la composition chimique des cellules et des tissus. En effet, la carcinogenèse hépatique est un processus en plusieurs étapes caractérisé par la progression de nodules de régénération, de nodules dysplasiques de bas grade puis de grade et enfin du CHC. Le traitement du CHC reste difficile et la transplantation du foie est la seule option thérapeutique curative à long terme. Le problème est qu'il n'y a pas de marqueur objectifs et quantifiables pour contrôler la qualité d’un greffon. Des biomarqueurs spécifiques marquant la progression du CHC font également défauts.Dans ce travail de thèse, nous avons évalué l’intérêt de la microspectroscopie infrarouge (IR) pour le diagnostic de la stéatose, qui est le facteur le plus important affectant la reprise de la fonction hépatique après greffe de foie. La microspectroscopie infrarouge permet de détecter de façon qualitative et quantitative les caractéristiques biochimiques liées aux différents constituants moléculaires présents dans l'échantillon biologique. Nos travaux ont montré que la progression de la stéatose hépatique correspond non seulement à l'accumulation de lipides, mais également à des changements spectaculaires dans la composition qualitative du tissu. En effet, le bas grade de stéatose présente une diminution de la teneur en glycogène et une augmentation concomitante de lipides par rapport au foie normal. La stéatose intermédiaire montre une augmentation de glycogène et des changements majeurs sont observés en ce qui concerne les lipides, avec une contribution significative des acides gras estérifiés, des chaînes de carbone allongées et des lipides insaturés. Ces caractéristiques sont encore plus prononcées dans les hauts degrés de stéatose. De plus, nous avons mis en évidence que des changements biochimiques majeurs se produisent dans la partie non-stéatosique du tissu malgré son aspect normal sur le plan histologique, ce qui suggère que l’organe dans son ensemble reflète le degré de la stéatose.La deuxième partie de la thèse est focalisée la carcinogenèse hépatique. Il s’agit d’un processus en plusieurs étapes qui se caractérise dans la plupart des foies cirrhotiques par la progression de nodules hyperplasiques de régénération vers des lésions précancéreuses telles que les nodules dysplasiques de bas grade puis de haut grade et enfin le CHC. Le diagnostic différentiel entre nodules dysplasiques en particulier de haut garde et CHC reste extrêmement difficile. Nous avons abordé le potentiel de la microspectroscopie IR pour le diagnostic des nodules cirrhotiques. Nous avons observé de profondes modifications de la composition biochimique du foie pathologique. En effet, des changements importants ont été détectés dans la composition des lipides, des protéines et des sucres mettant en évidence la reprogrammation métabolique dans la carcinogenèse. Les principaux changements ont été observés dans le domaine de fréquence 950-1480 cm-1 dans lequel plusieurs bandes permettaient la discrimination des nodules cirrhotiques, dysplasiques et tumoraux. Enfin, nous avons montré que le diagnostic peut être réalisé à l’aide d’un microscope de laboratoire qui peut être facilement mis en œuvre en milieu hospitalier<br>Hepatocellular carcinoma (HCC) is the sixth most common neoplasm and the second most common cause of death in the world. Hepatocarcinogenesis is a multistep process characterized in patients with chronic liver diseases by a spectrum of hepatic nodules that mark the progression from regenerative nodules to dysplastic lesions followed by HCC. Liver transplantation remains the curative therapeutic option able to treat both the HCC and the underlying liver disease. The issue is that there is no objective and quantifiable marker for quality control of liver graft. Specific biomarkers of early stages of HCC are also an unmet need.In this study, we have evaluated the potential of infrared (IR) microspectroscopy for the diagnosis of steatosis, one of the most important factors affecting the liver allograft function. Vibrational microspectroscopy, such as Fourier transform infrared microspectroscopy (FTIR), allows detecting spectral characteristics associated with different molecular components present in the biological sample, both qualitatively and quantitatively. Our first working hypothesis was that the progression of liver steatosis corresponds not only to the accumulation of lipids but also to dramatic changes in the qualitative composition of tissue. Indeed, a lower grade of steatosis showed a decrease in glycogen content and concomitant increase in lipids in comparison with normal liver. Intermediate steatosis exhibited an increase in glycogen and major changes in lipids, with a significant contribution of esterified fatty acids with elongated carbon chains and unsaturated lipids, and these features were more pronounced in a high grade of steatosis. Furthermore, we have shown, that FTIR approach allows a systemic discrimination of morphological features, leading to a separate investigation of steatotic vesicles and the non-steatotic counterpart of the tissue. This highlighted the fact that dramatic biochemical changes occur in the non-steatotic part of the tissue also despite its normal histological aspect, suggesting that the whole tissue reflects the grade of steatosis. The second part of the thesis focused on hepatocarcinogenesis; a multistep process that is characterized in most cirrhotic livers by the progression from hyperplastic regenerative nodules to low grade dysplastic nodules (LGDN), high grade dysplastic nodules (HGDN) and finally small HCC which corresponds either to vaguely nodular well differentiated HCC so called early HCC or to distinctly nodular moderately differentiated hepatocellular carcinomas. Since the differential diagnosis between precancerous dysplastic nodules and early HCC remains extremely difficult, we addressed the potential of FTIR microspectroscopy for grading cirrhotic nodules. The study was focused on 39 surgical specimens including normal livers as controls, dysplastic nodules, early HCC and the progressed HCC. Profound alterations of the biochemical composition of the pathological liver were demonstrated by FTIR microspectroscopy. Indeed, dramatic changes were observed in lipids, proteins and sugars highlighting the metabolic reprogramming in carcinogenesis. The major changes were observed in the frequency domain 950-1480 cm-1 in which several bands allowed significant discrimination of cirrhotic nodules, dysplastic lesions and HCC. Finally, a significant discrimination between benign, dysplastic nodules and early HCC remained possible using a FTIR microscope equipped with a laboratory-based infrared source that can be easily implemented in hospital environment. In conclusion, our study positions FTIR microspectroscopy as a versatile and powerful approach for investigating liver diseases, such as steatosis, dysplastic lesions and cancer. Further studies on larger series of patients as well as on biopsies will allow confirming the clinical reliability of such spectral signatures. Therefore, we anticipate that FTIR microspectroscopy will open new avenue in clinical diagnosis

Mid-infrared (MIR) spectroscopy has been recognized as an important analytical technique, and is widely applied for qualitative and quantitative analysis of materials with an increasing interest in addressing complex organic or biologic constituents. In the presented thesis, (a) the fundamental principles for IR spectroscopic applications via in vivo catheters in combination with multivariate data analysis technique were developed, and (b) the combination with a second analytical technique ¨C scanning electrochemical microscopy (SECM) - for enhancing the information obtained at complex or frequently changing matrices was demonstrated. The first part of this thesis focused on the combination of different MIR measurment techniques with specific focus on evanescent field absorption spectroscopy along with multivariate data analysis methods, for the discrimination of atherosclerotic and normal rabbit aorta tissues. Atherosclerotic and normal rabbit aorta tissues are characterized by marked differences in chemical composition governed by their water, lipid, and protein content. Strongly overlapping infrared absorption features of the different constituents and the complexity of the tissue matrix render the direct evaluation of molecular spectroscopic characteristics obtained from IR measurements challenging for classification. We have successfully applied multivariate data analysis and classification techniques based on principal component analysis (PCA), partial least squares regression (PLS), and linear discriminant analysis (LDA) to IR spectroscopic data obtained by infrared attenuated total reflectance (IR-ATR) measurements, reflection IR microscopy, and a recently developed IR-ATR catheter prototype for future in vivo diagnostic applications. Training and test data were collected ex vivo at atherosclerotic and normal rabbit aorta samples. The successful classification results at atherosclerotic and normal aorta samples utilizing the developed data evaluation routines reveals the potential of IR spectroscopy combined with multivariate classification strategies for in vitro, and ¨C in future - in vivo applications. The second part of this thesis aimed at the development of a novel multifunctional analytical platform by combining SECM with single-bounce IR-ATR spectroscopy for in situ studies of electrochemically active or electrochemically induced processes at the IR waveguide surface via simultaneous evanescent field absorption spectroscopy. The utility of the developed SECM-IR-ATR platform was demonstrated by spectroscopically monitoring microstructured polymer depositions induced via feedback mode SECM experiments using a 25μm Pt disk ultramicroelectrode (UME). The surface of a ZnSe ATR crystal was coated with a thin layer of 2,5-di-(2-thienyl)-pyrrole (SNS), which was then polymerized in a Ru(bpy) ₃ ² ⁺-mediated feedback mode SECM experiment. The polymerization reaction was simultaneously spectroscopically monitored by recording the absorption intensity changes of specific IR bands characteristic for SNS, thereby providing information on the polymerization progress, mechanism, and level of surface modification. Furthermore, a novel current-independent approach mechanism for positioning the UME in aqueous electrolyte solution was demonstrated by monitoring IR absorption changes of borosilicate glass (BSG) shielding the UME, and of water within the penetration depth of the evanescent field.

Neonatal necrotizing enterocolitis (NEC) is one of the most severe digestive tract emergencies in neonates, involving bowel edema, hemorrhage, and necrosis, and can lead to serious complications including death. Since it is difficult to diagnose early, the morbidity and mortality rates are high due to severe complications in later stages of NEC and thus early detection is key to the treatment of NEC. In this thesis, a novel automatic image acquisition and analysis system combining a color and depth (RGB-D) sensor with an infrared (IR) camera is proposed for NEC diagnosis. A design for sensors configuration and a data acquisition process are introduced. A calibration method between the three cameras is described which aims to ensure frames synchronization and observation consistency among the color, depth, and IR images. Subsequently, complete segmentation procedures based on the original color, depth, and IR information are proposed to automatically separate the human body from the background, remove other interfering items, identify feature points on the human body joints, distinguish the human torso and limbs, and extract the abdominal region of interest. Finally, first-order statistical analysis is performed on thermal data collected over the entire extracted abdominal region to compare differences in thermal data distribution between different patient groups. Experimental validation in a real clinical environment is reported and shows encouraging results.

Prostate cancer is a biologically heterogenous disease with considerable variation in clinical aggressiveness. Gleason grade, the universally accepted method for classification of prostate cancer, is subjective and gives limited predictive information regarding prostate cancer progression. There is a clinical need for an objective, reliable tool to help pathologists improve current prostate tissue analysis methods and better assess the malignant potential of prostate tumours. Fourier Transform Infrared (FTIR) microspectroscopy is a powerful bioanalytical technique that uses infrared light to interrogate biological tissue. The studies detailed in this thesis examine the ability of FTIR combined with multivariate analysis to discriminate between benign, premalignant and malignant prostate pathology in snap frozen, paraffinated and deparaffinated tissue. Prostate tissue was collected during and after urological procedures performed between 2005 and 2008. The tissue was analysed utilising a bench top FTIR system in point and image mapping modes. The histology under interrogation was identified by a uro- pathologist. Multivariate analysis was applied to the spectral dataset obtained. FTIR performance was evaluated. FTIR was able to reproducibly discriminate between benign and malignant prostate tissue in a pilot study. Cross validated diagnostic algorithms, constructed from the spectral dataset in this experiment, achieved sensitivities and specificities of 95% and 89% respectively. FTIR analysis of transverse paraffinated and deparaffinated radical prostatectomy sections achieved good differentiation of the benign, premalignant and malignant pathology groups. However the performance of diagnostic algorithms constructed from this dataset under cross validation was poor. The work in this thesis illustrates the potential of FTIR to provide an objective method to assist the pathologist in the assessment of prostate samples. The limitations of the technique and directions for future work are presented.

One of the largest challenges within modern medicine is the increase in global cancer rates especially in western countries, which is often attributed to ageing populations, dietary and lifestyle changes. One of the fastest growing cancers within the western world is oesophageal cancer, which without reliable early diagnosis is often fatal due to the cancer spreading. It is therefore crucial for the development of reliable methods and tools for early cancer detection. This is especially important for those who are most at risk, which includes Barrett's oesophagus patients. Infrared (IR) spectroscopy techniques have been proven capable of gaining large amounts of information on the chemical composition of biological samples. This thesis therefore focuses on using a variety of IR spectroscopy techniques, including Fourier transform infrared spectroscopy (FTIR) and scanning near-field optical microscopy (SNOM) to image oesophageal samples, tissue biopsies and cell line samples. The thesis demonstrates how machine learning algorithms can be used in conjunction with FTIR to provide a quick, non-biased tissue diagnostic method, free from the issues associated with current histology techniques. As well as focusing on the processing of FTIR data, the thesis will assess the ability of an aperture SNOM to image biological samples as it is able to achieve diffraction limit breaking spatial resolutions and has to potential to give previously impossible insights.

Bioengineering<br>M.S.<br>Raman spectroscopy is an effective optical analysis of the biochemically specific characterization of tissues without contrast agents or exogenous dyes. Applications of Raman spectroscopy include analysis and biomarker investigation, disease diagnosis and surgical guidance. One major challenge in Raman spectroscopy is removing inherent fluorescence background present in samples to acquire Raman signatures. In some tissues, like liver, kidney and darkly pigment skin, the auto-fluorescence background is strong enough to overwhelm the Raman peaks in conventional Near-Infrared (NIR) Raman systems. Recent publications have shown that using Raman systems with excitation sources with wavelengths beyond 830 nm and short-wave infrared (SWIR) InGaAs Array detectors resulted in dramatically reduced auto-fluorescence. The unique characteristics of Raman signals collected from SWIR systems versus NIR Raman systems requires inspection of the suitability of spectral pre-processing techniques. This thesis focused on the development of spectral processing techniques at three different steps; 1) detector background & noise reduction; 2) Auto-fluorescence background subtraction; 3) detection of outlier measurements to assist statistical classification. Detector background and noise reduction was compared between two different techniques, and a direct subtraction method resulted in better performance to reduce fixed pattern noise unique to InGaAs arrays. For the aim 2, three different algorithms for fluorescence background removal were developed, and a modified polynomial fitting method was found to be most appropriate for the low signal-to-noise (SNR) spectra. Finally, local outlier factor(LOF), a multivariate statistical outlier metric, was implemented in a two-stage fashion, and shown to be effective at identifying raw measurement errors and Raman spectra outliers. The overall outcome of this thesis was the evaluation of spectral processing techniques for SWIR Raman spectroscopy systems, and the development of specific techniques to optimize data quality and best prepare spectra for statistical analysis.<br>Temple University--Theses

This thesis presents work on the development of two distinct systems for the purpose of spectral imaging in the mid infrared (MIR), with particular focus on a method than can be of use in cancer diagnosis. Wavelengths are used that correspond to positions of absorbance peaks from the vibrational modes in molecules commonly found in biological tissue. Images from different wavelengths are combined to show the relative concentration of nuclei in tissue, an accepted marker of malignancy that can be seen in cancerous cells. One system, we have termed the 'digistain' system, uses a thermal source with narrow bandpass filters to select the wavelength, the other uses a pulsed tuneable quantum cascade laser (QCL) unit. Both systems show results that highlight a difference between healthy epithelium and epithelium that has entered a pre-cancerous stage. The digistain system has benefits in speed over other infrared spectral imaging systems, such as a scanning Raman system or a commercial multi-channel Fourier transform infrared (FTIR) system. Before a reliable direct comparison of the quantitative results of the digistain to histological grading of the same areas can be made, a method to identify the different tissue types that are present and mixed together must be created. The QCL system was also used for diffuse reflection imaging, with the conclusion that the differing surface roughness of the samples investigated played a larger role in creating contrast between areas of different chemical composition than did absorption.

Thesis (Ph.D.)--Boston University<br>Coronary artery disease accounts for nearly 50% of cardiovascular disease, the leading cause of death in the United States. The progression of atherosclerotic plaque is not yet fully understood. Histopathologic analysis of cadaver coronary plaques has suggested that certain subsets of coronary lesions, the vulnerable plaques, predispose patients to myocardial infarction. Prospective identification and treatment of vulnerable plaques has emerged as an important future goal for intravascular imaging and intervention. However, no single imaging modality has been shown to be capable of definitively identifying these lesions. Optical coherence tomography is a catheter-based imaging method that rapidly acquires three-dimensional images of coronary artery wall microstructure. While OCT has been documented to be capable of visualizing morphologic features associated with vulnerable plaques, it has not been shown to identify necrotic core or other putative chemicals/molecules associated with plaque progression and rupture. One solution is to add a secondary modality to OCT which detects molecules specific to necrotic cores. While conducting bench top spectroscopy measurements, our laboratory discovered that the intensity of near-infrared autofluorescence (NIRAF) is associated with plaque types. Using benchtop spectroscopy, this dissertation research established the relationship between the NIRAF signal intensity and spectral shape and atherosclerosis, and demonstrated its potential to differentiate necrotic core plaques from other arterial lesions. In addition to these spectroscopy-disease correlations, this thesis describes research conducted to identify the chemical/molecular origin of the NIRAF signal, using histopathology, confocal microscopy, spectroscopy, and chemical synthesis. The results indicate that protein modification in necrotic core is a potential mechanism for high NIRAF in advanced plaques. To translate OCT-NIRAF clinically, this dissertation describes the design of a double clad fiber that enables catheter-based detection of both OCT and NIRAF and a safety study to demonstrate that NIRAF excitation does not damage the artery wall. A preclinical OCT-NIRAF catheter was fabricated and used to image human coronary arteries ex vivo. These data showed that vulnerable plaques can potentially be identified using intracoronary OCT-NIRAF. The sum total of results from this thesis reseatch demonstrate the feasibility of conducting OCT-NIRAF imaging in human patients for the prospective identification ofvulnerable coronary plaques.

Mestrado em Biomedicina Molecular<br>Nowadays it is still difficult to perform an early and accurate diagnosis of dementia, therefore many research focus on the finding of new dementia biomarkers that can aid in that purpose. So scientists try to find a noninvasive, rapid, and relatively inexpensive procedures for early diagnosis purpose. Several studies demonstrated that the utilization of spectroscopic techniques, such as Fourier Transform Infrared Spectroscopy (FTIR) and Raman spectroscopy could be an useful and accurate procedure to diagnose dementia. As several biochemical mechanisms related to neurodegeneration and dementia can lead to changes in plasma components and others peripheral body fluids, blood-based samples and spectroscopic analyses can be used as a more simple and less invasive technique. This work is intended to confirm some of the hypotheses of previous studies in which FTIR was used in the study of plasma samples of possible patient with AD and respective controls and verify the reproducibility of this spectroscopic technique in the analysis of such samples. Through the spectroscopic analysis combined with multivariate analysis it is possible to discriminate controls and demented samples and identify key spectroscopic differences between these two groups of samples which allows the identification of metabolites altered in this disease. It can be concluded that there are three spectral regions, 3500-2700 cm -1, 1800-1400 cm-1 and 1200-900 cm-1 where it can be extracted relevant spectroscopic information. In the first region, the main conclusion that is possible to take is that there is an unbalance between the content of saturated and unsaturated lipids. In the 1800-1400 cm-1 region it is possible to see the presence of protein aggregates and the change in protein conformation for highly stable parallel β-sheet. The last region showed the presence of products of lipid peroxidation related to impairment of membranes, and nucleic acids oxidative damage. FTIR technique and the information gathered in this work can be used in the construction of classification models that may be used for the diagnosis of cognitive dysfunction.<br>Atualmente, não é possível fazer um diagnóstico precoce e diferencial da doença de Alzheimer, deste modo, é necessário encontrar biomarcadores que o permitam. Para isso, os cientistas tentam encontrar um procedimento nãoinvasivo, rápido, e relativamente barato. Os resultados de vários estudos demonstraram que a utilização de técnicas espectroscópicas, tais como a Espectroscopia de Infravermelho Transformada de Fourier (FTIR) e / ou espectroscopia de Raman, podem ser ferramentas úteis para diagnosticar a DA. Uma vez que, na DA, alguns mecanismos bioquímicos podem levar a mudanças em componentes do plasma, podem então ser utilizadas amostras de sangue nas análises espectroscópicas o que torna a técnica simples e menos invasiva. Com este trabalho pretende-se confirmar algumas das hipóteses de estudos anteriores em que o FTIR foi usado no estudo de amostras de plasma de possíveis doentes com DA e respetivos controlos e verificar a reprodutibilidade desta técnica espectroscópica na análise deste tipo de amostras. Através da análise espectroscopia combinada com análise multivariada é possível discriminar as amostras controlos e dementes e identificar as principais diferenças espectroscópicas entre estes dois grupos de amostras que permitem identificar os metabolitos alterados nesta patologia. Pode-se concluir que existem três regiões espectrais, 3500-2700 cm-1, 18001400 cm-1 e 1200-900 cm-1 onde se pode extrair informação espectroscópica relevante. Na primeira região, a principal conclusão que é possível tirar é que há um desequilíbrio entre o teor de lípidos saturados e insaturados. Na região entre 1800-1400 cm-1, é possível observar a presença de agregados de proteínas e a alteração na conformação das proteínas para folha β paralela altamente estável. A última região revelou a presença de produtos de peroxidação lipídica relacionados com a insuficiência de membranas, e danos oxidativos nos ácidos nucleicos. A técnica de FTIR e a informação reunida neste trabalho pode ser utilizada na construção de modelos de classificação que possam vir a ser utilizados para o diagnóstico de disfunções cognitivas.

A number of biomedical studies have shown that mid-infrared spectroscopic images can provide both morphological and biochemical information that can be used for the diagnosis of cancer. Whilst this technique has shown great potential it has yet to be employed by the medical profession. By replacing the conventional broadband thermal source employed in modern FTIR spectrometers with high-brightness, broadly tuneable laser based sources (QCLs and OPGs) we aim to solve one of the main obstacles to the transfer of this technology to the medical arena; namely poor signal to noise ratios at high spatial resolutions and short image acquisition times. In this thesis we take the first steps towards developing the optimum experimental configuration, the data processing algorithms and the spectroscopic image contrast and enhancement methods needed to utilise these high intensity laser based sources. We show that a QCL system is better suited to providing numerical absorbance values (biochemical information) than an OPG system primarily due to the QCL pulse stability. We also discuss practical protocols for the application of spectroscopic imaging to cancer diagnosis and present our spectroscopic imaging results from our laser based spectroscopic imaging experiments of oesophageal cancer tissue.

Gamification is an emerging phenomenon that has been advocated for its potential to improve organisational outcomes. The present study aimed to examine the effect of gamification in a perceptual diagnosis task. Forty participants completed a 22-minute visual search task. To investigate the role of game mechanics participants were divided into four conditions resulting from the factorial combination of the narrative mechanic (narrative and control condition) and the points mechanic (Points and no-points control condition). Attention effort, motivation, and work engagement were measured through performance metrics, functional near-infrared spectroscopy (fNIRS), and self-report questionnaires. The results revealed points significantly increased task performance while narrative significantly increased intrinsic motivation and prefrontal oxygenation. These findings may provide much needed contributions to the literature surrounding gamification. It was also revealed that fNIRS measures of frontal activation may be a reasonable objective indicator of initial cognitive effort. This presents significant real world applications for objectively measuring motivation.

Optical imaging is an emerging technology towards non-invasive breast cancer diagnostics. In recent years, portable and patient comfortable hand-held optical imagers are developed towards two-dimensional (2D) tumor detections. However, these imagers are not capable of three-dimensional (3D) tomography because they cannot register the positional information of the hand-held probe onto the imaged tissue. A hand-held optical imager has been developed in our Optical Imaging Laboratory with 3D tomography capabilities, as demonstrated from tissue phantom studies. The overall goal of my dissertation is towards the translation of our imager to the clinical setting for 3D tomographic imaging in human breast tissues. A systematic experimental approach was designed and executed as follows: (i) fast 2D imaging, (ii) coregistered imaging, and (iii) 3D tomographic imaging studies. (i) Fast 2D imaging was initially demonstrated in tissue phantoms (1% Liposyn solution) and in vitro (minced chicken breast and 1% Liposyn). A 0.45 cm3 fluorescent target at 1:0 contrast ratio was detectable up to 2.5 cm deep. Fast 2D imaging experiments performed in vivo with healthy female subjects also detected a 0.45 cm3 fluorescent target superficially placed ~2.5 cm under the breast tissue. (ii) Coregistered imaging was automated and validated in phantoms with ~0.19 cm error in the probe’s positional information. Coregistration also improved the target depth detection to 3.5 cm, from multi-location imaging approach. Coregistered imaging was further validated in-vivo, although the error in probe’s positional information increased to ~0.9 cm (subject to soft tissue deformation and movement). (iii) Three-dimensional tomography studies were successfully demonstrated in vitro using 0.45 cm3 fluorescence targets. The feasibility of 3D tomography was demonstrated for the first time in breast tissues using the hand-held optical imager, wherein a 0.45 cm3 fluorescent target (superficially placed) was recovered along with artifacts. Diffuse optical imaging studies were performed in two breast cancer patients with invasive ductal carcinoma. The images showed greater absorption at the tumor cites (as observed from x-ray mammography, ultrasound, and/or MRI). In summary, my dissertation demonstrated the potential of a hand-held optical imager towards 2D breast tumor detection and 3D breast tomography, holding a promise for extensive clinical translational efforts.

Submitted by Claudinei Pracidelli (cpracide@ipen.br) on 2015-08-07T14:13:11Z No. of bitstreams: 0<br>Made available in DSpace on 2015-08-07T14:13:11Z (GMT). No. of bitstreams: 0<br>Tese (Doutorado em Tecnologia Nuclear)<br>IPEN/T<br>Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP

Every year approximately 2800 Swedes are diagnosed with malignant melanoma, the form of cancer that is most rapidly increasing in incidence in the Western world. The earlier we can identify and diagnose a malignant melanoma, the better is the prognosis. In Sweden, 155 000 benign naevi, harmless skin tumours or moles, are surgically excised each year, many of them because melanoma cannot be dismissed by non-invasive methods. The excisions result in substantial medical costs and cause unrest and suffering of the individual patient. For untrained physicians, it is often difficult to make an accurate diagnosis of melanoma, thus a tool that could help to strengthen the diagnosis of suspected melanomas would be highly valuable. This thesis describes the development and assessment of a non-invasive method for early skin cancer detection. Using near infrared (NIR) and skin impedance spectroscopy, healthy and diseased skin of various subjects was examined to develop a new instrument for detecting malignant melanoma. Due to the complex nature of skin and the numerous variables involved, the spectroscopic data were analysed multivariately using Principal Component Analysis (PCA) and partial leas square discriminant analysis (PLS-DA). The reproducibility of the measurements was determined by calculating Scatter Values (SVs), and the significance of separations between overlapping groups in score plots was determined by calculating intra-model distances. The studies indicate that combining skin impedance and NIR spectroscopy measurements adds value, therefore a new probe-head for simultaneous NIR and skin impedance measurements was introduced. Using both spectroscopic techniques it was possible to separate healthy skin at one body location from healthy skin at another location due to the differences in skin characteristics at various body locations. In addition, statistically significant differences between overlapping groups of both age and gender in score plots were detected. However, the differences in skin characteristics at different body locations had stronger effects on the measurements than both age and gender. Intake of coffee and alcohol prior to measurement did not significantly influence the outcome data. Measurements on dysplastic naevi were significantly separated in a score plot and the influence of diseased skin was stronger than that of body location. This was confirmed in a study where measurements were performed on 12 malignant melanomas, 19 dysplastic naevi and 19 benign naevi. The malignant melanomas were significantly separated from both dysplastic naevi and benign naevi. Overall, the presented findings show that the instrument we have developed provides fast, reproducible measurements, capable of distinguishing malignant melanoma from dysplastic naevi and benign naevi non-invasively with 83% sensitivity and 95% specificity. Thus, the results are highly promising and the instrument appears to have high potential diagnostic utility.

El diagnóstico final de la mayoría de tipos de cáncer lo realiza un médico experto en anatomía patológica que examina muestras tisulares o celulares sospechosas extraídas del paciente. Actualmente, esta evaluación depende en gran medida de la experiencia del médico y se lleva a cabo de forma cualitativa mediante técnicas de imagen tradicionales como la microscopía óptica. Esta tarea tediosa está sujeta a altos grados de subjetividad y da lugar a niveles de discordancia inadecuados entre diferentes patólogos, especialmente en las primeras etapas de desarrollo del cáncer. La espectroscopía infrarroja por Transformada de Fourier (siglas FTIR en inglés) es una tecnología ampliamente utilizada en la industria que recientemente ha demostrado una capacidad creciente para mejorar el diagnóstico de diferentes tipos de cáncer. Esta técnica aprovecha las propiedades del infrarrojo medio para excitar los modos vibratorios de los enlaces químicos que forman las muestras biológicas. La principal señal generada consiste en un espectro de absorción que informa sobre la composición química de la muestra iluminada. Los microespectrómetros FTIR modernos, compuestos por complejos componentes ópticos y detectores matriciales de alta sensibilidad, permiten capturar en un laboratorio de investigación común imágenes hiperespectrales de alta calidad que aúnan información química y espacial. Las imágenes FTIR son estructuras de datos ricas en información que se pueden analizar individualmente o junto con otras modalidades de imagen para realizar diagnósticos patológicos objetivos. Por lo tanto, esta técnica de imagen emergente alberga un alto potencial para mejorar la detección y la graduación del riesgo del paciente en el cribado y vigilancia de cáncer. Esta tesis estudia e implementa diferentes metodologías y algoritmos de los campos interrelacionados de procesamiento de imagen, visión por ordenador, aprendizaje automático, reconocimiento de patrones, análisis multivariante y quimiometría para el procesamiento y análisis de imágenes hiperespectrales FTIR. Estas imágenes se capturaron con un moderno microscopio FTIR de laboratorio a partir de muestras de tejidos y células afectadas por cáncer colorrectal y de piel, las cuales se prepararon siguiendo protocolos alineados con la práctica clínica actual. Los conceptos más relevantes de la espectroscopía FTIR se investigan profundamente, ya que deben ser comprendidos y tenidos en cuenta para llevar a cabo una correcta interpretación y tratamiento de sus señales especiales. En particular, se revisan y analizan diferentes factores fisicoquímicos que influyen en las mediciones espectroscópicas en el caso particular de muestras biológicas y pueden afectar críticamente su análisis posterior. Todos estos conceptos y estudios preliminares entran en juego en dos aplicaciones principales. La primera aplicación aborda el problema del registro o alineación de imágenes hiperespectrales FTIR con imágenes en color adquiridas con microscopios tradicionales. El objetivo es fusionar la información espacial de distintas muestras de tejido medidas con esas dos modalidades de imagen y centrar la discriminación en las regiones seleccionadas por los patólogos, las cuales se consideran más relevantes para el diagnóstico de cáncer colorrectal. En la segunda aplicación, la espectroscopía FTIR se lleva a sus límites de detección para el estudio de las entidades biomédicas más pequeñas. El objetivo es evaluar las capacidades de las señales FTIR para discriminar de manera fiable diferentes tipos de células de piel que contienen fenotipos malignos. Los estudios desarrollados contribuyen a la mejora de métodos de decisión objetivos que ayuden al patólogo en el diagnóstico final del cáncer. Además, revelan las limitaciones de los protocolos actuales y los problemas intrínsecos de la tecnología FTIR moderna, que deberían abordarse para permit<br>The final diagnosis of most types of cancers is performed by an expert clinician in anatomical pathology who examines suspicious tissue or cell samples extracted from the patient. Currently, this assessment largely relies on the experience of the clinician and is accomplished in a qualitative manner by means of traditional imaging techniques, such as optical microscopy. This tedious task is subject to high degrees of subjectivity and gives rise to suboptimal levels of discordance between different pathologists, especially in early stages of cancer development. Fourier Transform infrared (FTIR) spectroscopy is a technology widely used in industry that has recently shown an increasing capability to improve the diagnosis of different types of cancer. This technique takes advantage of the ability of mid-infrared light to excite the vibrational modes of the chemical bonds that form the biological samples. The main generated signal consists of an absorption spectrum that informs of the chemical composition of the illuminated specimen. Modern FTIR microspectrometers, composed of complex optical components and high-sensitive array detectors, allow the acquisition of high-quality hyperspectral images with spatially-resolved chemical information in a common research laboratory. FTIR images are information-rich data structures that can be analysed alone or together with other imaging modalities to provide objective pathological diagnoses. Hence, this emerging imaging technique presents a high potential to improve the detection and risk stratification in cancer screening and surveillance. This thesis studies and implements different methodologies and algorithms from the related fields of image processing, computer vision, machine learning, pattern recognition, multivariate analysis and chemometrics for the processing and analysis of FTIR hyperspectral images. Those images were acquired with a modern benchtop FTIR microspectrometer from tissue and cell samples affected by colorectal and skin cancer, which were prepared by following protocols close to the current clinical practise. The most relevant concepts of FTIR spectroscopy are thoroughly investigated, which ought to be understood and considered to perform a correct interpretation and treatment of its special signals. In particular, different physicochemical factors are reviewed and analysed, which influence the spectroscopic measurements for the particular case of biological samples and can critically affect their later analysis. All these knowledge and preliminary studies come into play in two main applications. The first application tackles the problem of registration or alignment of FTIR hyperspectral images with colour images acquired with traditional microscopes. The aim is to fuse the spatial information of distinct tissue samples measured by those two imaging modalities and focus the discrimination on regions selected by the pathologists, which are meant to be the most relevant areas for the diagnosis of colorectal cancer. In the second application, FTIR spectroscopy is pushed to their limits of detection for the study of the smallest biomedical entities. The aim is to assess the capabilities of FTIR signals to reliably discriminate different types of skin cells containing malignant phenotypes. The developed studies contribute to the improvement of objective decision methods to support the pathologist in the final diagnosis of cancer. In addition, they reveal the limitations of current protocols and intrinsic problems of modern FTIR technology, which should be tackled in order to enable its transference to anatomical pathology laboratories in the future.<br>El diagnòstic final de la majoria de tipus de càncer ho realitza un metge expert en anatomia patològica que examina mostres tissulars o cel¿lulars sospitoses extretes del pacient. Actualment, aquesta avaluació depèn en gran part de l'experiència del metge i es porta a terme de forma qualitativa mitjançant tècniques d'imatge tradicionals com la microscòpia òptica. Aquesta tasca tediosa està subjecta a alts graus de subjectivitat i dóna lloc a nivells de discordança inadequats entre diferents patòlegs, especialment en les primeres etapes de desenvolupament del càncer. L'espectroscòpia infraroja per Transformada de Fourier (sigles FTIR en anglès) és una tecnologia àmpliament utilitzada en la indústria que recentment ha demostrat una capacitat creixent per millorar el diagnòstic de diferents tipus de càncer. Aquesta tècnica aprofita les propietats de l'infraroig mitjà per excitar els modes vibratoris dels enllaços químics que formen les mostres biològiques. El principal senyal generat consisteix en un espectre d'absorció que informa sobre la composició química de la mostra il¿luminada. Els microespectrómetres FTIR moderns, compostos per complexos components òptics i detectors matricials d'alta sensibilitat, permeten capturar en un laboratori d'investigació comú imatges hiperespectrals d'alta qualitat que uneixen informació química i espacial. Les imatges FTIR són estructures de dades riques en informació que es poden analitzar individualment o juntament amb altres modalitats d'imatge per a realitzar diagnòstics patològics objectius. Per tant, aquesta tècnica d'imatge emergent té un alt potencial per a millorar la detecció i la graduació del risc del pacient en el cribratge i vigilància de càncer. Aquesta tesi estudia i implementa diferents metodologies i algoritmes dels camps interrelacionats de processament d'imatge, visió per ordinador, aprenentatge automàtic, reconeixement de patrons, anàlisi multivariant i quimiometria per al processament i anàlisi d'imatges hiperespectrals FTIR. Aquestes imatges es van capturar amb un modern microscopi FTIR de laboratori a partir de mostres de teixits i cèl¿lules afectades per càncer colorectal i de pell, les quals es van preparar seguint protocols alineats amb la pràctica clínica actual. Els conceptes més rellevants de l'espectroscòpia FTIR s'investiguen profundament, ja que han de ser compresos i tinguts en compte per dur a terme una correcta interpretació i tractament dels seus senyals especials. En particular, es revisen i analitzen diferents factors fisicoquímics que influeixen en els mesuraments espectroscòpiques en el cas particular de mostres biològiques i poden afectar críticament la seua anàlisi posterior. Tots aquests conceptes i estudis preliminars entren en joc en dues aplicacions principals. La primera aplicació aborda el problema del registre o alineació d'imatges hiperespectrals FTIR amb imatges en color adquirides amb microscopis tradicionals. L'objectiu és fusionar la informació espacial de diferents mostres de teixit mesurades amb aquestes dues modalitats d'imatge i centrar la discriminació en les regions seleccionades pels patòlegs, les quals es consideren més rellevants per al diagnòstic de càncer colorectal. En la segona aplicació, l'espectroscòpia FTIR es porta als seus límits de detecció per a l'estudi de les entitats biomèdiques més xicotetes. L'objectiu és avaluar les capacitats dels senyals FTIR per discriminar de manera fiable diferents tipus de cèl¿lules de pell que contenen fenotips malignes. Els estudis desenvolupats contribueixen a la millora de mètodes de decisió objectius que ajuden el patòleg en el diagnòstic final del càncer. A més, revelen les limitacions dels protocols actuals i els problemes intrínsecs de la tecnologia FTIR moderna, que haurien d'abordar per permetre la seva transferència als laboratoris d'anatomia patològica en el futur.<br>Peñaranda Gómez, FJ. (2018). Application of artificial vision algorithms to images of microscopy and spectroscopy for the improvement of cancer diagnosis [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/99748<br>TESIS

An early diagnosis of melanoma is essential to reduce mortality of patients. The diagnosis is also fundamental to predict the outcome of patients and to select the most adapted treatment. Current diagnostic assessments are obtained after visual inspection of the histological section of the primary tumor. The pathologist has first to determine the malignant nature of the lesion and then to assess the potential of the lesion to form metastases. Depending on several characteristics of the primary tumor (mainly tumor thickness, ulceration and mitotic rate), the sentinel node is surgically removed and the detection of tumor cells is based on its histopathological examination. These assessments are time consuming, to some degree subjective and are particularly challenging. Among melanoma patients that are not subject to sentinel node surgery, 6.5 % will develop metastases while 20 % of patients that undergo sentinel node surgery will effectively present metastases. The search for biomarkers that can identify malignant cells, evaluate potential of invasion or help selecting a treatment is still on.<p>In this thesis we used a new and promising technique of imaging based on infrared spectroscopy to study melanoma primary tumors and metastatic lymph nodes. Infrared spectroscopy brings information on the biochemical composition of the main components of the cells. When combined with a microscope and with multivariate statistical analyses, images that are generated allow the identification of melanoma cells and stromal cells in the biopsy. We also focused on the immune infiltration as it was shown to carry an important prognosis value for melanoma patients.<p>The first part of the thesis was a prerequisite for the rest of the study. It addresses the effects of the process of fixation that tissues obtained by surgical resection undergo for their long term preservation. In chapter III, we showed that Formalin-Fixation and Paraffin-Embedding (FFPE) procedure induces small but significant modifications in the infrared spectra of cells but these are very similar for different cell lines. In turn, it preserves the potential to identify closely-related cell lines by infrared spectroscopy.<p>We thus pursued our study on primary melanomas. In chapter IV, we first developed an automatic tool capable of identifying melanoma cells and the main cells of the tumor microenvironment in tissue sections. Importantly, we built a second model that brings information on the presence of metastases on the basis of the spectral signature of the primary tumor.<p>The next chapter is dedicated to the prediction of the response of melanoma to dacarbazine, the first-line chemotherapy to treat stage IV patients. Infrared spectra of the primary tumor were shown to contain information capable of predicting whether dacarbazine will be a useful treatment.<p>In the last two chapters, we focused on lymphocytes. In chapter VI, we first demonstrated that helper and cytotoxic T cells purified from peripheral blood can be identified on the basis of their infrared signature. Then, in chapter VII we investigated metastatic lymph nodes. We created different statistical models using infrared spectra that first identified the melanoma cells invading the lymph nodes and secondly, the different subpopulations of lymphocytes (B and T cells).<p>In conclusion, we developed an automatic and reliable tool of imaging to help pathologists in the anatomopathological assessment of primary lesions and lymph nodes./Le mélanome est la forme de cancer cutané la plus mortelle, provoquant environ 80% des décès dus à un cancer de la peau. Lorsque le mélanome est localisé, la chirurgie est le principal traitement et est suffisante pour 80% des patients. A l’opposé, lorsque le mélanome primaire a formé des métastases, le cancer devient beaucoup plus difficile à traiter et la survie de ces patients diminue drastiquement. Seuls 10% des patients vont vivre 5 ans lorsqu’ils développent des métastases à distance. C’est pourquoi un diagnostic précoce est essentiel pour diminuer la mortalité causée par le mélanome. L’étape du diagnostic est également très importante pour donner un pronostic et pour planifier les traitements. Le diagnostic actuel du mélanome est basé sur l’analyse en microscopie optique de sections de la tumeur primaire. Sur base de la morphologie cellulaire et de l’architecture du tissu, cette étape permet premièrement d’identifier le caractère cancéreux de la lésion et deuxièmement d’évaluer son potentiel métastatique. Une analyse du ganglion sentinelle permet également de détecter la présence de métastases. Dans le cadre de cette thèse, nous proposons d’utiliser une nouvelle technique d’imagerie basée sur la spectroscopie infrarouge qui apporte une information complète et unique sur la biochimie de la cellule et des tissus. Les résultats présentés ici indiquent que lorsque les spectres infrarouges sont combinés à des analyses statistiques multivariées, des images sont reconstituées et révèlent les structures et les composants cellulaires majeurs présents dans les coupes de mélanomes. Une étude préliminaire a d’abord pu démontrer que la fixation au formol subies par les biopsies pour les conserver n’entrave pas l’étude de celles-ci par spectroscopie infrarouge. Nous nous sommes alors intéressés aux tumeurs primaires de mélanome et avons développé un modèle statistique, à partir des spectres infrarouges, identifiant automatiquement les cellules de mélanome dans le tissu ainsi que les autres cellules du microenvironnement de la tumeur. Dans ce chapitre, nous avons également créé un autre modèle statistique capable de prédire le potentiel métastatique de la tumeur primaire en se basant sur sa signature spectrale. Nous avons ensuite mis en évidence une signature spectrale corrélée à la réponse à la dacarbazine chez des patients traités pour leurs métastases. Nous avons également montré que des sous-populations de lymphocytes purifiées d’échantillons sanguins pouvaient être identifiées sur base de leur spectre. Cette capacité de la spectroscopie infrarouge à distinguer les différents types de lymphocytes a ensuite été démontrée pour les lymphocytes infiltrant les métastases. Finalement, nous avons mis en évidence l’utilité de cette technique d’imagerie pour la détection de métastases ganglionnaires.<p><br>Doctorat en sciences agronomiques et ingénierie biologique<br>info:eu-repo/semantics/nonPublished

Des fibres optiques en verres de chalcogénure transmettant dans le moyen infrarouge (MIR) ont été développées par le laboratoire Verres et Céramiques de l’université de Rennes 1. Des travaux ont ensuite montré les potentialités de ces fibres comme outil diagnostic pour la spectroscopie MIR appliquée aux biofluides. Le spectre moyen infrarouge d’un échantillon complexe est le reflet de sa composition moléculaire qui, lorsque celui-ci est un biofluide, peut être assimilé à une image métabolique instantanée d’un individu. Cette technique constitue donc un outil intéressant pour le diagnostic médical. La société Diafir fut crée à la suite du programme ANR émergence FIR-MED pour développer les potentialités de la spectroscopie par fibre optique. L’objectif de l’entreprise est de développer un système composé d’un spectromètre spécifiquement adapté au capteur à fibre optique et d’un algorithme associé pour une réponse diagnostique ne nécessitant pas de connaissance particulière en spectroscopie infrarouge. Dans le cadre de ces travaux de thèse associant l’IRDL et la société Diafir, des projets variés d’applications médicales de la technologie ont été abordés avec pour objectif de développer une méthodologie d’analyse des spectres MIR. Pour cela, il a été nécessaire dans un premier temps de caractériser le signal obtenu à partir des capteurs et d’optimiser et valider des protocoles de mesure applicables aux différents biofluides de manière à réduire au mieux les sources de variabilité d’ordre physique et environnemental. La construction d’un diagnostic médical à partir de spectres infrarouge qui sont des données en grande dimension implique de sélectionner un petit nombre de variables spectrales explicatives. Des méthodes de sélection de variables ont été sélectionnées afin d’éviter l’effet « boite noire » en établissant le lien avec les fonctions biochimiques impactées par les pathologies. Cette approche spectrale infrarouge a notamment permis de mettre en évidence, au cours du développement de pathologies, l’existence de transitions a priori non détectées par les dosages biochimiques classiques<br>Chalcogenide glass optical fibres exhibiting unique properties of mid-infrared (MIR) transparency have been developed by the Laboratoire Verres et Céramiques of Rennes 1 University. Our studies investigate the potential of such fibres as a tool for MIR spectroscopy applied to biofluids based diagnostic. The MIR spectrum of complex samples features its molecular composition which, when a biofluid is considered, can be assimilate to an instant metabolic imaging of an individual. The Diafir Company was created following the ANR emergence FIR-MED program to develop the potential of optical fibre biomedical spectroscopy. The company's goal is to develop a system that is composed of the optical fibre sensor, a spectrometer specifically designed to these sensors and an associated algorithm for a diagnostic response without specific knowledge of infrared spectroscopy. As part of this thesis work, linking the IRDL and the Diafir Company, various projects of biomedical applications were driven with the aim of developing a MIR spectra analysis methodology. Accordingly, it was necessary initially to characterize the signal obtained from the sensors and to optimize and validate robust measurement protocols for each biofluid tested with the aim to reduce the physical and environmental sources of variability. The medical diagnosis construction from infrared spectra, that are high dimensional data, involves selecting from the whole spectral data set a small number of explanatory variables. Purposely, particular variables selection algorithms were selected to avoid the effect of "black box" by establishing the link with the biochemical functions affected by the disease. This infrared spectral approach allowed identifying previously unrevealed transitions in the time course of pathologies which were not detected from conventional biochemical markers

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Durante o processo de usinagem, o conhecimento da temperatura é um dos fatores mais importante na análise do estado da ferramenta. Permite o controle dos fatores mais importantes que influenciam, no uso, na vida e no desgaste da ferramenta. A temperatura na região de contato entre a peça e a ferramenta é resultante do processo de remoção de material durante a operação de corte e é difícil de se obter uma vez que, ou a peça, ou a ferramenta estão em movimento. Uma maneira de se medir a temperatura nessa situação é detectando a radiação de infravermelho. Este trabalho tem objetivo de apresentar uma nova metodologia de diagnóstico e monitoramento de operações de usinagem com o uso de imagens de infravermelho. A imagem de infravermelho fornece um mapa em tons de cinza da temperatura dos elementos participantes do processo: ferramenta, peça e cavaco. Cada tom de cinza na imagem corresponde a uma temperatura para cada material. A correspondência entre tons de cinza e a temperatura é dada pela prévia calibração da câmera de infravermelho para os materiais participantes do processo. O sistema desenvolvido neste trabalho usa uma câmera de infravermelho, uma frame grabber e um software composto por 3 módulos: o primeiro módulo faz a aquisição da imagem de infravermelho e o processamento; o segundo módulo faz a extração e o cálculo do vetor de características das imagens. Finalmente o terceiro módulo usa um algoritmo fuzzy e fornece como saída o diagnóstico do estado da ferramenta.<br>During machining process the temperature knowledge is one of the most important factors in tool analysis. It allows to control main factors that influence tool use, life time and wear. The temperature in the contact area between the work piece and the tool is resulting from the material remova! in cutting operation and it is too difficult to be obtained because the tool, or the work piece is in motion. One way to measure the temperature in this situation is detecting the infrared radiation. This work presents a new methodology for diagnosis and monitoring of machining processes with the use of infrared images. The infrared image provides a map in gray tones of the elements temperature in the process: tool, work piece and chips. Each gray tone corresponds to a certain temperature for each one of those materials and the relationship between the gray tones and the temperature is goven by previous infrared camera calibration. The system developed in this work uses an infrared camera, a frame grabber board and a software composed by three modules. The first module provides the image acquisition and processing. The second one does the image feature extraction and calculates the feature vector. Finally, the third module uses fuzzy logic to evaluate the feature vector and to supply the tool state diagnostic as output.

Mestrado em Biomedicina Molecular<br>Current clinical AD diagnosis criteria used to identify the disorder in patients who have already overt the advanced stage of dementia. This is too late for some kind of successful disease adjustment and consequently, early recognition of AD needs to be improved. Therefore, it is really needed different approaches for discovering new AD biomarkers, such as the application of metabolomics techniques (e.g. FTIR). The potential of FTIR in the clinical field has recently received particular attention, since it uses vibration frequencies of molecules present in the analysed sample to produce a metabolic fingerprint, which is then specific for each sample. This dissertation aims to identify biochemical alterations that might be related to dementia, being possible to distinguish between control and disease groups of plasma samples, through application of FTIR methodology at the 4000-600 cm-1 spectral region. Using plasma samples makes the process being minimally invasive, with other relevant clinical advantages. Besides the collection of blood samples used in this project, the volunteers were also submitted to cognitive evaluation trough Mini Mental State Examination (MMSE) and Clinical Dementia Rating (CDR), with other relevant clinical information being also collected. All the analysed samples were matched by age and sex. For a better discrimination between control and disease samples, Principal Component Analysis (PCA) was applied to spectra data at specific regions, namely 3500-2700 cm-1, 1700-1400 cm-1, and 1200-900 cm-1. This allowed to identify the main pathological changes that occurred at the biochemical level during neurodegenerative disorder development. In the former spectral region, disease samples presented a higher content of saturated lipids in relation to the unsaturated ones, which translates in a high potential brain damage. Besides, it was also noted the presence of carboxylic acids that are usually related to lipid hyperoxidation, production of reactive carbonyls and proteins structural and functional alterations. In turn, the spectral region 1700-1400 cm-1 allowed to identify differences in protein conformation between control and disease samples, and these last ones were still related with occurrence of protein aggregates. In other hand, the 1200-900 cm-1 region could be associated to cellular damage provoked by oxidative stress in disease samples. As an important note to take, FTIR analysis could have the potential to be applied in future not only for cognitive impairment diagnosis but also for identification of disease stage and prognostic evaluation, besides assessment of disease developing risk for control subjects.<br>Os atuais critérios clínicos de diagnóstico da doença de Alzheimer geralmente identificam a patologia apenas quando os pacientes já atingiram a fase de demência, ou seja, o estágio mais avançado da doença. Isto revela-se demasiado tarde para que qualquer tipo de terapêutica seja bem-sucedida e, consequentemente é necessário desenvolver uma metodologia de diagnóstico que permita um reconhecimento mais precoce da doença. Desta forma, é preciso adotar diferentes abordagens para a descoberta de novos biomarcadores para a doença de Alzheimer, tais como a utilização de técnicas de metabolómica (ex. FTIR). O potencial do FTIR no campo clínico recebeu recentemente particular atenção, sendo que esta técnica utiliza as frequências de vibração das moléculas presentes na amostra analisada para produzir uma “impressão digital” metabólica, a qual é específica para cada amostra. Esta dissertação tem como objetivo a identificação de potenciais alterações bioquímicas que possam estar relacionadas com demência, tornando possível a distinção entre grupos controlo e de doentes no seio do conjunto de amostras de plasma analisadas. A utilização de amostras de plasma torna o processo minimamente invasivo, de entre outras vantagens clínicas. Para além da colheita das amostras de sangue utilizadas neste projeto, os voluntários foram submetidos a uma avaliação cognitiva através da realização do MMSE e do CDR, com outra informação clínica relevante a ser também recolhida. Todas as amostras analisadas foram emparelhadas de acordo com a idade e o sexo. Para uma melhor distinção entre amostras controlo e de doentes foi aplicada a metodologia de PCA aos dados dos espectros obtidos em regiões específicas, nomeadamente em 3500-2700 cm-1, 1700-1400 cm-1, e 1200-900 cm-1. Isto permitiu identificar as principais alterações patológicas que ocorrem a nível bioquímico durante o desenvolvimento da doença neurodegenerativa. Na primeira região espectral referida, as amostras dos doentes apresentaram um maior conteúdo de lípidos saturados comparativamente aos não saturados, o que se traduz num potencial risco cerebral maior. Para além disso, foi observada a presença de ácidos carboxílicos, usualmente relacionados com hiperoxidação de lípidos, produção de carbonilos reativos e alterações estruturais e funcionais de proteínas. Por sua vez, a região espectral 1700-1400 cm-1 permitiu identificar diferenças na conformação de proteínas entre amostras controlo e de doentes, tendo estas últimas sido ainda relacionadas com a ocorrência de agregados proteicos. Por outro lado, a região 1200-900 cm-1 pôde ser relacionada com presença de danos celulares provocados por stress oxidativo nas amostras de doentes. Como importante nota a reter, a análise por FTIR pode ter o potencial para ser aplicada no futuro não apenas para diagnóstico de disfunção cognitiva, mas também para identificação do estádio da doença e realização de prognósticos, para além da avaliação do risco de desenvolvimento da doença em sujeitos controlo.

Breast cancer is the most common cancer in women. It is a highly heterogeneous disease in terms of histology, therapeutic response and patient outcomes. Early and accurate detection of breast cancer is crucial as the patient prognosis varies greatly depending on the diagnosis of the disease. Nonetheless current breast cancer classification methods fail to precisely sub-classify the disease, resulting in potential inadequate therapeutic management of patients and subsequent poor clinical outcomes. Substantial effort is therefore put in cancer research to develop methods and find new biomarkers efficiently identifying and characterizing breast tumor cells. Moreover it is now well-recognized that the intensive cross-talk between cancer cells and their microenvironment (including non-tumor cells) highly influences cancer progression. Recently, a growing body of clinical evidence reported the prognostic and predictive value associated with the presence of tumor infiltrating lymphocytes (TILs) in the microenvironment of breast tumors. Although the evaluation of TILs would be of great value for the management of patients and the development of new immunotherapies, it is currently not assessed in routine practice. Furthermore Fourier transform infrared (FTIR) imaging has shown its usefulness to study a panel of human cancers. Infrared (IR) spectroscopy coupled to microscopy provides images composed of multiple spectra reflecting the biochemical composition and subtle modifications within biological samples. IR imaging therefore provides useful information to improve breast cancer identification and characterization. The ultimate aim of this thesis is to improve breast cancer diagnosis using FTIR imaging to better identify and characterize cancer cells and the tumor microenvironment of breast cancers. In a first step we carried out a feasibility study aiming at evaluating the impact of the sample fixation process on IR spectra. While spectra were undeniably influenced by this biochemical alteration, our results indicated that closely-related cell types were influenced similarly and could still be discriminated on the basis of their spectral features. We then demonstrated the capability of IR imaging to discriminate a tumor from a normal tissue environment based on the spectral features of tumor cells and the surrounding extracellular matrix. A particular focus was placed on the identification of lymphocyte spectral signatures of cells isolated from blood or present within secondary lymphoid organs such as tonsils. Our results revealed that IR imaging was sensitive enough to discriminate lymphocyte subpopulations and to identify a particular spectral signature that we assigned to lymphocyte activation. Finally we highlighted the potential value of IR imaging as complementary tool to identify and characterize TILs in breast tumor samples. Altogether, our results suggest that IR imaging provides interesting and reliable information to improve breast cancer characterization and to assess the immune microenvironment of breast tumors.<p>/<p>Le cancer du sein est le carcinome le plus fréquent chez la femme. C’est une maladie très hétérogène du point de vue histologique, de la réponse thérapeutique et de l’évolution clinique. Une détection rapide et précise de la maladie est cruciale, un diagnostic du cancer du sein dès les premiers stades de la maladie permet une meilleure prise en charge du patient et est directement associé à un meilleur pronostic. Néanmoins la classification actuelle des cancers du sein ne permet souvent pas de caractériser la maladie de manière précise, ce qui donne lieu à la mise en place de traitements moins ciblés et une évolution clinique peu favorable. Pour remédier à cela, des efforts conséquents sont réalisés en recherche, dans le but de mettre au point des méthodes capables d’identifier et de caractériser les cellules tumorales. De plus il est actuellement reconnu que le micro-environnement tumoral (composé des cellules non-tumorales) influence fortement la progression du cancer. Récemment de nombreuses études ont montré que la présence de lymphocytes au niveau des tumeurs mammaires (TILs) était corrélée à un meilleur facteur pronostic et prédictif. Bien que l’évaluation des TILs soit de grande importance dans le cadre des immunothérapies, cet élément n’est actuellement pas pris en compte dans les analyses de routine. Par ailleurs, l’imagerie infrarouge par transformée de Fourier (FTIR) a démontré son utilité dans l’étude de plusieurs cancers humains. La spectroscopie infrarouge (IR) couplée à la microscopie fourni des images composées de multiples spectres qui reflètent la composition biochimique et les modifications dans les échantillons biologiques. De ce fait l’imagerie infrarouge procure des informations utiles pour améliorer l’identification et la caractérisation du cancer du sein. L’objectif général de cette thèse est d’améliorer le diagnostic du cancer du sein par imagerie FTIR pour mieux identifier et caractériser les cellules cancéreuses et le micro-environnement tumoral des tumeurs mammaires. Dans un premier temps nous avons effectué une étude de faisabilité afin d’évaluer l’impact du protocole de fixation des tissus sur les spectres IR. Bien que les spectres soient indéniablement influencés par cette altération biochimique, nos résultats indiquent que des types cellulaires proches sont influencés de manière similaire et peuvent donc être discriminés sur base de leurs caractéristiques spectrales. Nous avons ensuite démontré la capacité de l’imagerie IR de distinguer un environnement tumoral d’un environnement normal sur base des particularités spectrales des cellules tumorales et de la matrice extracellulaire. Une attention particulière a ensuite été portée afin d’identifier des signatures spectrales de cellules immunitaires du sang et au sein d’organes lymphoïdes secondaires, tels que les amygdales. Nos résultats ont révélé que l’imagerie IR permet d'identifier une signature spectrale particulière, que nous avons associée à une stimulation lymphocytaire. Finalement nous avons mis en évidence l’utilité de l’imagerie IR en tant qu’outil complémentaire pour identifier et caractériser les TILs dans les échantillons tumoraux mammaires. De manière générale, nos résultats suggèrent que l’imagerie IR fournit des informations intéressantes et fiables pour améliorer la caractérisation et l’évaluation du micro-environnement immunitaire dans les tumeurs mammaires.<br>Doctorat en Sciences agronomiques et ingénierie biologique<br>info:eu-repo/semantics/nonPublished

Un déséquilibre dans les mécanismes de défense de la cornée peut entraîner une invasion par des micro-organismes (MO) et générer une kératite infectieuse (KI), ou encore un syndrome sec. Les KI sont la première cause de cécité monoculaire. Le syndrome sec, également fréquent, est sujet à de nombreuses études cliniques pour l’évaluation de nouveaux traitements. L’objectif de cette thèse est de mettre au point des méthodes d’imagerie pour le diagnostic et le suivi des pathologies de la surface oculaire au travers de deux projets innovants : 1/ le projet FLUOCOR consistant à développer une solution complète de diagnostic rapide in vivo des MO les plus souvent responsables des KI afin de débuter immédiatement le traitement adapté et améliorer le pronostic visuel final. Cette solution comprendra des BioMarqueurs fluorescents (BMfs) spécifiques des agents infectieux, fluorescents dans le rouge ou le proche infrarouge non éblouissant et un nouvel instrument optique de détection. Des BMfs basés sur le couplage de BODIPY innovant avec des molécules ciblant les MO ont été obtenus. Des tests in vitro ont montré une bonne spécificité mais les tests ex vivo sur cornées humaines ont montré une fixation non spécifique sur les cellules épithéliales. Pour pallier ce manque de spécificité, le couplage de ces BODIPY sur des anticorps dirigés contre les MO est en cours. 2/ le projet FLUOSCOPE qui a permis de développer une nouvelle stratégie d’imagerie de la surface oculaire pour le suivi du syndrome sec, de la méthode d’instillation des colorants jusqu’au traitement d’images, en passant par la conception d’un instrument optique désormais industrialisé par les laboratoires Théa<br>An imbalance in the defence system of cornea can result in several diseases, like infectious keratitis (IK) in case of invasion by microorganisms (MO) or dry eye in case of insufficient tear quality and/or quality. IK are the first cause of unilateral blindness worldwide. Sicca syndrome, also frequent, is the subject of numerous clinical trials assessing new treatments. The aim of the PhD Thesis work is to develop new imaging methods for the diagnosis and follow-up of diseases of the ocular surface. Two innovative project were conducted: 1/ the FLUOCOR project consists in developing a complete solution of rapid in vivo etiologic diagnosis of IK, for the most frequent and/or severe infections to allow rapid starting of the most adapted treatment in order to improve the final visual prognosis. This solution will comprise fluorescent biomarkers (excitable by sustainable non blinding red or near infrared lights) specific to the target MO, and a new optical imaging device for their detection. Biomarkers based on new BODIPY coupled with molecules targeting the MO were obtained with a good in vitro specificity. Nevertheless, on ex vivo human corneas they stained superficial epithelial cells. In order to overcome this difficulty, the coupling of BODIPY on specific antibodies targeting the MO is ongoing; 2/ the FLUOSCOPE project that allowed development of a new strategy of ocular surface imaging for the diagnosis and follow up of sicca syndrome. The complete chain was revisited from the instillation of the dye to the objective quantification of staining by image analysis, through the development of a prototype of imaging device, now industrialized by les Laboratoires Thea

A new molecular imaging modality has been developed to detect and locate positive axillary and sentinel lymph nodes non-invasively in breast cancer patients undergoing lymphoscintigraphy. The modality is based on fluorescent photon detection to locate the presence of indocyanine green (ICG) in the lymph subsequent to peritumoral injection of ICG into the breast. The imaging system consists of a gain-modulated intensified charge-coupled device (ICCD) camera, which captures low-intensity, near-infrared, and frequency-modulated photons. A four-fold ‘optical lymphography’ study was conducted to (1) examine fluorescence depth penetration and ICCD system accuracy at clinically relevant depths, (2) compare image quality of the ICCD system vs. conventional gamma imaging, (3) measure ICG pharmacokinetics in vivo, and (4) develop a clinical protocol while examining pre-clinical factors such as the outcome of combining ICG with sulfur colloids used in lymphoscintigraphy. The frequency-domain ICCD system was found to precisely detect modulation amplitude, IAC, and phase, θ, at depths up to 9 cm and with IAC accuracy less than 20% and θ less than 2º using an 80-mW laser incident on phantoms having ranging tissue optical properties. Significant differences in the mean depth of penetration owing to 0.62-ns lifetime and 100-MHz frequency increases were detected. An in vivo optical vs. nuclear image quality comparison demonstrated statistically similar (α=0.05) target-to-background ratios for optical (1.4+/-0.3) and nuclear (1.5+/-0.2). Alternatively, resulting image signal-to-noise ratios (SNR) from the ICCD system were greater than that achieved with a conventional gamma camera (pvalue<<0.01). Analysis of SNR versus contrast showed greater sensitivity of optical over nuclear imaging for subcutaneous tumors. In vivo and rapid detection of ICG in the blood-stream of nude mice was accomplished with a home-built avalanche photodiode dynamic fluorescence measurement system. Intensity data upon i.v. injection were regressed with a pharmacokinetic model describing the partitioning of ICG from the blood to the surrounding tissues. ICG blood-clearance was detected approximately 15 min after injection. Lastly, a human subject protocol was written, practiced, and federally approved for the application of optical lymphography. Furthermore, ICG was unaffected when mixed with sulfur colloids thus supporting the feasibility for combining fluorescence imaging with lymphoscintigraphy in breast cancer patients.

Diese Arbeit entstand im Rahmen des Projektes „Molekulare Endospektroskopie“ an der Technischen Universität Dresden. Der Titel drückt aus, dass durch Kopplung von Endoskopie und Spektroskopie Gewebe auf molekularer Ebene charakterisiert wird. Infrarot- (IR-) und Raman-Spektroskopie bieten dabei besondere Vorteile, da sie zu den molekülspektroskopischen Verfahren mit dem höchsten Informationsgehalt gehören. Beide Methoden beruhen auf Molekülschwingungen, deren Spektren einen chemischen Fingerabdruck über die Zusammensetzung und Struktur der Proben liefern. Der Autor leitete eine wissenschaftliche Nachwuchsgruppe, die die Grundlagen der schwingungs-spektroskopischen Methoden zur Bildgebung von Gewebe und Zellen entwickelte und auf klinische Probleme – vor allem aus dem neuroonkologischen Bereich – anwendete. Diese kumulative Habilitationsschrift fasst vierzehn Veröffentlichungen zusammen, wobei in der letzten die Untersuchung eines Hirntumormodells von Mäusen mit einer faseroptischen Sonde beschrieben wurde. Zunächst werden verschiedene Methoden der Biophotonik verglichen, um die hier eingesetzten Techniken in diesen Kontext zu stellen. Danach werden biomedizinische Anwendungen von Fourier-Transform-Infrarot- (FTIR-) und Raman-Imaging beschrieben. Die eigenen Beiträge sind untergliedert in (i) Raman- und FTIR-Imaging in der Neuroonkologie, (ii) FTIR-mikroskopisches Imaging von Gewebedünnschnitten und (iii) Raman- und FTIR-mikroskopisches Imaging von einzelnen Zellen. Abschließend wird in den Schlussfolgerungen und dem Ausblick diskutiert, welche Rolle die molekulare Endospektroskopie als neue instrumentell-analytische Methode in der medizinischen Diagnostik übernehmen kann<br>This work summarizes the results of the project “Molecular Endospectroscopy” at the Dresden University of Technology. The title expresses that tissue is characterized on the molecular level by coupling endoscopy and spectroscopy. Infrared (IR) and Raman spectroscopy offer advantages for these applications because they belong to the methods of molecular spectroscopy with the highest information content. Both methods probe molecular vibrations that provide a chemical fingerprint for the composition and structure of samples. The author was leader of a junior research group which developed vibrational spectroscopic methods for imaging of cells and tissues and applied them to clinical problems, in particular from the field of neuro-oncology. The current cumulative habilitation thesis is based on fourteen publications. The last one describes studies of a murine brain tumor model using a fiber-optic probe. In the first part various biophotonic methods are compared. Then biomedical applications of Fourier transform infrared (FTIR) and Raman imaging are reported. The papers are grouped into the chapters (i) Raman and FTIR imaging in neuro-oncology, (ii) FTIR microscopic imaging of tissue sections and (iii) Raman and FTIR microscopic imaging of single cells. It is discussed in the conclusions and outlook how molecular endospectroscopy as a new analytical tool can complement the standard diagnostic methods

This overview reports 31 studies, which have been performed by the author since 1989 to define the diagnostic value of thermometry and infrared imaging in rehabilitation and rheumatology. Some investigations were designed to characterise either treatment modalities, to clarify the role of temperature measurements as a method for follow-up or treatment monitoring in certain diseases. Thermal imaging has an important impact in assisting the diagnosis of many diseases. A relationship between temperature and clinical signs was established in the following disorders: epicondylitis (correlation of hot spots with pain provocated by firm pressure or resisted movement, and pressure threshold), complex regional pain syndrome (elevated temperature is paralleled by swelling and pain, temperature elevation of the hand after radius fracture after plaster removal predicts typical X-ray changes), thoracic outlet syndrome (high correlation of the region of paresthesia and low temperature readings), muscular inactivity, acute stage of Herpes zoster and Raynaud's phenomenon. Thermal imaging is of little value for the assessment of disability in patients with knee pain and of questionable value in patients with carpal tunnel syndrome or fibromyalgia. Painful tendon insertions or acupuncture points on the auricle cannot be detected by thermal imaging. Temperature signs in epicondylitis, complex regional pain syndrome and thoracic outlet can be successfully used for treatment monitoring. This might be also the case in radiotherapy of malignant breast disease. Infrared thermography, performed immediately after physical exercise can help to identify activated muscles. The value of thermal imaging for monitoring patients with lymphedema remains questionable. Temperature signs in epicondylitis, complex regional pain syndrome and thoracic outlet can be successfully used for treatment monitoring. This might be also the case in radiotherapy of malignant breast disease. Infrared thermography, performed immediately after physical exercise can help to identify activated muscles. The value of thermal imaging for monitoring patients with lymphedema remains questionable. On the other hand as a result of these studies, it became quite clear that the heat regulatory system is connected with other regulation systems of the body. Many of these influence the perfusion of vessels, which can result in temperature changes on the surface. In addition to the circulation system, pain and muscle function are the most important links to temperature regulation. Therefore any change or therapeutic modification of these systems might be seen on thermal images.

Thesis (Ph. D.) -- University of Maryland, College Park, 2004.<br>Thesis research directed by: Mechanical Engineering. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.

The ability to rapidly, sensitively, and accurately detect the presence of a pathogen is a vital capability for first responders in the assessment and treatment of scenarios such as disease outbreak and bioterrorism. Nucleic acid tests such as the polymerase chain reaction (PCR) are supplanting traditional techniques due to the improved speed, specificity, sensitivity, and simplicity. Still, amplification by PCR is often the bottleneck when processing genetic samples. Conventional PCR machines are bulky, slow, and consume large reagent volumes and an affordable, compact, efficient, easy-to-use alternative has yet to emerge. In this work, a microfluidic PCR platform was developed consisting of a low-cost, multi-chamber polymer microchip and a laser-mediated thermocycler capable of independent thermal control of each reaction chamber. Innovations in polymer microchip modeling, fabrication, and characterization yielded a low-cost solution for sample handling. A simple optical system featuring an infrared laser diode and solenoid-driven optical shutter was combined with a microfluidic temperature measurement system utilizing embedded thermocouples to achieve rapid thermocycling capable of multiplexed temperature control. We validated the instrument with sensitive amplifications of multiple viral targets simultaneously. This technology is a breakthrough in practical microfluidic PCR instrumentation, providing the foundation for a paradigm shift in low-cost, high-throughput genetic diagnostics.

In the manufacturing process of float glass often atmospheric pressure chemical vapour deposition (APCVD) reactors are integrated on-line for the deposition of functional thin solid films. Such functional films have applications in architectural glass, flat panel displays and solar cells. As glass moves downstream in the process, the thin film is deposited at temperatures between 500 to 700°C. The high temperatures make it difficult to monitor the deposition process and thin film quality control is commonly done at the end of the line or at lower temperatures. A time delay therefore exists between the point of thin film deposition and subsequent quality control, which can lead to large quantities of defective product being produced before faults are detected. It is therefore desirable to monitor in the APCVD reactor for rapid feedback of unexpected deviations from desired process conditions, reaction progress and fault detection. High uniformity of film properties across the substrate are important, but APCVD reactors are often empirically designed and the detailed chemical reaction mechanism is unknown. This leads to inefficient gas flow patterns and precursor utilization as well as difficulties in the design of new reactors. The APCVD deposition of tin oxide from the mono-butyl-tin tri-chloride (MBTC) is an example of such a process. Optical monitoring instruments in-situ and in-line on the APCVD reactor provided rapid feedback about process stability and progress non-invasively. Near infrared diode laser absorption spectroscopy (NIR-LAS) monitored the concentration of the reaction species hydrogen chloride (HCl) in-situ and spatially in the coating zone. A mid-infrared grating absorption spectrometer (IR-GAS) with novel pyro-electric array detector monitored the concentration of precursor entering the coating system simultaneously. In combination these instruments provide the means for rapid process feedback. Fourier transform infrared absorption spectroscopy (FTIR) was used to investigate the unknown decomposition pathway of the precursor to find the yet unknown key tin radical that initiates film growth. Stable species forming during MBTC decomposition over a temperature range of 170 to 760°C were investigated but the tin intermediate remains unknown. Computational fluid dynamics (CFD) is routinely employed in research and industry for the numerical simulation of CVD processes in order to predict reactor flow patterns, deposition rates, chemical species distribution or temperature profiles. Two and three dimensional models with complex geometries and detailed reaction models exist. A three dimensional computational fluid dynamics (CFD) model of the used APCVD reactor was built using the Fluent CFD software. The numerical simulation included a chemical model that predicted qualitatively the chemical species distribution of hydrogen chloride in the gas phase. This was confirmed through comparison with NIR-LAS results. Design shortcomings due to inefficient flow patterns were also identified. In combination the optical tools developed provide the means for safe and efficient manufacturing of thin films in APCVD reactors. CFD simulations can be used to increase precursor utilization and film uniformity in the development of new reactor designs.

A new optical imaging modality has been developed for small animal in vivo imaging of near-infrared fluorescence resulting from fluorescent contrast agents specifically targeted to molecular markers of cancer. The imaging system is comprised of an intensified charge-coupled device (ICCD) for the detection of ultra-low levels of re-emitted fluorescence following the delivery of an expanded beam of excitation light. The design of the ICCD detection system allows for both continuous wave (CW) and frequency-domain modes of operation. Since the accurate acquisition of frequency-domain photon migration (FDPM) data is important for tomographic imaging, the imaging system was also validated using experimentally obtained FDPM measurements of homogenous turbid media and diffusion theory to obtain estimates of the optical properties characteristic of the media. The experiments demonstrated that the absorption and reduced scattering coefficients are determined least accurately when relative rel measurements of average light intensity IDC are employed either alone or in a rel combination with relative modulation amplitude data IAC and/or relative phase shift data rel . However, when FDPM measurements of are employed either alone or in rel combination with IAC data, the absorption and reduced scattering coefficients may be found accurate to within 15% and 11%, respectively, of the values obtained from standard single-pixel measurements; a result that suggests that FDPM data obtained from an ICCD detection system may in fact be useful in tomographic imaging. Furthermore, intensified-detection allows for sub-second exposure times, permitting the acquisition of dynamic fluorescence images immediately following administration of the contrast agent. Experimental results demonstrate that when coupled with a suitable pharmacokinetic model describing targeted dye distribution throughout the body, dynamic fluorescence imaging may be used to discriminate spontaneous canine adenocarcinoma from normal mammary tissue. A separate experiment demonstrates that pharmacokinetic analysis of dynamic fluorescence images enables one to estimate the rate constant governing Kaposi's sarcoma tumor uptake of an integrin-targeted dye and integrin receptor turnover rate. The rate constant for uptake was calculated to be 0.16-sec-1 while the turnover rate of the integrin receptor was estimated to occur within 24-hours.

Thesis (M.S.) -- University of Maryland, College Park, 2006.<br>Thesis research directed by: Dept. of Aerospace Engineering. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.

This thesis focuses on the utilisation of mid-infrared techniques in technological atmospheric pressure, non-thermal plasma (NTP) diagnostics. Two mid-infrared techniques were demonstrated in this work namely laser absorption and Fourier transform infrared (FTIR) spectroscopy. The performance of external-cavity quantum cascade laser (EC-QCL), a relatively new laser type with broad tuning capability was also demonstrated as potential diagnostics tool for technological NTP applications. A dual plate dielectric barrier discharge (DBD) and a packed-bed NTP reactor were designed and fabricated to perform plasma process. Quantitative analysis of the laser absorption and FTIR spectroscopy techniques for gas detection were validated by using standard gas samples. Real-time CO monitoring by means of in-situ laser absorption spectroscopy measurements were performed for gas phase diagnostics in the decomposition of TEOS by means of plasma-enhanced chemical vapour deposition (PE-CVD) and in CO2 reforming of CH4 by means of NTP. In-line FTIR measurements simultaneously recorded the gas spectrum at the exhaust of the plasma reactors. Information from both measurements was found to provide useful information on the plasma processes and chemistry for the NTP applications. Finally, wavelength stability and linearity performance of a broad tuning range EC-QCL were evaluated by using the Allan variance technique. (LOD) at SNR = 1 was estimated to be ~ 2 ppm, achieved under atmospheric pressure, at the room temperature, and a path length of 41 cm for NO detection produced from the decomposition of dichloromethane (DCM) by means of NTP.

Thermography is a useful tool for analyzing spinal nerve root irritation, but interpretation of digital infrared images is often qualitative and subjective. A new quantitative, computer-aided method for analyzing thermograms, utilizing the human dermatome map, is presented. Image processing and pattern recognition principles needed to accomplish this goal are discussed. Algorithms for segmentation, boundary detection and interpretation of thermograms are presented. An interactive, user-friendly program to perform this analysis has been developed. Due to the relatively large number of images in an exam, speed and simplicity were emphasized in algorithm development. The results obtained correlate well with clinical data and show promise for aiding the diagnosis of spinal nerve root irritation.

A novel nonintrusive soot diagnostics methodology was developed, validated and applied for in-situ determination of temperature, volume fraction and refractive index of soot aggregates formed inside flames by using near-infrared emission spectrometry. Research was conducted in three main parts, first one addressing development and validation of a comprehensive &quot<br>direct&quot<br>model for simulation of line-of-sight radiative emission from axisymmetric sooty flames by coupling sub-models for radiative transfer, radiative properties and optical constants. Radiative property estimation for soot agglomerates was investigated by experimentally validating discrete dipole approximation against microwave measurements and using it as reference to assess applicability of simpler Rayleigh-Debye-Gans approximation for fractal aggregates (RDG-FA). Comparisons between predictions of two methods for soot-like model aggregates demonstrated that radiative property predictions of RDG-FA are acceptably accurate for relatively small soot aggregates encountered in small-scale flames. Part two concerns experimental investigation of an axisymmetric ethylene/air diffusion flame by Fourier Transform Near-Infrared spectroscopy. Measurement of line-of-sight emission intensity spectra was performed along with analyses on calibration, noise, uncertainty and reproducibility. A noise characterization approach was introduced to account for spatial fluctuations which were found to dominate over spectral noise. Final part focuses on development, evaluation and application of an inversion methodology that inputs spectral emission intensity measurements from optically thin flames, removes noise, identifies soot refractive index from spectral gradients and retrieves soot temperature and volume fraction fields by tomographic reconstruction. Validation with simulated data and favorable application to measurements indicate that proposed methodology is a promising option for nonintrusive soot diagnostics in flames.

A novel nonintrusive soot diagnostics methodology was developed, validated and applied for in-situ determination of temperature, volume fraction and refractive index of soot aggregates formed inside flames by using near-infrared emission spectrometry. Research was conducted in three main parts, first one addressing development and validation of a comprehensive direct model for simulation of line-of-sight radiative emission from axisymmetric sooty flames by coupling sub-models for radiative transfer, radiative properties and optical constants. Radiative property for soot agglomerates was investigated by experimentally validating DDA method against microwave measurements and using it as a reference to assess applicability of simpler RDG-FA approximation. Part two concerns experimental investigation of an axisymmetric ethylene/air diffusion flame by Fourier Transform Near-Infrared spectroscopy. Measurement of line-of-sight emission intensity spectra was performed along with analyses on calibration, noise, uncertainty and reproducibility. Final part focuses on development, evaluation and application of an inversion methodology that inputs spectral emission intensity measurements from optically thin flames, removes noise, identifies soot refractive index from spectral gradients and retrieves soot temperature and volume fraction fields by tomographic reconstruction. Validation with simulated data and favourable application to measurements indicate that proposed methodology is a promising option for nonintrusive soot diagnostics in flames<br>Une méthodologie originale de diagnostique des suies a été développée, validée et mise en œuvre pour la détermination in-situ de la température, la fraction volumique et l'indice de réfraction des agrégats de suie formés dans les flammes, en utilisant la spectrométrie d'émission dans le proche infrarouge. Les travaux ont été conduits en trois parties. La première a concerné le développement et la validation d'un modèle direct complet de simulation de l'émission radiative des flammes sur une ligne de visée. Les propriétés radiatives des agrégats de suie ont été étudiées en validant expérimentalement la méthode DDA avec des mesures micro-ondes et en l'utilisant ensuite pour évaluer l'applicabilité de l'approximation RDG-FA. La deuxième partie a impliqué l'analyse expérimentale de l'émission radiative de flammes de diffusion éthylène/air en mettant en œuvre la spectrométrie à Transformée de Fourier dans le Proche Infra-Rouge. La mesure des flux de rayonnement émis sur une ligne de visée a été réalisée en conjonction avec une analyse de l'étalonnage, du bruit, des incertitudes et de la reproductibilité. La dernière partie a consisté en le développement, l'évaluation et l'application d'une méthodologie d'inversion qui a pour données d'entrée les spectres d'émission de flammes optiquement minces, élimine le bruit, identifie l'indice de réfraction des suies à partir des gradients spectraux et fournit la température et la fraction volumique par reconstruction tomographique. La validation avec des données simulées et une application aux spectres mesurés indiquent que la méthodologie proposée est prometteuse pour le diagnostic non intrusif des suies dans les flammes

La thermographie infrarouge constitue un outil de diagnostic très utile dans le domaine du bâtiment et du génie civil. Cependant un diagnostic quantitatif reste difficile, et l'émissivité des surfaces étudiées joue un rôle important. Le présent travail est une étude sur la mesure d'émissivité pour le diagnostic quantitatif des structures par thermographie. Un des enjeux est de compléter une base de données d'émissivité pour des matériaux du bâtiment et du génie civil ; pour cela il a été nécessaire de développer des appareils de mesure portables. Deux appareils ont été développés au CERTES, utilisant des méthodes indirectes. Ces méthodes consistent à mesurer la réflexion d'un flux infrarouge modulé et nécessite une référence de réflectance connue. Le premier appareil module le flux par modulation lente de température (mesure en 16mn) ; il est adapté aux surfaces diffusantes et hétérogènes comme les bétons bitumineux et les matériaux de construction du bâtiment. L'autre appareil utilise un système d'écran permettant une modulation plus rapide (mesure en quelques secondes). Il est plus polyvalent. Il est aussi plus facilement transportable et permet également d'obtenir une évaluation du caractère plus ou moins spéculaire de la surface. Ces deux appareils couvrent au choix une bande spectrale large (1 à 40µm) pour évaluer les propriétés radiatives des surfaces et une bande étroite (8 à 14µm) adaptée à la sensibilité des caméras infrarouges. Une étude comparative sur les mesures d'émissivité a été entreprise avec le LNE (Laboratoire National de Métrologie et d'Essais). Les échantillons utilisés pour cette étude comparative ont permis de tester les différents dispositifs pour des matériaux ayant des propriétés radiatives très variées. Des mesures ont été effectuées au laboratoire et sur site sur une large gamme de matériaux usuels du bâtiment et du génie civil<br>Thermography is a very useful diagnosis tool in buildings and civil engineering structures. However quantitative diagnosis remains difficult, and having accurate values of surface emissivity is an important factor. The present work is a study about emissivity measurement for quantitative diagnosis with thermography. We needed accurate measurement of the emissivity of a number of civil engineering materials, in order to create a database. Thus, it was necessary to develop new portable measurement devices. Two devices using an indirect measurement method were developed at CERTES laboratory. The method uses the measurement of the reflectivity from a modulated IR source and requires calibration with a highly reflective surface. The first device uses a low-frequency, thermal modulation well-adapted to laboratory measurements, whereas the second one is a portable system using a mechanical modulation at a faster frequency, more appropriate to outdoor measurements. Both devices allow measurements in the broad (1—50µm) and narrow (8—14µm) bands. Experiments were performed on a large number of materials commonly used in buildings and civil engineering structures. The final objective of this work is to build a database of emissivity for these materials. A comparison of laboratory and on-site measurements of emissivity values obtained in both spectral bands is presented along with an estimation and an analysis of measurement uncertainties. A comparative study with measurement obtained at LNE (Laboratoire National de Métrologie et d'Essais, French laboratory of metrology) was performed, using a range of materials with widely different radiative properties. An analysis of discrepancies and their possible causes is presented

This Project is aimed at developing and fabricating mid-infrared (MIR) transmitting germanium-antimony-selenium (Ge-Sb-Se) chalcogenide glass fibres for passive transmission in MIR sensing and as new high-purity low-loss optical fibres for active MIR supercontinuum generation (SCG). The work reported in this Thesis can be divided into three main categories: (i) a study of four Ge-Sb-Se glass compositions (atomic %): (Ge19Sb15Se66), (Ge20Sb10Se70), (Ge24Sb4Se72) and (Ge22Sb8Se70), in terms of their thermal properties, optical properties and cytotoxicity to match potential glass pairs for small-core step-index MIR SCG fibres; (ii) to develop and optimise methods of achieving high-purity chalcogenide glasses and (iii) a preliminary study of the structure of Ge-Sb-Se glasses along the stoichiometric tie-line x(GeSe2)-(1x)( Sb2Se3), to guide future selection of candidate glass pairs to draw to step-index fibre. The MIR spectral region covers the wavelengths 3-50 μm and characteristic vibrational absorption spectra unique to each molecular type. Vibrational spectroscopy can detect subtle changes in the specific spectral response within this region. Molecular vibrations are indicative of changes within biological cells relative to normal biological cells, signifying the presence or absence of a disease. This Project contributes to the collaborative MINERVA Project which is developing a remote skin cancer detection system using MIR absorption spectroscopy aiming to carry out disease diagnosis in vivo. Providing broadband photons at MIR wavelengths has previously presented difficulties. Conventional MIR blackbody light sources are weak and optical fibres for transmitting MIR light to/from tissue in vivo can be limited by strong material absorption such as silica glass > 2.4 μm and tellurite, and heavy metal fluoride, > 4.75μm. In contrast, chalcogenide glasses have been shown to transmit MIR light out to 25 μm and MIR SCG from ~ 2 – 15.1 µm has recently been demonstrated in chalcogenide glass fibre. This Thesis reports on the characterisation of four Ge-Sb-Se glass compositions to match potential glass pairs for fabrication of step-index fibres based on particular thermal properties and desired fibre numerical aperture (NA). Three glass pairs are drawn to fibre: Pair I (Ge22Sb8Se70) and (Ge24Sb4Se72), Pair II (Ge19Sb15Se66) and (Ge20Sb10Se70), and Pair III (Ge20Sb10Se70) and (Ge24Sb4Se72). Difficulties emerged and are examined in the extrusion and fibre drawing processes arising from a mismatch in the glass pair’s physical properties. Thus, a hierarchy of the order of selection of physical properties is suggested, with matching the glass transition temperature (Tg) deemed to be the top priority. The optical properties of the fabricated fibres are characterised in terms of predicted NA, near-field imaging and optical loss measurements. The minimum loss achieved (2.42 dB/m at 6.66 µm wavelength) is for Pair I (Core: Ge22Sb8Se70 and cladding: Ge24Sb4Se72). The effect of heat-treating to purify the precursor elements Sb and Se on subsequent fibre loss is observed and it is established that glass purity was a critical factor affecting the intensity of hydride and oxide impurity absorption bands punctuating the 2.5 – 10 µm wavelength transmission region. Therefore, distillation methods are explored as a means of generating high-purity chalcogenide glasses and a new distillation rig is developed. Preliminary cytotoxicity tests on a fibre fabricated from Pair I are conducted to provide the foundations of a procedure for future chalcogenide glass fibre cytotoxicity testing. The initial data demonstrated the potential of etching the Ge-Sb-Se chalcogenide glass fibres in propylamine to reduce any cytotoxic response caused by the Ge-Sb-Se fibres. Neutron diffraction experiments are combined with Tg and density measurements along the stoichiometric tie-line x(GeSe2)-(1-x)( Sb2Se3), to aid in a greater understanding of the structure-property relationship of Ge-Sb-Se glasses for the future selection of candidate glass step-index fibre pairs. The preliminary work established that the stoichiometric glasses are predominantly made up of [GeSe4] and [SbSe3] units. From the neutron diffraction data, it is suggested that the average bond length of a Sb-Se bond was 2.62 ± 0.001 Å and the average bond length of a Ge-Se bond was 2.37 ± 0.001 Å. Extracting the coordination of the Ge and Sb elements is found to be difficult on account of an overlap of the Ge-Se and Sb-Se peaks. Therefore further analysis, using nuclear magnetic resonance (NMR) and X-ray diffraction (XRD) is suggested. It is shown that, as the vitreous structure changes from higher levels of [SbSe3] units to incorporate more [GeSe4] (thus a reduction of Sb), the Tg of the glass increases and the density decreases. A close match in Tg (< 23 °C) is recommended as critical for the successful fabrication of a Ge-Sb-Se chalcogenide glass fibre. Thus, knowledge of the trend in Tg, dependent on the ratio of [SbSe3] units to [GeSe4] units, is an initial step in selecting theoretical Ge-Sb-Se compositions with a closer match of thermal properties as candidate glass step-index fibre pairs. Having a more accurate guide to select theoretically Ge-Sb-Se glass compositions to match thermal properties is suggested to save time synthesising and characterising obsolete compositions. It is concluded that Ge-Sb-Se chalcogenide glass fibres, developed through this Project, are strong candidates towards achieving MIR SCG small-core fibres, with the potential application for the transmission of MIR to and from potentially cancerous skin tissue samples. Therefore, enabling in vivo mapping for an immediate diagnostic response.