Colorectal Cancer Tissue Classification Based on Machine Learning

For digital pathology, automatic recognition of different tissue types in histological images is important for diagnostic assistance and healthcare. Since histological images generally contain more than one tissue type, multi-class texture analysis plays a critical role to solve this problem. This study examines the important statistical features including Gray Level Co-occurrence Matrix (GLCM), Discrete Wavelet Transform (DWT), Spatial filters, Wiener filter, Gabor filters, Haralick features, fractal filters, and local binary pattern (LBP) for colorectal cancer tissue identification by using support vector machine (SVM) and decision fusion of feature selection. The average experimental results achieve high identification rate which is significantly superior to the existing known methods. In summary, the proposed method based on machine learning outperforms the techniques described in the literatures and achieve high classification accuracy rate at 93.17% for eight classes and 96.02% for ten classes which demonstrate promising applications for cancer tissue classification of histological image

Epithelium and Stroma Identification in Histopathological Images using Unsupervised and Semi-supervised Superpixel-based Segmentation

We present superpixel-based segmentation frameworks for unsupervised and semi-supervised epithelium-stroma identification in histopathological images or oropharyngeal tissue micro arrays. A superpixel segmentation algorithm is initially used to split-up the image into binary regions (superpixels) and their colour features are extracted and fed into several base clustering algorithms with various parameter initializations. Two Consensus Clustering (CC) formulations are then used: the Evidence Accumulation Clustering (EAC) and the voting-based consensus function. These combine the base clustering outcomes to obtain a more robust detection of tissue compartments than the base clustering methods on their own. For the voting-based function, a technique is introduced to generate consistent labellings across the base clustering results. The obtained CC result is then utilized to build a self-training Semi-Supervised Classification (SSC) model. Unlike supervised segmentations, which rely on large number of labelled training images, our SSC approach performs a quality segmentation while relying on few labelled samples. Experiments conducted on forty-five hand-annotated images of oropharyngeal cancer tissue microarrays show that (a) the CC algorithm generates more accurate and stable results than individual clustering algorithms; (b) the clustering performance of the voting-based function outperforms the existing EAC; and (c) the proposed SSC algorithm outperforms the supervised methods, which is trained with only a few labelled instances

Prototipo CAD de segmentación automática de cáncer de pulmón en imágenes histopatológicas TMA

El cáncer de pulmón es una enfermedad letal que para el 2012 se situó como la quinta causa de muerte a nivel mundial, la tercera en Europa y la primera en España con casi 20.000 nuevos casos cada año; aproximadamente el 85 % de los sujetos que padecen cáncer de pulmón, morirán por esta enfermedad. El principal obstáculo en la lucha contra esta patología es su detección tardía. El desarrollo que ha experimentado el campo de la imagen médica en aspectos como la adquisición, almacenamiento y visualización ha contribuido al mejoramiento de la calidad del análisis y diagnóstico de las diferentes patologías (entre ellas el cáncer de pulmón) convirtiéndola actualmente en un componente indispensable en medicina. En las últimas décadas, se han realizado numerosos esfuerzos para detectar de manera precoz el cáncer de pulmón mediante el desarrollo de distintas tecnologías, entre ellas los sistemas de diagnóstico asistido por computador (CAD), los cuales mediante el análisis automático de la imagen médica brindan al especialista una segunda opinión diagnostica, con el objetivo de obtener diagnósticos mas precisos que permitan formular tratamientos mas adecuados. La imagen médica histopatológica es el "gold standard. en detección temprana de la mayoría de patológicas incluido el cáncer de pulmón. La tarea de detección suele ser bastante tediosa e que implica una importante inversión de tiempo y esfuerzo por parte de los expertos en histopatología. El crecimiento de los bancos de tejidos ya ha superado las habilidades manuales de análisis disponibles. Además, la revisión de patología experta sufre variaciones ínter e intra observador. Lo anterior evidencia la gran necesidad de automatizar el análisis de imagen médica en histopatológica. En este trabajo se hace una aproximación a la detección de cáncer de pulmón en imagen médica, concretamente abordando el problema de segmentación de tejido tumoral y no tumoral sobre imágenes histopatológicas TMA, mediante el desarrollo de un prototipo de sistema de diagnóstico asistido por computador CAD

Development of deep learning methods for head and neck cancer detection in hyperspectral imaging and digital pathology for surgical guidance

Surgeons performing routine cancer resections utilize palpation and visual inspection, along with time-consuming microscopic tissue analysis, to ensure removal of cancer. Despite this, inadequate surgical cancer margins are reported for up to 10-20% of head and neck squamous cell carcinoma (SCC) operations. There exists a need for surgical guidance with optical imaging to ensure complete cancer resection in the operating room. The objective of this dissertation is to evaluate hyperspectral imaging (HSI) as a non-contact, label-free optical imaging modality to provide intraoperative diagnostic information. For comparison of different optical methods, autofluorescence, RGB composite images synthesized from HSI, and two fluorescent dyes are also acquired and investigated for head and neck cancer detection. A novel and comprehensive dataset was obtained of 585 excised tissue specimens from 204 patients undergoing routine head and neck cancer surgeries. The first aim was to use SCC tissue specimens to determine the potential of HSI for surgical guidance in the challenging task of head and neck SCC detection. It is hypothesized that HSI could reduce time and provide quantitative cancer predictions. State-of-the-art deep learning algorithms were developed for SCC detection in 102 patients and compared to other optical methods. HSI detected SCC with a median AUC score of 85%, and several anatomical locations demonstrated good SCC detection, such as the larynx, oropharynx, hypopharynx, and nasal cavity. To understand the ability of HSI for SCC detection, the most important spectral features were calculated and correlated with known cancer physiology signals, notably oxygenated and deoxygenated hemoglobin. The second aim was to evaluate HSI for tumor detection in thyroid and salivary glands, and RGB images were synthesized using the spectral response curves of the human eye for comparison. Using deep learning, HSI detected thyroid tumors with 86% average AUC score, which outperformed fluorescent dyes and autofluorescence, but HSI-synthesized RGB imagery performed with 90% AUC score. The last aim was to develop deep learning algorithms for head and neck cancer detection in hundreds of digitized histology slides. Slides containing SCC or thyroid carcinoma can be distinguished from normal slides with 94% and 99% AUC scores, respectively, and SCC and thyroid carcinoma can be localized within whole-slide images with 92% and 95% AUC scores, respectively. In conclusion, the outcomes of this thesis work demonstrate that HSI and deep learning methods could aid surgeons and pathologists in detecting head and neck cancers.Ph.D

Automated analysis of colorectal cancer

Colorectal cancer (CRC) is the second largest cause of cancer deaths in the UK, with approximately 16,000 per year. Over 41,000 people are diagnosed annually, and 43% of those will die within ten years of diagnosis. The treatment of CRC patients relies on pathological examination of the disease to identify visual features that predict growth and spread, and response to chemoradiotherapy. These prognostic features are identified manually, and are subject to inter and intra-scorer variability. This variability stems from the subjectivity in interpreting large images which can have very varied appearances, as well as the time consuming and laborious methodology of visually inspecting cancer cells. The work in this thesis presents a systematic approach to developing a solution to address this problem for one such prognostic indicator, the Tumour:Stroma Ratio (TSR). The steps taken are presented sequentially through the chapters, in order of the work carried out. These specifically involve the acquisition and assessment of a dataset of 2.4 million expert-classified images of CRC, and multiple iterations of algorithm development, to automate the process of generating TSRs for patient cases. The algorithm improvements are made using conclusions from observer studies, conducted on a psychophysics experiment platform developed as part of this work, and further work is undertaken to identify issues of image quality that affect automated solutions. The developed algorithm is then applied to a clinical trial dataset with survival data, meaning that the algorithm is validated against two separate pathologist-scored, clinical trial datasets, as well as being able to test its suitability for generating independent prognostic markers