Computer-aided detection of colonic polyps with level set-based adaptive convolution in volumetric mucosa to advance CT colonography toward a screening modality

As a promising second reader of computed tomographic colonography (CTC) screening, the computer-aided detection (CAD) of colonic polyps has earned fast growing research interest. In this paper, we present a CAD scheme to automatically detect colonic polyps in CTC images. First, a thick colon wall representation, ie, a volumetric mucosa (VM) with several voxels wide in general, was segmented from CTC images by a partial-volume image segmentation algorithm. Based on the VM, we employed a level set-based adaptive convolution method for calculating the first- and second-order spatial derivatives more accurately to start the geometric analysis. Furthermore, to emphasize the correspondence among different layers in the VM, we introduced a middle-layer enhanced integration along the image gradient direction inside the VM to improve the operation of extracting the geometric information, like the principal curvatures. Initial polyp candidates (IPCs) were then determined by thresholding the geometric measurements. Based on IPCs, several features were extracted for each IPC, and fed into a support vector machine to reduce false positives (FPs). The final detections were displayed in a commercial system to provide second opinions for radiologists. The CAD scheme was applied to 26 patient CTC studies with 32 confirmed polyps by both optical and virtual colonoscopies. Compared to our previous work, all the polyps can be detected successfully with less FPs. At the 100% by polyp sensitivity, the new method yielded 3.5 FPs/dataset

Computer-aided detection of polyps in CT colonography

Master'sMASTER OF ENGINEERIN

Feature extraction to aid disease detection and assessment of disease progression in CT and MR colonography

Computed tomographic colonography (CTC) is a technique employed to examine the whole colon for cancers and premalignant adenomas (polyps). Oral preparation is taken to fully cleanse the colon, and gas insufflation maximises the attenuation contrast between the enoluminal colon surface and the lumen. The procedure is performed routinely with the patient both prone and supine to redistribute gas and residue. This helps to differentiate fixed colonic pathology from mobile faecal residue and also helps discover pathology occluded by retained fluid or luminal collapse. Matching corresponding endoluminal surface locations with the patient in the prone and supine positions is therefore an essential aspect of interpretation by radiologists; however, interpretation can be difficult and time consuming due to the considerable colonic deformations that occur during repositioning. Hence, a method for automated registration has the potential to improve efficiency and diagnostic accuracy. I propose a novel method to establish correspondence between prone and supine CT colonography acquisitions automatically. The problem is first simplified by detecting haustral folds which are elongated ridgelike endoluminal structures and can be identified by curvature based measurements. These are subsequently matched using appearance based features, and their relative geometric relationships. It is shown that these matches can be used to find correspondence along the full length of the colon, but may also be used in conjunction with other registration methods to achieve a more robust and accurate result, explicitly addressing the problem of colonic collapse. The potential clinical value of this method has been assessed in an external clinical validation, and the application to follow-up CTC surveillance has been investigated. MRI has recently been applied as a tool to quantitatively evaluate the therapeutic response to therapy in patients with Crohn's disease, and is the preferred choice for repeated imaging. A primary biomarker for this evaluation is the measurement of variations of bowel wall thickness on changing from the active phase of the disease to remission; however, a poor level of interobserver agreement of measured thickness is reported and therefore a system for accurate, robust and reproducible measurements is desirable. I propose a novel method which will automatically track sections of colon, by estimating the positions of elliptical cross sections. Subsequently, estimation of the positions of the inner and outer bowel walls are made based on image gradient information and therefore a thickness measurement value can be extracted

Development of a new, minimally invasive, full thickness excision technique for early colonic neoplasia

Introduction of bowel cancer screening programmes internationally has resulted in a significant shift in diagnosis towards early stage disease. In addition, the number of patients diagnosed with complex benign colorectal polyps is increasing. Advanced endoscopic techniques including endoscopic mucosal resection (EMR) and endoscopic submucosal dissection (ESD) as well as transanal endoscopic microsurgery (TEMS) are being increasingly utilised for excision of early rectal neoplasia. An equivalent surgical technique is currently not available for colonic lesions, and endoscopic techniques are associated with a high risk of complications such as bleeding, perforation and recurrence than in the rectum. Hemicolectomy with en bloc mesenteric excision remains the gold standard treatment for patients with early, node negative colon cancer and large colonic polyps. Even when performed laparoscopically within an enhanced recovery protocol, problems such as death, anastomotic leakage and other complications occurring in up to 40% of patients make colectomy a morbid intervention. The introduction to this thesis reviews the literature on the development and staging of colorectal cancer as well as currently available endoscopic and surgical techniques. In order to improve our understanding of the morbidity associated with hemicolectomy for the treatment of benign colonic polyps, two studies examined short term outcomes after surgery. The results suggest similar 30-day outcomes to those after cancer resection. In addition, a two-part study was designed to assess bowel function and related quality of life in patients who underwent hemicolectomy for colonic neoplasia, a subject that is poorly documented in the literature. As an introduction to the laboratory work, a systematic review of endoscopic full thickness excision techniques is presented. The final three chapters of the thesis describe ex-vivo development and outcome data after a porcine survival study of a laparo-endoscopic excision technique for colonic lesions as a potential alternative to hemicolectomy.Open Acces

Automatic colonic polyp detection using curvature analysis for standard and low dose CT data

Colon cancer is the second leading cause of cancer related deaths in the developed nations. Early detection and removal of colorectal polyps via screening is the most effective way to reduce colorectal cancer (CRC) mortality. Computed Tomography Colonography (CTC) or Virtual Colonoscopy (VC) is a rapidly evolving non-invasive technique and the medical community view this medical procedure as an alternative to the standard colonoscopy for the detection of colonic polyps. In CTC the first step for automatic polyp detection for 3D visualization of the colon structure and automatic polyp detection addresses the segmentation of the colon lumen. The segmentation of colon lumen is far from a trivial task as in practice many datasets are collapsed due to incorrect patient preparation or blockages caused by residual water/materials left in the colon. In this thesis a robust multi-stage technique for automatic segmentation of the colon is proposed tha t maximally uses the anatomical model of a generic colon. In this regard, the colon is reconstructed using volume by length analysis, orientation, length, end points, geometrical position in the volumetric data, and gradient of the centreline of each candidate air region detected in the CT data. The proposed method was validated using a total of 151 standard dose (lOOmAs) and 13 low-dose (13mAs-40mAs) datasets and the collapsed colon surface detection was always higher than 95% with an average of 1.58% extra colonic surface inclusion. The second major step of automated CTC attempts the identification of colorectal polyps. In this thesis a robust method for polyp detection based on surface curvature analysis has been developed and evaluated. The convexity of the segmented colon surface is sampled using the surface normal intersection, Hough transform, 3D histogram, Gaussian distribution, convexity constraint and 3D region growing. For each polyp candidate surface the morphological and statistical features are extracted and the candidate surface is classified as a polyp/fold structure using a Feature Normalized Nearest Neighbourhood classifier. The devised polyp detection scheme entails a low computational overhead (typically takes 3.60 minute per dataset) and shows 100% sensitivity for polyps larger than 10mm, 92% sensitivity for polyps in the range 5 to 10mm and 64.28% sensitivity for polyp smaller than 5mm. The developed technique returns in average 4.01 false positives per dataset. The patient exposure to ionising radiation is the major concern in using CTC as a mass screening technique for colonic polyp detection. A reduction of the radiation dose will increase the level of noise during the acquisition process and as a result the quality of the CT d a ta is degraded. To fully investigate the effect of the low-dose radiation on the performance of automated polyp detection, a phantom has been developed and scanned using different radiation doses. The phantom polyps have realistic shapes (sessile, pedunculated, and flat) and sizes (3 to 20mm) and were designed to closely approximate the real polyps encountered in clinical CT data. Automatic polyp detection shows 100% sensitivity for polyps larger than 10mm and shows 95% sensitivity for polyps in the range 5 to 10mm. The developed method was applied to CT data acquired at radiation doses between 13 to 40mAs and the experimental results indicate th a t robust polyp detection can be obtained even at radiation doses as low as 13mAs

Registration of prone and supine CT colonography images and its clinical application

Computed tomographic (CT) colonography is a technique for detecting bowel cancer and potentially precancerous polyps. CT imaging is performed on the cleansed and insufflated bowel in order to produce a virtual endoluminal representation similar to optical colonoscopy. Because fluids and stool can mimic pathology, images are acquired with the patient in both prone and supine positions. Radiologists then match endoluminal locations visually between the two acquisitions in order to determine whether pathology is real or not. This process is hindered by the fact that the colon can undergo considerable deformation between acquisitions. Robust and accurate automated registration between prone and supine data acquisitions is therefore pivotal for medical interpretation, but a challenging problem. The method proposed in this thesis reduces the complexity of the registration task of aligning the prone and supine CT colonography acquisitions. This is done by utilising cylindrical representations of the colonic surface which reflect the colon's specific anatomy. Automated alignment in the cylindrical domain is achieved by non-rigid image registration using surface curvatures, applicable even when cases exhibit local luminal collapses. It is furthermore shown that landmark matches for initialisation improve the registration's accuracy and robustness. Additional performance improvements are achieved by symmetric and inverse-consistent registration and iteratively deforming the surface in order to compensate for differences in distension and bowel preparation. Manually identified reference points in human data and fiducial markers in a porcine phantom are used to validate the registration accuracy. The potential clinical impact of the method has been evaluated using data that reflects clinical practise. Furthermore, correspondence between follow-up CT colonography acquisitions is established in order to facilitate the clinical need to investigate polyp growth over time. Accurate registration has the potential to both improve the diagnostic process and decrease the radiologist's interpretation time. Furthermore, its result could be integrated into algorithms for improved computer-aided detection of colonic polyps

An Investigation of the Diagnostic Potential of Autofluorescence Lifetime Spectroscopy and Imaging for Label-Free Contrast of Disease

The work presented in this thesis aimed to study the application of fluorescence lifetime spectroscopy (FLS) and fluorescence lifetime imaging microscopy (FLIM) to investigate their potential for diagnostic contrast of diseased tissue with a particular emphasis on autofluorescence (AF) measurements of gastrointestinal (GI) disease. Initially, an ex vivo study utilising confocal FLIM was undertaken with 420 nm excitation to characterise the fluorescence lifetime (FL) images obtained from 71 GI samples from 35 patients. A significant decrease in FL was observed between normal colon and polyps (p = 0.024), and normal colon and inflammatory bowel disease (IBD) (p = 0.015). Confocal FLIM was also performed on 23 bladder samples. A longer, although not significant, FL for cancer was observed, in paired specimens (n = 5) instilled with a photosensitizer. The first in vivo study was a clinical investigation of skin cancer using a fibre-optic FL spectrofluorometer and involved the interrogation of 27 lesions from 25 patients. A significant decrease in the FL of basal cell carcinomas compared to healthy tissue was observed (p = 0.002) with 445 nm excitation. A novel clinically viable FLS fibre-optic probe was then applied ex vivo to measure 60 samples collected from 23 patients. In a paired analysis of neoplastic polyps and normal colon obtained from the same region of the colon in the same patient (n = 12), a significant decrease in FL was observed (p = 0.021) with 435 nm excitation. In contrast, with 375 nm excitation, the mean FL of IBD specimens (n = 4) was found to be longer than that of normal tissue, although not statistically significant. Finally, the FLS system was applied in vivo in 17 patients, with initial data indicating that 435 nm excitation results in AF lifetimes that are broadly consistent with ex vivo studies, although no diagnostically significant differences were observed in the signals obtained in vivo.Open Acces

Segmentation and polyp detection in virtual colonoscopy : a complete system for computer aided diagnosis

El cancer colorectal es una de las mayores causas de muerte por cancer en el mundo. La deteccion temprana de polipos es fundamental para su tratamiento, permitiendo alcanzar tasas del 90% de curabilidad. La tecnica habitual para la deteccion de polipos, debido a su elevada performance, es la colonoscopia optica (tecnica invasiva y extremadamente cara). A mediados de los '90 surge la tecnica denominada colonoscopia virtual. Esta tecnica consiste en la reconstruccion 3D del colon a partir de cortes de tomografia computada. Es por ende una tecnica no invasiva, y relativamente barata, pero la cantidad de falsos positivos y falsos negativos producida por estos metodos esta muy por encima de los maximos aceptados en la practica medica. Los avances recientes en las tecnicas de imagenologia parecerian hacer posible la reduccion de estas tasas. Como consecuencia de esto, estamos asistiendo a un nuevo interes por la colonoscopia virtual. En este trabajo se presenta un sistema completo de diagnostico asistido por computadora. La primera etapa del sistema es la segmentacion, que consiste en la reconstruccion 3D de la superficie del colon a partir del volumen tomografico. El aporte principal en este paso es el suavizado de la imagen. A partir de la superficie, se detectan aquellas zonas candidatas de ser polipos mediante una estrategia multi-escala que permite delinear con precision la zona. Luego para cada candidato se extraen caracteristicas geometricas y de textura, que son calculadas tambien en el tejido que rodea la zona a efectos de compararlas. Finalmente las zonas candidatas se clasifican utilizando SVM. Los resultados obtenidos son prometedores, permitiendo detectar un 100% de los polipos mayoresColorectal cancer is the second leading cause of cancer-related death in the United States, and the third cause worldwide. The early detection of polyps is fundamental, allowing to reduce mortality rates up to 90%. Nowadays, optical colonoscopy is the most used detection method due in part to its relative high performance. Virtual Colonoscopy is a promising alternative technique that emerged in the 90's. It uses volumetric Computed Tomographic data of the cleansed and air-distended colon, and the examination is made by a specialist from the images in a computer. Therefore, this technique is less invasive and less expensive than optical colonoscopy, but up to now the false positive and false negative rates are above the accepted medical limits. Recent advances in imaging techniques have the potential to reduce these rates; consequently, we are currently re-experiencing an increasing interest in Virtual Colonoscopy. In this work we propose a complete pipeline for a Computer-Aided Detection algorithm. The system starts with a novel and simple segmentation step. We then introduce geometrical and textural features that take into account not only the candidate polyp region, but the surrounding area at multiple scales as well. This way, our proposed CAD algorithm is able to accurately detect candidate polyps by measuring local variations of these features. Candidate patches are then classi ed using SVM. The whole algorithm is completely automatic and produces state-of-the-art results, achieving 100% sensitivity for polyps greater than 6mm in size with less than one false positive per case, and 100% sensitivity for polyps greater than 3mm in size with 2:2 false positives per case

Facilitating Colorectal Cancer Diagnosis with Computed Tomographic Colonography

Computed tomographic colonography (CTC) is a diagnostic technique involving helical volume acquisition of the cleansed, distended colorectum to detect colorectal cancer or potentially premalignant polyps. This Thesis summarises the evidence base, identifies areas in need of further research, quantifies sources of bias and presents novel techniques to facilitate colorectal cancer diagnosis using CTC. CTC literature is reviewed to justify the rationale for current implementation and to identify fruitful areas for research. This confirms excellent diagnostic performance can be attained providing CTC is interpreted by trained, experienced observers employing state-of-the-art implementation. The technique is superior to barium enema and consequently, it has been embraced by radiologists, clinicians and health policy-makers. Factors influencing generalisability of CTC research are investigated, firstly with a survey of European educational workshop participants which revealed limited CTC experience and training, followed by a systematic review exploring bias in research studies of diagnostic test accuracy which established that studies focussing on these aspects were lacking. Experiments to address these sources of bias are presented, using novel methodology: Conjoint analysis is used to ascertain patients‘ and clinicians’ attitudes to false-positive screening diagnoses, showing that both groups overwhelmingly value sensitivity over specificity. The results inform a weighted statistical analysis for CAD which is applied to the results of two previous studies showing the incremental benefit is significantly higher for novices than experienced readers. We have employed eye-tracking technology to establish the visual search patterns of observers reading CTC, demonstrated feasibility and developed metrics for analysis. We also describe development and validation of computer software to register prone and supine endoluminal surface locations demonstrating accurate matching of corresponding points when applied to a phantom and a generalisable, publically available, CTC database. Finally, areas in need of future development are suggested