Medical imaging plays a vital role in the medical field because it is widely used in diseases diagnosis and treatment of patients. There are different modalities of medical imaging such as ultrasounds, x-rays, Computed Tomography (CT), Magnetic Resonance (MR), and Positron Emission Tomography (PET). Most of these modalities usually suffer from noise and other sampling artifacts. The diagnosis process in these modalities depends mainly on the interpretation of the radiologists. Consequently, the diagnosis is subjective as it is based on the radiologist experience. Medical image segmentation is an important process in the field of image processing. It has a significant role in many applications such as diagnosis, therapy planning, and advanced surgeries. There are many segmentation techniques to be applied on medical images. However, most of these techniques are still depending on the experts, especially for initializing the segmentation process. The artifacts of images can affect the segmentation output. In this thesis, we propose a new approach for automatic prostate segmentation of Trans-Rectal UltraSound (TRUS) images by dealing with the speckle not as noise but as informative signals. The new approach is an automation of the conventional region growing technique. The proposed approach overcomes the requirement of manually selecting a seed point for initializing the segmentation process. In addition, the proposed approach depends on unique features such as the intensity and the spatial Euclidean distance to overcome the effect of the speckle noise of the images. The experimental results of the proposed approach show that it is fast and accurate. Moreover, it performs well on the ultrasound images, which has the common problem of the speckle noise.

<p>The behavior of light after interacting with a biological medium reveals a wealth of information that may be used to distinguish between normal and disease states. This may be achieved by simply imaging the morphology of tissues or individual cells, and/or by more sophisticated methods that quantify specific surrogate biomarkers of disease. To this end, the work presented in this dissertation demonstrates novel tools derived from low coherence interferometry (LCI) that quantitatively measure wavelength-dependent scattering and absorption properties of biological samples, with high spectral resolution and micrometer spatial resolution, to provide insight into disease states. </p><p>The presented work first describes a dual window (DW) method, which decomposes a signal sampled in a single domain (in this case the frequency domain) to a distribution that simultaneously contains information from both the original domain and the conjugate domain (here, the temporal or spatial domain). As the name suggests, the DW method utilizes two independently adjustable windows, each with different spatial and spectral properties to overcome limitations found in other processing methods that seek to obtain the same information. A theoretical treatment is provided, and the method is validated through simulations and experiments. With this tool, the spatially dependent spectral behavior of light after interacting with a biological medium may be analyzed to extract parameters of interest, such as the scattering and absorption properties. </p><p>The DW method is employed to investigate scattering properties of samples using Fourier domain LCI (fLCI). In this method, induced temporal coherence effects provide insight into structural changes in dominant scatterers, such as cell nuclei within tissue, which can reveal the early stages of cancerous development. fLCI is demonstrated in complex, three-dimensional samples using a scattering phantom and an ex-vivo animal model. The results from the latter study show that fLCI is able to detect changes in the morphology of tissues undergoing precancerous development. </p><p>The DW method is also employed to enable a novel form of optical coherence tomography (OCT), an imaging modality that uses coherence gating to obtain micrometer-scale, cross-sectional information of tissues. The novel method, named molecular imaging true color spectroscopic OCT (METRiCS OCT), analyses the depth dependent absorption of light to ascertain quantitative information of chromophore concentration, such as hemoglobin. The molecular information is also processed to yield a true color representation of the sample, a unique capability of this approach. A number of experiments, including hemoglobin absorbing phantoms and in-vivo imaging of a chick embryo model and dorsal skinfold window chamber model, demonstrate the power of the method. </p><p>The final method presented in this dissertation, consists of a spectroscopic approach that interrogates the dispersive biochemical properties of samples to independently probe the scattering and absorption coefficients. To demonstrate this method, named non-linear phase dispersion spectroscopy (NLDS), a careful analysis of LCI signals is presented. The method is verified using measurements from samples that scatter and absorb light. Lastly, NLDS is combined with phase microscopy to achieve molecular imaging with sub-micron spatial resolution. Imaging of red blood cells (RBCs) shows that the method enables highly sensitive measurements that can quantify hemoglobin content from single RBCs.</p> / Dissertation

The  anatomic  human  body  is  increasingly  visible  in  public  culture.  Representations  of  the  body  sourced  from  or  imitative  of  the  images  produced  by  medical  imaging   technology  are  bloodless  depictions  that  highlight  the  body’s  internal  structures  and  elide its viscerality. Despite the deliberate exclusion of the flesh, many of these images are saturated  in  erotic  potential,  both  implicitly  and  explicitly.  These  images  emerge  in  a  culture   preoccupied  with  the  visualization  and  control  of  women’s  bodies  and  sexualities. Feminist  scholars  have  long  been  critical  of  the  ways  in  which  popular  media   constructs  the  body  as  an  object  for  erotic  consumption;;  the  anatomic  images  I  consider   here  go  one  step  further.  The  mainstream  gaze  has  previously  been  limited  to  the  exterior   surfaces  of  the  body,  with  the  penetrating  gaze  into  the  body’s  interior  restricted  to  the   medical  and  legal  establishments.  The  penetrating  gaze  is  increasingly  democratized  as   x-ray  and  other  interior  views  of  the  body  become  more  prevalent.The  texts  under  discussion  in  this  thesis  traverse  the  opaque  barrier  of  the  skin  and  serve  to  construct  the  totality   of  the  human  body  as  an  object  to  be  examined  and  consumed. While  X-­rated  x-­rays  can,  sometimes,  offer  a  potential  site  of  resistance  to  gen-­ dered  surveillance  of  the  anatomic  body,  their  increasing  ubiquity  demonstrates  the   escalation  of  a  dominating  surveillant  regime  intent  on  penetrating  and  controlling  the   anatomic  body.  The  images’  uncritical  public  consumption  provides  an  insidious  route  by which that regime may be normalized, furthered and even glorified. / text

The goal of this thesis is to study the potential of optical spectroscopy as a clinical diagnostic tool for melanoma and nonmelanoma skin cancer. Skin cancer is the most common cancer in the United States. Like most cancers, early diagnosis and treatment improves patient prognosis for both melanoma and nonmelanoma skin cancer. However, current “gold standard” for diagnosis is invasive, costly and time-consuming. A diagnostic procedure consists of a clinical examination of the suspicious lesion, followed by biopsy and histopathology, with an additional turnaround time of approximately one week. There is a need for an accurate, objective, noninvasive, and faster method to aid physician in diagnosing cancerous lesions, increasing diagnosis accuracy while preventing unnecessary biopsies. We propose Spectral Diagnosis, a system capable of noninvasive in vivo spectroscopic examination of human skin. The research objectives are: (1) Probe pressure effects on in vivo spectroscopy measurements of human skin, (2) Clinical trial of Spectral Diagnosis, (3) Design, construction, and characterization of a confocal Raman microspectroscope. Spectral Diagnosis utilizes an optical fiber probe that transmits and collects optical spectra in contact with the suspected lesion. We identified short term and light probe pressure effects to be minimal on diagnostic parameters, and should not negatively influence diagnostic performance. We conducted a clinical trial at the University of Texas MD Anderson Cancer Center, and our results show that principal components from three spectroscopy modalities (diffuse reflectance spectroscopy, laser induced fluorescence spectroscopy, and Raman spectroscopy) provide excellent melanoma and nonmelanoma skin cancer diagnosis. We also constructed and characterized a Raman microspectroscope, with the goal of developing a physiological-based fitting model to better understand the analysis of in vivo Raman spectroscopy data from human skin tissue. / text

<p> In MRI, it is more desirable to scan less data as possible because it reduces MRI scanning time. We want to get a clear image by reconstructing the signals we acquire from the MRI machine. Special scanning or sampling techniques are needed to overcome this issue based on various mathematical methods. </p><p> We present an improved random sampling pattern for SAKE (simultaneous autocalibrating and k-space estimation) reconstruction and an iterative GRAPPA reconstruction using Wiener filter. </p><p> In our iterative method using Wiener filter, in contrast to the conventional GRAPPA where only the auto calibration signals (ACS) are used to find the convolution weights, our proposed method iteratively updates the convolution weights using both the acquired and reconstructed data from previous iterations in the entire k-space. To avoid error propagation, the method applies adaptive Wiener filter on the reconstructed data. Experimental results demonstrate that even with a smaller number of ACS lines the proposed method improves the SNR when compared to GRAPPA. </p><p> In compressed sensing MRI, it is very important to design sampling pattern for random sampling. For example, SAKE (simultaneous auto-calibrating and k-space estimation) is a parallel MRI reconstruction method using random undersampling. It formulates image reconstruction as a structured low-rank matrix completion problem. Variable density (VD) Poisson discs are typically adopted for 2D random sampling. The basic concept of Poisson disc generation is to guarantee samples are neither too close to nor too far away from each other. However, it is difficult to meet such a condition especially in the high density region. Therefore the sampling becomes inefficient. In this paper, we present an improved random sampling pattern for SAKE reconstruction. The pattern is generated based on a conflict cost with a probability model. The conflict cost measures how many dense samples already assigned are around a target location, while the probability model adopts the generalized Gaussian distribution which includes uniform and Gaussian-like distributions as special cases. Our method preferentially assigns a sample to a k-space location with the least conflict cost on the circle of the highest probability. To evaluate the effectiveness of the proposed random pattern, we compare the performance of SAKEs using both VD Poisson discs and the proposed pattern. Experimental results for brain data show that the proposed pattern yields lower normalized mean square error (NMSE) than VD Poisson discs.</p>

<p>MRI can benefit from an increase in the sensitivity of contrast agents. The CEST MRI technique in particular suffers from very poor sensitivity when using diamagnetic contrast agents. Polymerized CEST MRI contrast agents could increase the sensitivity per macromolecule over monomer contrast agents. The increase in sensitivity is related to the increase in number of contrast agents per polymer. A contrast agent with increased sensitivity can be used to image on the molecular level in vivo, where the concentration of targets is very low. A polymerized diaCEST contrast agent was synthesized by coupling a salicylic acid analogue to a poly (acrylic acid) backbone. The CEST effect of the coupled analogue was compared to its uncoupled form for different concentrations and pH values. A RL-QUEST method was used to calculate the exchange rate of the analogue for different pH values before and after coupling. The polymerized diaCEST agent was attempted to be loaded into DOPC and bis-SorbPC liposomes, and was also attempted to be targeted to folate receptors in a KB cell culture. These studies establish the foundation for translation of polymerized diaCEST contrast agents to additional in vitro and in vivo investigations. </p>

In current digital imaging systems, new components such as digital display, image compression, image processing, as well as film digitization and film printing are introduced, in addition to analogue or digital imaging modalities. Although the current trend is towards fully digital systems, analog images (films) represent a high percentage of the volume of medical image data in the interim transition period from analog to digital. Soft copy display of medical image using CRT monitors, which plays a critical role in diagnostic information extraction, is one of the most vulnerable to failure and performance degradation component of the display workstation. Medical film digitizers and film printers play an important transitory role as analog-to-digital bridges in current PACS. Lossless compression algorithms are widely used in digital medical imaging systems for efficient image storage, transmission, and display, while lossy ones, offering significantly higher compression ratios, are emerging. An important factor for the acceptance of lossy compression in clinical practice is the assessment of “visually lossless” compression thresholds. The above components, as well as the services involving them in telemedicine or PACS systems, introduce additional needs of performance evaluation. In this thesis a performance evaluation protocol, applicable to each of the new components of digital medical imaging systems, as well as to telemedicine or PACS services, is proposed. The proposed protocol is based on a set of transfer characteristics assessment, such as characteristic curve, high contrast transfer, low contrast transfer, noise, uniformity, and geometric distortion, common to all components, and additional component specific parameters (i.e. veiling glare for CRT monitors). The application of the protocol for each component is based on the use of digital test objects, designed using a software tool, which enables (a) user-driven selection of patterns, associated to evaluation parameters, to be included, and (b) user-driven pattern specifications, according to requirements of individual components. The protocol has been applied for the assessment of transfer characteristics of: (a) three film digitizers, (b) two CRT monitors, (c) two film printers, and (d) two compression algorithms, used or intended for use in digital medical imaging systems, to demonstrate its completeness with respect to evaluation parameters, its sensitivity (i.e., the capability to differentiate between components of the same category and with similar performance), and its adaptability with respect to the specifications of the individual component being tested. Of the three film digitizers tested two are CCD based, Lumiscan 20 and Agfa DuoScan, and one is laser based, Lumiscan 75. Measurements performed show superior performance of the Lumiscan 75 digitizer with respect to its characteristic curve and amount of noise introduced. The Agfa DuoScan has superior performance with respect to spatial resolution. For low contrast discrimination the Agfa DuoScan has superior performance for low optical densities, up to 1.8 o.d. units, while for higher optical densities the Lumiscan 75 digitizer show better performance. The Lumiscan 20 film digitizer has a linear characteristic curve and acceptable noise handling up to 2.8 o.d. units, but low spatial resolution. Of the two CRT monitors tested, Sony E500 and Samsung 950p, the former exhibits slight performance superiority, but they are both characterized by limited performance with respect to maximum luminance, resolution (high contrast response), and low contrast discrimination. Of the two film printers tested, AGFA DrayStar 2000 and Kodak DrayView 8100, the latter shows better performance with respect to characteristic curve, high contrast response and low contrast discrimination. The assessment results for the JPEG compression algorithm tested (OTE-TS implementation) indicate the compression ratio of 15:1, as a visually lossless threshold in case of low contrast lesion detection in x-ray chest images, in agreement with previous observer performance studies. The wavelet based compression algorithm tested (Pegasus Imaging Corp. implementation) is JPEG 2000 compatible with respect to the wavelet filters used. Its visually lossless threshold, derived from contrast threshold curves associated with microcalcification cluster detection in mammograms, is at compression ratio 35:1, and it is lowered at 30:1 if a perceptibility criterion for image quality degradation is applied. The validation study, based on ROC analysis of observers’ performance, confirmed these values, as the threshold for cluster detection is at compression ratio 40:1, and it is lowered to 25:1 by observers’ image quality grading. Component performance evaluation results indicate that the proposed protocol can be successfully used for comparative evaluation of film digitizers, film printers and CRT monitors. In case of compression algorithms, the proposed protocol can be used: (a) as a preliminary step for testing the algorithm during development, (b) for comparative evaluation of algorithms, and (c) in the efficient planning of a ROC study with respect to range of interest of compression ratios. The wide applicability of the proposed protocol is based on a generic set of common transfer characteristics with respect to components and services, and is also empowered by the userdriven design of the digital test objects used. Test objects design is flexible, due to their soft character, enabling adaptation of the design to the technical specifications of each type of individual component. / Η τρέχουσα τάση στην ιατρική απεικόνιση είναι τα πλήρη ψηφιακά απεικονιστικά συστήματα. Κύρια χαρακτηριστικά των ψηφιακών απεικονιστικών συστημάτων είναι πρώτον ο διαχωρισμός καταγραφής και παρουσίασης εικόνας, μέσω ψηφιακών ανιχνευτών και οθονών CRT αντίστοιχα, και δεύτερον η ψηφιακή επεξεργασία/ανάλυση και μετάδοση ιατρικής εικόνας, στα πλαίσια συστημάτων PACS και Τηλε-ιατρικής. Μεταβατικά, οι ψηφιοποιητές και οι εκτυπωτές ιατρικού φιλμ διαδραματίζουν ένα σπουδαίο ρόλο ως “γέφυρες” μεταξύ αναλογικών και ψηφιακών συστημάτων. Η αποδοτική αποθήκευση, μετάδοση και παρουσίαση ψηφιακών ιατρικών εικόνων επέβαλλε τη χρήση αλγορίθμων συμπίεσης. Προς το παρόν, οι αντιστρέψιμοι αλγόριθμοι (lossless) είναι κλινικά αποδεκτοί, ενώ οι μη αντιστρέψιμοι (lossy), οι οποίοι χαρακτηρίζονται από μεγάλους λόγους συμπίεσης, αποτελούν τρέχον πεδίο έρευνας. Οι νέες συνιστώσες των ψηφιακών ιατρικών απεικονιστικών συστημάτων δημιουργούν την ανάγκη ανάπτυξης πρωτοκόλλων ελέγχου απόδοσης για τη διασφάλιση υψηλής ποιότητας ιατρικής εικόνας. Στα πλαίσια της διατριβής αυτής αναπτύχθηκε ένα πρωτόκολλο ελέγχου απόδοσης, γενικής χρήσεως, ικανό να ανταποκρίνεται σε όλες τις ανωτέρω συνιστώσες και υπηρεσίες. Το πρωτόκολλο βασίζεται σε ένα σύνολο χαρακτηριστικών μεταφοράς, κοινό για όλες τις συνιστώσες, όπως η χαρακτηριστική καμπύλη, η μεταφορά υψηλής αντίθεσης, η μεταφορά χαμηλής αντίθεσης, ο θόρυβος, η ομοιογένεια και η γεωμετρική παραμόρφωση, καθώς και σε χαρακτηριστικά εξειδικευμένα για κάθε συνιστώσα. Η εφαρμογή του πρωτοκόλλου στηρίζεται στη χρήση ψηφιακών ομοιωμάτων (digital test objects) που σχεδιάζονται με χρήση λογισμικού που σχεδιάστηκε και αναπτύχθηκε στα πλαίσια της διατριβής. Η εφαρμοσιμότητα του πρωτοκόλλου πιστοποιήθηκε σε: (α) τρεις ψηφιοποιητές ιατρικού φιλμ (Lumiscan 75, Lumiscan 20 και Agfa DuoScan), (β) δύο οθόνες ψηφιακής παρουσίασης (Sony E500 και Samsung 950p), (γ) δύο εκτυπωτές ιατρικού φιλμ (Agfa DrayStar 200 και Kodak DrayView 8100) και (δ) δύο αλγορίθμους συμπίεσης (OTE-TS JPEG και Pegasus wavelet-based), που χρησιμοποιούνται ή προτείνονται για χρήση σε ιατρικά απεικονιστικά συστήματα. Ειδικότερα ελέγχθηκαν: (ι) η πληρότητα του κοινού συνόλου χαρακτηριστικών μεταφοράς, (ιι) η ευαισθησία τους, δηλαδή η ικανότητα διαφοροποίησης μεταξύ συνιστωσών της ίδιας κατηγορίας και (ιιι) η προσαρμοστικότητα των ψηφιακών ομοιωμάτων στις τεχνικές προδιαγραφές των επιμέρους συνιστωσών. Από τους ψηφιοποιητές ιατρικού φιλμ που ελέγχθηκαν, ο Lumiscan 75 έχει καλύτερη απόδοση ως προς την χαρακτηριστική καμπύλη και το θόρυβο. Ο ψηφιοποιητής Agfa DuoScan έχει καλύτερη απόδοση ως προς την μεταφορά υψηλής αντίθεσης. Ως προς την μεταφορά χαμηλής αντίθεσης, ο ψηφιοποιητής Agfa DuoScan έχει καλύτερη απόδοση για χαμηλές οπτικές πυκνότητες, μέχρι 1.8. o.d. μονάδες, ενώ ο ψηφιοποιητής Lumiscan 75 έχει καλύτερη απόδοση για υψηλές οπτικές πυκνότητες. Ο ψηφιοποιητής Lumiscan 20, έχει γραμμική χαρακτηριστική καμπύλη και ικανοποιητικό χειρισμό θορύβου για οπτικές πυκνότητες μικρότερες από 2.8 o.d. μονάδες, αλλά χαρακτηρίζεται από χαμηλή απόδοση ως προς την μεταφορά υψηλής αντίθεσης. Σχετικά με την απόδοση οθονών η Sony E500 έχει καλύτερη απόδοση, όμως και οι δύο οθόνες χαρακτηρίζονται από χαμηλή απόδοση ως προς την χαρακτηριστική καμπύλη και την μεταφορά υψηλής και χαμηλής αντίθεσης. Σχετικά με την απόδοση εκτυπωτών ιατρικού φιλμ ο Kodak DrayView 8100 να έχει καλύτερη απόδοση ως προς την χαρακτηριστική καμπύλη και την μεταφορά υψηλής και χαμηλής αντίθεσης. Ως προς τους αλγορίθμους συμπίεσης, επιβεβαιώθηκε το οπτικά αντιστρέψιμο κατώφλι (visually lossless threshold) του αλγορίθμου JPEG (OTE-TS υλοποίηση), με λόγο συμπίεσης 15:1, που αντιστοιχεί σε ανίχνευση πνευμονικών αλλοιώσεων χαμηλής αντίθεσης στην ακτινογραφία θώρακος. Για τον αλγόριθμο wavelet που μελετήθηκε (Pegasus Imaging Corp. υλοποίηση), ο οποίος είναι συμβατός με το πρότυπο JPEG 2000 ως προς το φίλτρο wavelet, προτείνεται οπτικά αντιστρέψιμο κατώφλι με λόγο συμπίεσης 35:1, στην περίπτωση ανίχνευσης ομάδων αποτιτανώσεων στη μαστογραφία. Με τη χρήση κριτηρίου αντίληψης υποβάθμισης ποιότητας εικόνας (perceptibility criterion for image quality degradation) το κατώφλι μειώνεται σε 30:1. Τα κατώφλια επιβεβαιώθηκαν και με ανάλυση ROC, η οποία ανάδειξε το οπτικά αντιστρέψιμο κατώφλι για ανίχνευση ομάδων αποτιτανώσεων σε 40:1, ενώ με τη διαβάθμιση ποιότητας εικόνας από τους παρατηρητές, το κατώφλι μειώνεται σε 25:1. Τα αποτελέσματα συγκριτικής απόδοσης των ψηφιοποιητών, των οθονών και των εκτυπωτών ανάδειξαν ότι το προτεινόμενο πρωτόκολλο ανταποκρίνεται στις απαιτήσεις των ανωτέρω συνιστωσών. Ως προς τους αλγόριθμους συμπίεσης, το προτεινόμενο πρωτόκολλο μπορεί να χρησιμοποιηθεί για: (α) βελτιστοποίηση των αλγορίθμων κατά τη διαδικασία ανάπτυξης, (β) συγκριτικό έλεγχο μεταξύ διαφορετικών αλγορίθμων, και (γ) αποδοτική σχεδίαση μελέτης ROC, μέσω του περιορισμού του εύρους των λόγων συμπίεσης. Η ευρεία εφαρμοσιμότητα του προτεινόμενου πρωτοκόλλου βασίζεται στο κοινό σύνολο χαρακτηριστικών μεταφοράς για συνιστώσες και υπηρεσίες, και ενδυναμώνεται με την χρήση ψηφιακών ομοιωμάτων. Ο σχεδιασμός των ψηφιακών ομοιωμάτων επιτρέπει την προσαρμογή τους στις ανάγκες του χρήστη και των τεχνικών προδιαγραφών της κάθε συνιστώσας.

Medical image analysis is a ubiquitous and essential part of modem health care. A crucial first step to this is segmentation, which is often complicated by many factors including subject diversity, pathology, noise corruption, and poor image resolution. Traditionally, manual tracing by experts was done. While considered accurate, this process is time consuming and tedious, especially when performed slice-by-slice on three-dimensional (3D) images over large datasets or on two-dimensional (2D) but topologically complicated images such as a retinography. On the other hand, fully-automated methods are typically faster, but work best with data-dependent, carefully tuned parameters and still require user validation and refinement. This thesis contributes to the field of medical image segmentation by proposing a highly-automated, interactive approach that effectively merges user knowledge and efficient computing. To this end, our work focuses on graph-based methods and offer globally optimal solutions. First, we present a novel method for 3D segmentation based on a 3D Livewire approach. This approach is an extension of the 2D Livewire framework, and this method is capable of handling objects with large protrusions, concavities, branching, and complex arbitrary topologies. Second, we propose a method for efficiently segmenting 2D vascular networks, called ‘Live-Vessel’. Live-Vessel simultaneously extracts vessel centrelines and boundary points, and globally optimizes over both spatial variables and vessel radius. Both of our proposed methods are validated on synthetic data, real medical data, and are shown to be highly reproducible, accurate, and efficient. Also, they were shown to be resilient to high amounts of noise and insensitive to internal parameterization.

Thesis (M. Sc.)--University of Canterbury, 2006. / Typescript (photocopy). "Year: 2004-2006." Includes bibliographical references (leaves 108-112). Also available via the World Wide Web.

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