Capturing Global Spatial Context for Accurate Cell Classification in Skin Cancer Histology

The spectacular response observed in clinical trials of immunotherapy in patients with previously uncurable Melanoma, a highly aggressive form of skin cancer, calls for a better understanding of the cancer-immune interface. Computational pathology provides a unique opportunity to spatially dissect such interface on digitised pathological slides. Accurate cellular classification is a key to ensure meaningful results, but is often challenging even with state-of-art machine learning and deep learning methods. We propose a hierarchical framework, which mirrors the way pathologists perceive tumour architecture and define tumour heterogeneity to improve cell classification methods that rely solely on cell nuclei morphology. The SLIC superpixel algorithm was used to segment and classify tumour regions in low resolution H&E-stained histological images of melanoma skin cancer to provide a global context. Classification of superpixels into tumour, stroma, epidermis and lumen/white space, yielded a 97.7% training set accuracy and 95.7% testing set accuracy in 58 whole-tumour images of the TCGA melanoma dataset. The superpixel classification was projected down to high resolution images to enhance the performance of a single cell classifier, based on cell nuclear morphological features, and resulted in increasing its accuracy from 86.4% to 91.6%. Furthermore, a voting scheme was proposed to use global context as biological a priori knowledge, pushing the accuracy further to 92.8%. This study demonstrates how using the global spatial context can accurately characterise the tumour microenvironment and allow us to extend significantly beyond single-cell morphological classification.Comment: Accepted by MICCAI COMPAY 2018 worksho

O uso da Divergência de Kullback-Leibler e da Divergência Generalizada como medida de similaridade em sistemas CBIR

The content-based image retrieval is important for various purposes like disease diagnoses from computerized tomography, for example. The relevance, social and economic of image retrieval systems has created the necessity of its improvement. Within this context, the content-based image retrieval systems are composed of two stages, the feature extraction and similarity measurement. The stage of similarity is still a challenge due to the wide variety of similarity measurement functions, which can be combined with the different techniques present in the recovery process and return results that aren’t always the most satisfactory. The most common functions used to measure the similarity are the Euclidean and Cosine, but some researchers have noted some limitations in these functions conventional proximity, in the step of search by similarity. For that reason, the Bregman divergences (Kullback Leibler and I-Generalized) have attracted the attention of researchers, due to its flexibility in the similarity analysis. Thus, the aim of this research was to conduct a comparative study over the use of Bregman divergences in relation the Euclidean and Cosine functions, in the step similarity of content-based image retrieval, checking the advantages and disadvantages of each function. For this, it was created a content-based image retrieval system in two stages: offline and online, using approaches BSM, FISM, BoVW and BoVW-SPM. With this system was created three groups of experiments using databases: Caltech101, Oxford and UK-bench. The performance of content-based image retrieval system using the different functions of similarity was tested through of evaluation measures: Mean Average Precision, normalized Discounted Cumulative Gain, precision at k, precision x recall. Finally, this study shows that the use of Bregman divergences (Kullback Leibler and Generalized) obtains better results than the Euclidean and Cosine measures with significant gains for content-based image retrieval.Coordenação de Aperfeiçoamento de Pessoal de Nível SuperiorDissertação (Mestrado)A recuperação de imagem baseada em conteúdo é importante para diversos fins, como diagnósticos de doenças a partir de tomografias computadorizadas, por exemplo. A relevância social e econômica de sistemas de recuperação de imagens criou a necessidade do seu aprimoramento. Dentro deste contexto, os sistemas de recuperação de imagens baseadas em conteúdo são compostos de duas etapas: extração de característica e medida de similaridade. A etapa de similaridade ainda é um desafio, devido à grande variedade de funções de medida de similaridade, que podem ser combinadas com as diferentes técnicas presentes no processo de recuperação e retornar resultados que nem sempre são os mais satisfatórios. As funções geralmente mais usadas para medir a similaridade são as Euclidiana e Cosseno, mas alguns pesquisadores têm notado algumas limitações nestas funções de proximidade convencionais, na etapa de busca por similaridade. Por esse motivo, as divergências de Bregman (Kullback Leibler e Generalizada) têm atraído a atenção dos pesquisadores, devido à sua flexibilidade em análise de similaridade. Desta forma, o objetivo desta pesquisa foi realizar um estudo comparativo sobre a utilização das divergências de Bregman em relação às funções Euclidiana e Cosseno, na etapa de similaridade da recuperação de imagens baseadas em conteúdo, averiguando as vantagens e desvantagens de cada função. Para isso, criou-se um sistema de recuperação de imagens baseado em conteúdo em duas etapas: off-line e on-line, utilizando as abordagens BSM, FISM, BoVW e BoVW-SPM. Com esse sistema, foram realizados três grupos de experimentos utilizando os bancos de dados: Caltech101, Oxford e UK-bench. O desempenho do sistema de recuperação de imagem baseada em conteúdo utilizando as diferentes funções de similaridade foram testadas por meio das medidas de avaliação: Mean Average Precision, normalized Discounted Cumulative Gain, precisão em k, e precisão x revocação. Por fim, o presente estudo aponta que o uso das divergências de Bregman (Kullback Leibler e Generalizada) obtiveram melhores resultados do que as medidas Euclidiana e Cosseno, com ganhos relevantes para recuperação de imagem baseada em conteúdo