Fast and accurate tumor segmentation of histology images using persistent homology and deep convolutional features

Tumor segmentation in whole-slide images of histology slides is an important step towards computer-assisted diagnosis. In this work, we propose a tumor segmentation framework based on the novel concept of persistent homology profiles (PHPs). For a given image patch, the homology profiles are derived by efficient computation of persistent homology, which is an algebraic tool from homology theory. We propose an efficient way of computing topological persistence of an image, alternative to simplicial homology. The PHPs are devised to distinguish tumor regions from their normal counterparts by modeling the atypical characteristics of tumor nuclei. We propose two variants of our method for tumor segmentation: one that targets speed without compromising accuracy and the other that targets higher accuracy. The fast version is based on the selection of exemplar image patches from a convolution neural network (CNN) and patch classification by quantifying the divergence between the PHPs of exemplars and the input image patch. Detailed comparative evaluation shows that the proposed algorithm is significantly faster than competing algorithms while achieving comparable results. The accurate version combines the PHPs and high-level CNN features and employs a multi-stage ensemble strategy for image patch labeling. Experimental results demonstrate that the combination of PHPs and CNN features outperforms competing algorithms. This study is performed on two independently collected colorectal datasets containing adenoma, adenocarcinoma, signet and healthy cases. Collectively, the accurate tumor segmentation produces the highest average patch-level F1-score, as compared with competing algorithms, on malignant and healthy cases from both the datasets. Overall the proposed framework highlights the utility of persistent homology for histopathology image analysis

Fast ScanNet : fast and dense analysis of multi-gigapixel whole-slide images for cancer metastasis detection

Lymph node metastasis is one of the most important indicators in breast cancer diagnosis, that is traditionally observed under the microscope by pathologists. In recent years, with the dramatic advance of high-throughput scanning and deep learning technology, automatic analysis of histology from whole- slide images has received a wealth of interest in the field of medical image computing, which aims to alleviate pathologists’ workload and simultaneously reduce misdiagnosis rate. However, automatic detection of lymph node metastases from whole-slide images remains a key challenge because such images are typically very large, where they can often be multiple gigabytes in size. Also, the presence of hard mimics may result in a large number of false positives. In this paper, we propose a novel method with anchor layers for model conversion, which not only leverages the efficiency of fully convolutional architectures to meet the speed requirement in clinical practice, but also densely scans the whole- slide image to achieve accurate predictions on both micro- and macro-metastases. Incorporating the strategies of asynchronous sample prefetching and hard negative mining, the network can be effectively trained. The efficacy of our method are corroborated on the benchmark dataset of 2016 Camelyon Grand Challenge. Our method achieved significant improvements in comparison with the state-of-the-art methods on tumour localization accuracy with a much faster speed and even surpassed human performance on both challenge tasks

Topology and attention in computational pathology

Histopathology serves as the gold standard in the process of cancer diagnosis and unravelling the disease heterogeneity. In routine practice, a trained histopathologist performs visual examination of tissue glass slides under the microscope. The objective of the visual examination is to observe the morphological appearance of tissue sections, analyse the density of tumour rich areas, spatial arrangement, and architecture of diferent types of cells. However, careful visual examination of tissue slides is a demanding task especially when workloads are high, and the subjective nature of the histological grading inevitably leads to inter- and even intra-observer variability. Attaining high accuracy and objective quantification of tissue specimens in cancer diagnosis are some of the ongoing challenges in modern histopathology. With the recent advent of digital pathology, tissue glass slides can now be scanned with digital slides scanners to produce whole slide images (WSIs). A WSI contains a high-resolution pixel representation of tissue slide, stored in a pyramidal structure and typically containing 1010 pixels. Automated algorithms are generally based on the concepts of digital image analysis which can analyse WSIs to improve the precision and reproducibility in cancer diagnostics. The reliability of the results of an algorithm can be objectively measured and improved against an objective standard. In this thesis, we focus on developing automated methods for quantitative assessment of histology WSIs with the aim of improving the precision and reproducibility of cancer diagnosis. More specifically, the designed automated computational pathology algorithms are based on deep learning models in conjunction with algebraic topology and visual attention mechanisms. To the best of our knowledge, the applicability of attention and topology based methods have not been explored in the domain of computational pathology. In this regard, we propose an algorithm for computing persistent homology profiles (topological features) and propose two variants for effective and reliable tumour segmentation of colorectal cancer WSIs. We show that incorporation of deep features along with topological features improves the overall performance for tumour segmentation. We then present the first-ever systematic study (contest) for scoring the human epidermal growth factor receptor 2 (HER2) biomarker on breast cancer histology WSIs. Further, we devise a reinforcement learning based attention mechanism for HER2 scoring that sequentially identifies and analyses the diagnostically relevant regions within a given image, mimicking the histopathologist who would not usually analyse every part of the slide at the highest magnification. We demonstrate the proposed model outperforms other methods participated in our systematic study, most of them were using state-of-the-art deep convolutional networks. Finally, we propose a multi-task learning framework for simultaneous cell detection and classifi- cation, which we named as Hydra-Net. We then compute an image based biomarker which we refer as digital proximity signature (DPS), to predict overall survival in diffuse large B-cell lymphoma (DLBCL) patients. Our results suggest that patients with high collagen-tumour proximity are likely to experience better overall survival

Искусственный интеллект при колоректальном раке: обзор

The study objective: the study objective is to examine the use of artificial intelligence (AI) in the diagnosis, treatment, and prognosis of Colorectal Cancer (CRC) and discuss the future potential of AI in CRC. Material and Methods. The Web of Science, Scopus, PubMed, Medline, and eLIBRARY databases were used to search for the publications. A study on the application of Artificial Intelligence (AI) to the diagnosis, treatment, and prognosis of Colorectal Cancer (CRC) was discovered in more than 100 sources. In the review, data from 83 articles were incorporated. Results. The review article explores the use of artificial intelligence (AI) in medicine, specifically focusing on its applications in colorectal cancer (CRC). It discusses the stages of AI development for CRC, including molecular understanding, image-based diagnosis, drug design, and individualized treatment. The benefits of AI in medical image analysis are highlighted, improving diagnosis accuracy and inspection quality. Challenges in AI development are addressed, such as data standardization and the interpretability of machine learning algorithms. The potential of AI in treatment decision support, precision medicine, and prognosis prediction is discussed, emphasizing the role of AI in selecting optimal treatments and improving surgical precision. Ethical and regulatory considerations in integrating AI are mentioned, including patient trust, data security, and liability in AI-assisted surgeries. The review emphasizes the importance of an AI standard system, dataset standardization, and integrating clinical knowledge into AI algorithms. Overall, the article provides an overview of the current research on AI in CRC diagnosis, treatment, and prognosis, discussing its benefits, challenges, and future prospects in improving medical outcomes.Цель исследования - оценка возможностей использования искусственного интеллекта (ИИ) в диагностике, лечении и прогнозировании колоректального рака (КРР), а также обсуждение потенциала ИИ в лечении КРР. Материал и методы. Проведен поиск научных публикаций в поисковых системах Web of Science, Scopus, PubMed, Medline и eLIBRARY. Было просмотрено более 100 источников по применению ИИ для диагностики, лечения и прогнозирования КРР. В обзор включены данные из 83 статей. Результаты. Проведен анализ литературы, посвященной применению искусственного интеллекта в медицине, особое внимание уделено его использованию при колоректальном раке. Обсуждаются этапы развития ИИ при КРР, включая молекулярную верификацию, лучевую диагностику, разработку лекарств и индивидуальное лечение. Подчеркнуты преимущества ИИ в анализе медицинских изображений, таких как КТ, МРТ и ПЭТ, что повышает точность диагностики. Рассматриваются такие проблемы развития ИИ, как стандартизация данных и интерпретируемость алгоритмов машинного обучения. Подчеркивается роль ИИ в выборе оптимальной тактики лечения и повышении эффективности хирургического вмешательства. Учитываются этические и нормативные аспекты ИИ, включая доверие пациентов, безопасность данных и ответственность в проведении операций с использованием ИИ. Обсуждаются преимущества ИИ в диагностике, лечении и прогнозировании колоректального рака, проблемы и перспективы улучшения результатов лечения

MILD-Net: Minimal Information Loss Dilated Network for Gland Instance Segmentation in Colon Histology Images

The analysis of glandular morphology within colon histopathology images is an important step in determining the grade of colon cancer. Despite the importance of this task, manual segmentation is laborious, time-consuming and can suffer from subjectivity among pathologists. The rise of computational pathology has led to the development of automated methods for gland segmentation that aim to overcome the challenges of manual segmentation. However, this task is non-trivial due to the large variability in glandular appearance and the difficulty in differentiating between certain glandular and non-glandular histological structures. Furthermore, a measure of uncertainty is essential for diagnostic decision making. To address these challenges, we propose a fully convolutional neural network that counters the loss of information caused by max-pooling by re-introducing the original image at multiple points within the network. We also use atrous spatial pyramid pooling with varying dilation rates for preserving the resolution and multi-level aggregation. To incorporate uncertainty, we introduce random transformations during test time for an enhanced segmentation result that simultaneously generates an uncertainty map, highlighting areas of ambiguity. We show that this map can be used to define a metric for disregarding predictions with high uncertainty. The proposed network achieves state-of-the-art performance on the GlaS challenge dataset and on a second independent colorectal adenocarcinoma dataset. In addition, we perform gland instance segmentation on whole-slide images from two further datasets to highlight the generalisability of our method. As an extension, we introduce MILD-Net+ for simultaneous gland and lumen segmentation, to increase the diagnostic power of the network.Comment: Initial version published at Medical Imaging with Deep Learning (MIDL) 201

DRMS for Patient-Level Lymph Node Status Classification

Generally, automatic diagnosis of the presence of metastases in lymph nodes has therapeutic implications for breast cancer patients. Detection and classification of breast cancer metastases have high clinical relevance, especially in whole-slide images of histological lymph node sections. Fast early detection leads to huge improvement of patient’s survival rate. However, currently pathologists mainly detect the metastases with microscopic assessments. This diagnosis procedure is extremely laborious and prone to inevitable missed diagnoses. Therefore, automated, accurate patient-level classification would hold great promise to reduce the pathologist’s workload while also reduce the subjectivity of diagnosis. In this paper, we provide a novel deep regional metastases segmentation (DRMS) framework for the patient-level lymph node status classification. First, a deep segmentation network (DSNet) is proposed to detect the regional metastases in patch-level. Then, we adopt the density-based spatial clustering of applications with noise (DBSCAN) to predict the whole metastases from individual slides. Finally, we determine patient-level pN-stages by aggregating each individual slide-level prediction. In combination with the above techniques, the framework can make better use of the multi-grained information in histological lymph node section of whole-slice images. Experiments on large-scale clinical datasets (e.g., CAMELYON17) demonstrate that our method delivers advanced performance and provides consistent and accurate metastasis detection in clinical trials

Context-aware convolutional neural network for grading of colorectal cancer histology images

Digital histology images are amenable to the application of convolutional neural networks (CNNs) for analysis due to the sheer size of pixel data present in them. CNNs are generally used for representation learning from small image patches (e.g. 224 × 224) extracted from digital histology images due to computational and memory constraints. However, this approach does not incorporate high-resolution contextual information in histology images. We propose a novel way to incorporate a larger context by a context-aware neural network based on images with a dimension of 1792 × 1792 pixels. The proposed framework first encodes the local representation of a histology image into high dimensional features then aggregates the features by considering their spatial organization to make a final prediction. We evaluated the proposed method on two colorectal cancer datasets for the task of cancer grading. Our method outperformed the traditional patch-based approaches, problem-specific methods, and existing context-based methods. We also presented a comprehensive analysis of different variants of the proposed method