Large-scale computations on histology images reveal grade-differentiating parameters for breast cancer

Applying image features of proximal paracancerous tissues in predicting prognosis of patients with hepatocellular carcinoma

BACKGROUND

Most of the methods using digital pathological image for predicting Hepatocellular carcinoma (HCC) prognosis have not considered paracancerous tissue microenvironment (PTME), which are potentially important for tumour initiation and metastasis. This study aimed to identify roles of image features of PTME in predicting prognosis and tumour recurrence of HCC patients.

METHODS

We collected whole slide images (WSIs) of 146 HCC patients from Sun Yat-sen Memorial Hospital (SYSM dataset). For each WSI, five types of regions of interests (ROIs) in PTME and tumours were manually annotated. These ROIs were used to construct a Lasso Cox survival model for predicting the prognosis of HCC patients. To make the model broadly useful, we established a deep learning method to automatically segment WSIs, and further used it to construct a prognosis prediction model. This model was tested by the samples of 225 HCC patients from the Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC).

RESULTS

In predicting prognosis of the HCC patients, using the image features of manually annotated ROIs in PTME achieved C-index 0.668 in the SYSM testing dataset, which is higher than the C-index 0.648 reached by the model only using image features of tumours. Integrating ROIs of PTME and tumours achieved C-index 0.693 in the SYSM testing dataset. The model using automatically segmented ROIs of PTME and tumours achieved C-index of 0.665 (95% CI: 0.556-0.774) in the TCGA-LIHC samples, which is better than the widely used methods, WSISA (0.567), DeepGraphSurv (0.593), and SeTranSurv (0.642). Finally, we found the Texture SumAverage Skew HV on immune cell infiltration and Texture related features on desmoplastic reaction are the most important features of PTME in predicting HCC prognosis. We additionally used the model in prediction HCC recurrence for patients from SYSM-training, SYSM-testing, and TCGA-LIHC datasets, indicating the important roles of PTME in the prediction.

CONCLUSIONS

Our results indicate image features of PTME is critical for improving the prognosis prediction of HCC. Moreover, the image features related with immune cell infiltration and desmoplastic reaction of PTME are the most important factors associated with prognosis of HCC.

The Cross-Scale Association between Pathomics and Radiomics Features in Immunotherapy-Treated NSCLC Patients: A Preliminary Study

BACKGROUND

Recent advances in cancer biomarker development have led to a surge of distinct data modalities, such as medical imaging and histopathology. To develop predictive immunotherapy biomarkers, these modalities are leveraged independently, despite their orthogonality. This study aims to explore the cross-scale association between radiological scans and digitalized pathology images for immunotherapy-treated non-small cell lung cancer (NSCLC) patients.

METHODS

This study involves 36 NSCLC patients who were treated with immunotherapy and for whom both radiology and pathology images were available. A total of 851 and 260 features were extracted from CT scans and cell density maps of histology images at different resolutions. We investigated the radiopathomics relationship and their association with clinical and biological endpoints. We used the Kolmogorov-Smirnov (KS) method to test the differences between the distributions of correlation coefficients with the two imaging modality features. Unsupervised clustering was done to identify which imaging modality captures poor and good survival patients.

RESULTS

Our results demonstrated a significant correlation between cell density pathomics and radiomics features. Furthermore, we also found a varying distribution of correlation values between imaging-derived features and clinical endpoints. The KS test revealed that the two imaging feature distributions were different for PFS and CD8 counts, while similar for OS. In addition, clustering analysis resulted in significant differences in the two clusters generated from the radiomics and pathomics features with respect to patient survival and CD8 counts.

CONCLUSION

The results of this study suggest a cross-scale association between CT scans and pathology H&E slides among ICI-treated patients. These relationships can be further explored to develop multimodal immunotherapy biomarkers to advance personalized lung cancer care.

Machine learning in computational histopathology: Challenges and opportunities

Digital histopathological images, high-resolution images of stained tissue samples, are a vital tool for clinicians to diagnose and stage cancers. The visual analysis of patient state based on these images are an important part of oncology workflow. Although pathology workflows have historically been conducted in laboratories under a microscope, the increasing digitization of histopathological images has led to their analysis on computers in the clinic. The last decade has seen the emergence of machine learning, and deep learning in particular, a powerful set of tools for the analysis of histopathological images. Machine learning models trained on large datasets of digitized histopathology slides have resulted in automated models for prediction and stratification of patient risk. In this review, we provide context for the rise of such models in computational histopathology, highlight the clinical tasks they have found success in automating, discuss the various machine learning techniques that have been applied to this domain, and underscore open problems and opportunities.

A state-of-the-art survey of artificial neural networks for Whole-slide Image analysis: From popular Convolutional Neural Networks to potential visual transformers

In recent years, with the advancement of computer-aided diagnosis (CAD) technology and whole slide image (WSI), histopathological WSI has gradually played a crucial aspect in the diagnosis and analysis of diseases. To increase the objectivity and accuracy of pathologists' work, artificial neural network (ANN) methods have been generally needed in the segmentation, classification, and detection of histopathological WSI. However, the existing review papers only focus on equipment hardware, development status and trends, and do not summarize the art neural network used for full-slide image analysis in detail. In this paper, WSI analysis methods based on ANN are reviewed. Firstly, the development status of WSI and ANN methods is introduced. Secondly, we summarize the common ANN methods. Next, we discuss publicly available WSI datasets and evaluation metrics. These ANN architectures for WSI processing are divided into classical neural networks and deep neural networks (DNNs) and then analyzed. Finally, the application prospect of the analytical method in this field is discussed. The important potential method is Visual Transformers.

Detection of Necrosis in Digitised Whole-Slide Images for Better Grading of Canine Soft-Tissue Sarcomas Using Machine-Learning

The definitive diagnosis of canine soft-tissue sarcomas (STSs) is based on histological assessment of formalin-fixed tissues. Assessment of parameters, such as degree of differentiation, necrosis score and mitotic score, give rise to a final tumour grade, which is important in determining prognosis and subsequent treatment modalities. However, grading discrepancies are reported to occur in human and canine STSs, which can result in complications regarding treatment plans. The introduction of digital pathology has the potential to help improve STS grading via automated determination of the presence and extent of necrosis. The detected necrotic regions can be factored in the grading scheme or excluded before analysing the remaining tissue. Here we describe a method to detect tumour necrosis in histopathological whole-slide images (WSIs) of STSs using machine learning. Annotated areas of necrosis were extracted from WSIs and the patches containing necrotic tissue fed into a pre-trained DenseNet161 convolutional neural network (CNN) for training, testing and validation. The proposed CNN architecture reported favourable results, with an overall validation accuracy of 92.7% for necrosis detection which represents the number of correctly classified data instances over the total number of data instances. The proposed method, when vigorously validated represents a promising tool to assist pathologists in evaluating necrosis in canine STS tumours, by increasing efficiency, accuracy and reducing inter-rater variation.

Artificial intelligence in breast cancer histopathology

This is a review on the use of artificial intelligence for digital breast pathology. A systematic search on PubMed was conducted, identifying 17,324 research papers related to breast cancer pathology. Following a semimanual screening, 664 papers were retrieved and pursued. The papers are grouped into six major tasks performed by pathologists-namely, molecular and hormonal analysis, grading, mitotic figure counting, ki-67 indexing, tumour-infiltrating lymphocyte assessment, and lymph node metastases identification. Under each task, open-source datasets for research to build artificial intelligence (AI) tools are also listed. Many AI tools showed promise and demonstrated feasibility in the automation of routine pathology investigations. We expect continued growth of AI in this field as new algorithms mature.

Improved Bald Eagle Search Optimization with Synergic Deep Learning-Based Classification on Breast Cancer Imaging

Medical imaging has attracted growing interest in the field of healthcare regarding breast cancer (BC). Globally, BC is a major cause of mortality amongst women. Now, the examination of histopathology images is the medical gold standard for cancer diagnoses. However, the manual process of microscopic inspections is a laborious task, and the results might be misleading as a result of human error occurring. Thus, the computer-aided diagnoses (CAD) system can be utilized for accurately detecting cancer within essential time constraints, as earlier diagnosis is the key to curing cancer. The classification and diagnosis of BC utilizing the deep learning algorithm has gained considerable attention. This article presents a model of an improved bald eagle search optimization with a synergic deep learning mechanism for breast cancer diagnoses using histopathological images (IBESSDL-BCHI). The proposed IBESSDL-BCHI model concentrates on the identification and classification of BC using HIs. To do so, the presented IBESSDL-BCHI model follows an image preprocessing method using a median filtering (MF) technique as a preprocessing step. In addition, feature extraction using a synergic deep learning (SDL) model is carried out, and the hyperparameters related to the SDL mechanism are tuned by the use of the IBES model. Lastly, long short-term memory (LSTM) was utilized to precisely categorize the HIs into two major classes, such as benign and malignant. The performance validation of the IBESSDL-BCHI system was tested utilizing the benchmark dataset, and the results demonstrate that the IBESSDL-BCHI model has shown better general efficiency for BC classification.

Label Cleaning Multiple Instance Learning: Refining Coarse Annotations on Single Whole-Slide Images

Annotating cancerous regions in whole-slide images (WSIs) of pathology samples plays a critical role in clinical diagnosis, biomedical research, and machine learning algorithms development. However, generating exhaustive and accurate annotations is labor-intensive, challenging, and costly. Drawing only coarse and approximate annotations is a much easier task, less costly, and it alleviates pathologists' workload. In this paper, we study the problem of refining these approximate annotations in digital pathology to obtain more accurate ones. Some previous works have explored obtaining machine learning models from these inaccurate annotations, but few of them tackle the refinement problem where the mislabeled regions should be explicitly identified and corrected, and all of them require a - often very large - number of training samples. We present a method, named Label Cleaning Multiple Instance Learning (LC-MIL), to refine coarse annotations on a single WSI without the need for external training data. Patches cropped from a WSI with inaccurate labels are processed jointly within a multiple instance learning framework, mitigating their impact on the predictive model and refining the segmentation. Our experiments on a heterogeneous WSI set with breast cancer lymph node metastasis, liver cancer, and colorectal cancer samples show that LC-MIL significantly refines the coarse annotations, outperforming state-of-the-art alternatives, even while learning from a single slide. Moreover, we demonstrate how real annotations drawn by pathologists can be efficiently refined and improved by the proposed approach. All these results demonstrate that LC-MIL is a promising, lightweight tool to provide fine-grained annotations from coarsely annotated pathology sets.

Characterization of Nuclear Pleomorphism and Tubules in Histopathological Images of Breast Cancer

Breast cancer (BC) diagnosis is made by a pathologist who analyzes a portion of the breast tissue under the microscope and performs a histological evaluation. This evaluation aims to determine the grade of cellular differentiation and the aggressiveness of the tumor by the Nottingham Grade Classification System (NGS). Nowadays, digital pathology is an innovative tool for pathologists in diagnosis and acquiring new learning. However, a recurring problem in health services is the excessive workload in all medical services. For this reason, it is required to develop computational tools that assist histological evaluation. This work proposes a methodology for the quantitative analysis of BC tissue that follows NGS. The proposed methodology is based on digital image processing techniques through which the BC tissue can be characterized automatically. Moreover, the proposed nuclei characterization was helpful for grade differentiation in carcinoma images of the BC tissue reaching an 0.84 accuracy. In addition, a metric was proposed to assess the likelihood of a structure in the tissue corresponding to a tubule by considering spatial and geometrical characteristics between lumina and its surrounding nuclei, reaching an accuracy of 0.83. Tests were performed from different databases and under various magnification and staining contrast conditions, showing that the methodology is reliable for histological breast tissue analysis.

Comparing machine learning and deep learning regression frameworks for accurate prediction of dielectrophoretic force

An intelligent sensing framework using Machine Learning (ML) and Deep Learning (DL) architectures to precisely quantify dielectrophoretic force invoked on microparticles in a textile electrode-based DEP sensing device is reported. The prediction accuracy and generalization ability of the framework was validated using experimental results. Images of pearl chain alignment at varying input voltages were used to build deep regression models using modified ML and CNN architectures that can correlate pearl chain alignment patterns of Saccharomyces cerevisiae(yeast) cells and polystyrene microbeads to DEP force. Various ML models such as K-Nearest Neighbor, Support Vector Machine, Random Forest, Neural Networks, and Linear Regression along with DL models such as Convolutional Neural Network (CNN) architectures of AlexNet, ResNet-50, MobileNetV2, and GoogLeNet have been analyzed in order to build an effective regression framework to estimate the force induced on yeast cells and microbeads. The efficiencies of the models were evaluated using Mean Absolute Error, Mean Absolute Relative, Mean Squared Error, R-squared, and Root Mean Square Error (RMSE) as evaluation metrics. ResNet-50 with RMSPROP gave the best performance, with a validation RMSE of 0.0918 on yeast cells while AlexNet with ADAM optimizer gave the best performance, with a validation RMSE of 0.1745 on microbeads. This provides a baseline for further studies in the application of deep learning in DEP aided Lab-on-Chip devices.

A multi-level feature-fusion-based approach to breast histopathological image classification

Previously, convolutional neural networks mostly used deep semantic feature information obtained from several convolutions for image classification. Such deep semantic features have a larger receptive field, and the features extracted are more effective as the number of convolutions increases, which helps in the classification of targets. However, this method tends to lose the shallow local features, such as the spatial connectivity and correlation of tumor region texture and edge contours in breast histopathology images, which leads to its recognition accuracy not being high enough. To address this problem, we propose a multi-level feature fusion method for breast histopathology image classification. First, we fuse shallow features and deep semantic features by attention mechanism and convolutions. Then, a new weighted cross entropy loss function is used to deal with the misjudgment of false negative and false positive. And finally, the correlation of spatial information is used to correct the misjudgment of some patches. We have conducted experiments on our own datasets and compared with the base network Inception-ResNet-v2, which has a high accuracy. The proposed method achieves an accuracy of 99.0% and an AUC of 99.9%.

A review: The detection of cancer cells in histopathology based on machine vision

Machine vision is being employed in defect detection, size measurement, pattern recognition, image fusion, target tracking and 3D reconstruction. Traditional cancer detection methods are dominated by manual detection, which wastes time and manpower, and heavily relies on the pathologists' skill and work experience. Therefore, these manual detection approaches are not convenient for the inheritance of domain knowledge, and are not suitable for the rapid development of medical care in the future. The emergence of machine vision can iteratively update and learn the domain knowledge of cancer cell pathology detection to achieve automated, high-precision, and consistent detection. Consequently, this paper reviews the use of machine vision to detect cancer cells in histopathology images, as well as the benefits and drawbacks of various detection approaches. First, we review the application of image preprocessing and image segmentation in histopathology for the detection of cancer cells, and compare the benefits and drawbacks of different algorithms. Secondly, for the characteristics of histopathological cancer cell images, the research progress of shape, color and texture features and other methods is mainly reviewed. Furthermore, for the classification methods of histopathological cancer cell images, the benefits and drawbacks of traditional machine vision approaches and deep learning methods are compared and analyzed. Finally, the above research is discussed and forecasted, with the expected future development tendency serving as a guide for future research.

New bag-of-feature for histopathology image classification using reinforced cat swarm algorithm and weighted Gaussian mixture modelling

The progress in digital histopathology for computer-aided diagnosis leads to advancement in automated histopathological image classification system. However, heterogeneity and complexity in structural background make it a challenging process. Therefore, this paper introduces robust and reliable new bag-of-feature framework. The optimal visual words are obtained by applying proposed reinforcement cat swarm optimization algorithm. Moreover, the frequency of occurrence of each visual words is depicted through histogram using new weighted Gaussian mixture modelling method. Reinforcement cat swarm optimization algorithm is evaluated on the IEEE CEC 2017 benchmark function problems and compared with other state-of-the-art algorithms. Moreover, statistical test analysis is done on acquired mean and the best fitness values from benchmark functions. The proposed classification model effectively identifies and classifies the different categories of histopathological images. Furthermore, the comparative experimental result analysis of proposed reinforcement cat swarm optimization-based bag-of-feature is performed on standard quality metrics measures. The observation states that reinforcement cat swarm optimization-based bag-of-feature outperforms the other methods and provides promising results.

Breast histopathological image analysis using image processing techniques for diagnostic puposes: A methodological review

Breast cancer in women is the second most common cancer worldwide. Early detection of breast cancer can reduce the risk of human life. Non-invasive techniques such as mammograms and ultrasound imaging are popularly used to detect the tumour. However, histopathological analysis is necessary to determine the malignancy of the tumour as it analyses the image at the cellular level. Manual analysis of these slides is time consuming, tedious, subjective and are susceptible to human errors. Also, at times the interpretation of these images are inconsistent between laboratories. Hence, a Computer-Aided Diagnostic system that can act as a decision support system is need of the hour. Moreover, recent developments in computational power and memory capacity led to the application of computer tools and medical image processing techniques to process and analyze breast cancer histopathological images. This review paper summarizes various traditional and deep learning based methods developed to analyze breast cancer histopathological images. Initially, the characteristics of breast cancer histopathological images are discussed. A detailed discussion on the various potential regions of interest is presented which is crucial for the development of Computer-Aided Diagnostic systems. We summarize the recent trends and choices made during the selection of medical image processing techniques. Finally, a detailed discussion on the various challenges involved in the analysis of BCHI is presented along with the future scope.

Computer-Aided Histopathological Image Analysis Techniques for Automated Nuclear Atypia Scoring of Breast Cancer: a Review

Breast cancer is the most common type of malignancy diagnosed in women. Through early detection and diagnosis, there is a great chance of recovery and thereby reduce the mortality rate. Many preliminary tests like non-invasive radiological diagnosis using ultrasound, mammography, and MRI are widely used for the diagnosis of breast cancer. However, histopathological analysis of breast biopsy specimen is inevitable and is considered to be the golden standard for the affirmation of cancer. With the advancements in the digital computing capabilities, memory capacity, and imaging modalities, the development of computer-aided powerful analytical techniques for histopathological data has increased dramatically. These automated techniques help to alleviate the laborious work of the pathologist and to improve the reproducibility and reliability of the interpretation. This paper reviews and summarizes digital image computational algorithms applied on histopathological breast cancer images for nuclear atypia scoring and explores the future possibilities. The algorithms for nuclear pleomorphism scoring of breast cancer can be widely grouped into two categories: handcrafted feature-based and learned feature-based. Handcrafted feature-based algorithms mainly include the computational steps like pre-processing the images, segmenting the nuclei, extracting unique features, feature selection, and machine learning-based classification. However, most of the recent algorithms are based on learned features, that extract high-level abstractions directly from the histopathological images utilizing deep learning techniques. In this paper, we discuss the various algorithms applied for the nuclear pleomorphism scoring of breast cancer, discourse the challenges to be dealt with, and outline the importance of benchmark datasets. A comparative analysis of some prominent works on breast cancer nuclear atypia scoring is done using a benchmark dataset which enables to quantitatively measure and compare the different features and algorithms used for breast cancer grading. Results show that improvements are still required, to have an automated cancer grading system suitable for clinical applications.

3E-Net: Entropy-Based Elastic Ensemble of Deep Convolutional Neural Networks for Grading of Invasive Breast Carcinoma Histopathological Microscopic Images

Automated grading systems using deep convolution neural networks (DCNNs) have proven their capability and potential to distinguish between different breast cancer grades using digitized histopathological images. In digital breast pathology, it is vital to measure how confident a DCNN is in grading using a machine-confidence metric, especially with the presence of major computer vision challenging problems such as the high visual variability of the images. Such a quantitative metric can be employed not only to improve the robustness of automated systems, but also to assist medical professionals in identifying complex cases. In this paper, we propose Entropy-based Elastic Ensemble of DCNN models (3E-Net) for grading invasive breast carcinoma microscopy images which provides an initial stage of explainability (using an uncertainty-aware mechanism adopting entropy). Our proposed model has been designed in a way to (1) exclude images that are less sensitive and highly uncertain to our ensemble model and (2) dynamically grade the non-excluded images using the certain models in the ensemble architecture. We evaluated two variations of 3E-Net on an invasive breast carcinoma dataset and we achieved grading accuracy of 96.15% and 99.50%.

Deep Multi-Magnification Networks for multi-class breast cancer image segmentation

Pathologic analysis of surgical excision specimens for breast carcinoma is important to evaluate the completeness of surgical excision and has implications for future treatment. This analysis is performed manually by pathologists reviewing histologic slides prepared from formalin-fixed tissue. In this paper, we present Deep Multi-Magnification Network trained by partial annotation for automated multi-class tissue segmentation by a set of patches from multiple magnifications in digitized whole slide images. Our proposed architecture with multi-encoder, multi-decoder, and multi-concatenation outperforms other single and multi-magnification-based architectures by achieving the highest mean intersection-over-union, and can be used to facilitate pathologists' assessments of breast cancer.

Objective Diagnosis for Histopathological Images Based on Machine Learning Techniques: Classical Approaches and New Trends

Histopathology refers to the examination by a pathologist of biopsy samples. Histopathology images are captured by a microscope to locate, examine, and classify many diseases, such as different cancer types. They provide a detailed view of different types of diseases and their tissue status. These images are an essential resource with which to define biological compositions or analyze cell and tissue structures. This imaging modality is very important for diagnostic applications. The analysis of histopathology images is a prolific and relevant research area supporting disease diagnosis. In this paper, the challenges of histopathology image analysis are evaluated. An extensive review of conventional and deep learning techniques which have been applied in histological image analyses is presented. This review summarizes many current datasets and highlights important challenges and constraints with recent deep learning techniques, alongside possible future research avenues. Despite the progress made in this research area so far, it is still a significant area of open research because of the variety of imaging techniques and disease-specific characteristics.

Deep learning in digital pathology image analysis: a survey

Deep learning (DL) has achieved state-of-the-art performance in many digital pathology analysis tasks. Traditional methods usually require hand-crafted domain-specific features, and DL methods can learn representations without manually designed features. In terms of feature extraction, DL approaches are less labor intensive compared with conventional machine learning methods. In this paper, we comprehensively summarize recent DL-based image analysis studies in histopathology, including different tasks (e.g., classification, semantic segmentation, detection, and instance segmentation) and various applications (e.g., stain normalization, cell/gland/region structure analysis). DL methods can provide consistent and accurate outcomes. DL is a promising tool to assist pathologists in clinical diagnosis.

An End-to-end System for Automatic Characterization of Iba1 Immunopositive Microglia in Whole Slide Imaging

Traumatic brain injury (TBI) is one of the leading causes of death and disability worldwide. Detailed studies of the microglial response after TBI require high throughput quantification of changes in microglial count and morphology in histological sections throughout the brain. In this paper, we present a fully automated end-to-end system that is capable of assessing microglial activation in white matter regions on whole slide images of Iba1 stained sections. Our approach involves the division of the full brain slides into smaller image patches that are subsequently automatically classified into white and grey matter sections. On the patches classified as white matter, we jointly apply functional minimization methods and deep learning classification to identify Iba1-immunopositive microglia. Detected cells are then automatically traced to preserve their complex branching structure after which fractal analysis is applied to determine the activation states of the cells. The resulting system detects white matter regions with 84% accuracy, detects microglia with a performance level of 0.70 (F1 score, the harmonic mean of precision and sensitivity) and performs binary microglia morphology classification with a 70% accuracy. This automated pipeline performs these analyses at a 20-fold increase in speed when compared to a human pathologist. Moreover, we have demonstrated robustness to variations in stain intensity common for Iba1 immunostaining. A preliminary analysis was conducted that indicated that this pipeline can identify differences in microglia response due to TBI. An automated solution to microglia cell analysis can greatly increase standardized analysis of brain slides, allowing pathologists and neuroscientists to focus on characterizing the associated underlying diseases and injuries.

Cell Image Classification: A Comparative Overview

Cell image classification methods are currently being used in numerous applications in cell biology and medicine. Applications include understanding the effects of genes and drugs in screening experiments, understanding the role and subcellular localization of different proteins, as well as diagnosis and prognosis of cancer from images acquired using cytological and histological techniques. The article also reviews three main approaches for cell image classification most often used: numerical feature extraction, end-to-end classification with neural networks (NNs), and transport-based morphometry (TBM). In addition, we provide comparisons on four different cell imaging datasets to highlight the relative strength of each method. The results computed using four publicly available datasets show that numerical features tend to carry the best discriminative information for most of the classification tasks. Results also show that NN-based methods produce state-of-the-art results in the dataset that contains a relatively large number of training samples. Data augmentation or the choice of a more recently reported architecture does not necessarily improve the classification performance of NNs in the datasets with limited number of training samples. If understanding and visualization are desired aspects, TBM methods can offer the ability to invert classification functions, and thus can aid in the interpretation of results. These and other comparison outcomes are discussed with the aim of clarifying the advantages and disadvantages of each method. © 2020 International Society for Advancement of Cytometry.

Batch Mode Active Learning on the Riemannian Manifold for Automated Scoring of Nuclear Pleomorphism in Breast Cancer

Breast cancer is the most prevalent invasive type of cancer among women. The mortality rate of the disease can be reduced considerably through timely prognosis and felicitous treatment planning, by utilizing the computer aided detection and diagnosis techniques. With the advent of whole slide image (WSI) scanners for digitizing the histopathological tissue samples, there is a drastic increase in the availability of digital histopathological images. However, these samples are often unlabeled and hence they need labeling to be done through manual annotations by domain experts and experienced pathologists. But this annotation process required for acquiring high quality large labeled training set for nuclear atypia scoring is a tedious, expensive and time consuming job. Active learning techniques have achieved widespread acceptance in reducing this human effort in annotating the data samples. In this paper, we explore the possibilities of active learning on nuclear pleomorphism scoring over a non-Euclidean framework, the Riemannian manifold. Active learning technique adopted for the cancer grading is in the batch-mode framework, that adaptively identifies the apt batch size along with the batch of instances to be queried, following a submodular optimization framework. Samples for annotation are selected considering the diversity and redundancy between the pair of samples, based on the kernelized Riemannian distance measures such as log-Euclidean metrics and the two Bregman divergences - Stein and Jeffrey divergences. Results of the adaptive Batch Mode Active Learning on the Riemannian metric show a superior performance when compared with the state-of-the-art techniques for breast cancer nuclear pleomorphism scoring, as it makes use of the information from the unlabeled samples.

Tumor apelin immunoreactivity is correlated with body mass index in ovarian high grade serous carcinoma

Ovarian cancer has a high mortality rate. Serous carcinoma is the most common subtype and can be detected by distant or lymph node metastasis in advanced stages. Apelin, an adipokine associated with obesity, and its receptor, APJ, participate in lymphatic invasion. Angiogenesis also can affect lymph node involvement in serous ovarian carcinomas. We investigated apelin/APJ receptor immunoreactivity in stages III and IV ovarian cancer with or without lymph node involvement and correlated the results with body mass index (BMI) to determine whether the potential relation of the two affects the outcome of the cancer. We investigated 30 patients diagnosed between 2014 and 2016 with high grade serous ovarian cancer. Tumor:stroma ratio, indirect immunoperoxidase method, H-score and MATLAB analysis were performed. In obese and pre-obese patients, tumor apelin immunoreactivity was stronger than for patients with normal BMI. Tumor:stroma ratio was correlated with survival and lymph node involvement. Strong apelin and moderate APJ immunoreactivity was detected in both lymph node negative and positive patients. BMI was related to both survival outcome and apelin immunoreactivity. BMI, adipokines such as apelin, and the stromal compartment play critical roles in advanced stage serous carcinomas.

Viable and necrotic tumor assessment from whole slide images of osteosarcoma using machine-learning and deep-learning models

Pathological estimation of tumor necrosis after chemotherapy is essential for patients with osteosarcoma. This study reports the first fully automated tool to assess viable and necrotic tumor in osteosarcoma, employing advances in histopathology digitization and automated learning. We selected 40 digitized whole slide images representing the heterogeneity of osteosarcoma and chemotherapy response. With the goal of labeling the diverse regions of the digitized tissue into viable tumor, necrotic tumor, and non-tumor, we trained 13 machine-learning models and selected the top performing one (a Support Vector Machine) based on reported accuracy. We also developed a deep-learning architecture and trained it on the same data set. We computed the receiver-operator characteristic for discrimination of non-tumor from tumor followed by conditional discrimination of necrotic from viable tumor and found our models performing exceptionally well. We then used the trained models to identify regions of interest on image-tiles generated from test whole slide images. The classification output is visualized as a tumor-prediction map, displaying the extent of viable and necrotic tumor in the slide image. Thus, we lay the foundation for a complete tumor assessment pipeline from original histology images to tumor-prediction map generation. The proposed pipeline can also be adopted for other types of tumor.

Sparse Representation Over Learned Dictionaries on the Riemannian Manifold for Automated Grading of Nuclear Pleomorphism in Breast Cancer

Breast cancer is found to be the most pervasive type of cancer among women. Computer aided detection and diagnosis of cancer at the initial stages can increase the chances of recovery and thus reduce the mortality rate through timely prognosis and adequate treatment planning. The nuclear atypia scoring or histopathological breast tumor grading remains to be a challenging problem due to the various artifacts and variabilities introduced during slide preparation and also because of the complexity in the structure of the underlying tissue patterns. Inspired by the success of symmetric positive definite (SPD) matrices in many of the challenging tasks in machine learning and computer vision, a sparse coding and dictionary learning on SPD matrices is proposed in this paper for the breast tumor grading. The proposed covariance-based SPD matrices form a Riemannian manifold and are represented as the sparse combination of Riemannian dictionary atoms. Non-linearity of the SPD manifold is tackled by embedding into the reproducing kernel Hilbert space using kernels derived from log-Euclidean metric, Jeffrey and Stein divergences and compared with the non-kernel-based affine invariant Riemannian metric. The novelty of the work lies in exploiting the kernel approach for the Hilbert space embedding of the Riemannian manifold, that can achieve a better discrimination of the breast cancer tissues, following a sparse representation over learned dictionaries and henceforth it outperforms many of the state-of-the-art algorithms in breast cancer grading in terms of quantitative and qualitative analysis.

1399 H&E-stained sentinel lymph node sections of breast cancer patients: the CAMELYON dataset

Background

The presence of lymph node metastases is one of the most important factors in breast cancer prognosis. The most common way to assess regional lymph node status is the sentinel lymph node procedure. The sentinel lymph node is the most likely lymph node to contain metastasized cancer cells and is excised, histopathologically processed, and examined by a pathologist. This tedious examination process is time-consuming and can lead to small metastases being missed. However, recent advances in whole-slide imaging and machine learning have opened an avenue for analysis of digitized lymph node sections with computer algorithms. For example, convolutional neural networks, a type of machine-learning algorithm, can be used to automatically detect cancer metastases in lymph nodes with high accuracy. To train machine-learning models, large, well-curated datasets are needed.

Results

We released a dataset of 1,399 annotated whole-slide images (WSIs) of lymph nodes, both with and without metastases, in 3 terabytes of data in the context of the CAMELYON16 and CAMELYON17 Grand Challenges. Slides were collected from five medical centers to cover a broad range of image appearance and staining variations. Each WSI has a slide-level label indicating whether it contains no metastases, macro-metastases, micro-metastases, or isolated tumor cells. Furthermore, for 209 WSIs, detailed hand-drawn contours for all metastases are provided. Last, open-source software tools to visualize and interact with the data have been made available.

Conclusions

A unique dataset of annotated, whole-slide digital histopathology images has been provided with high potential for re-use.

A novel computational method for automatic segmentation, quantification and comparative analysis of immunohistochemically labeled tissue sections

Background

In the clinical practice, the objective quantification of histological results is essential not only to define objective and well-established protocols for diagnosis, treatment, and assessment, but also to ameliorate disease comprehension.

Software

The software MIAQuant_Learn presented in this work segments, quantifies and analyzes markers in histochemical and immunohistochemical images obtained by different biological procedures and imaging tools. MIAQuant_Learn employs supervised learning techniques to customize the marker segmentation process with respect to any marker color appearance. Our software expresses the location of the segmented markers with respect to regions of interest by mean-distance histograms, which are numerically compared by measuring their intersection. When contiguous tissue sections stained by different markers are available, MIAQuant_Learn aligns them and overlaps the segmented markers in a unique image enabling a visual comparative analysis of the spatial distribution of each marker (markers’ relative location). Additionally, it computes novel measures of markers’ co-existence in tissue volumes depending on their density.

Conclusions

Applications of MIAQuant_Learn in clinical research studies have proven its effectiveness as a fast and efficient tool for the automatic extraction, quantification and analysis of histological sections. It is robust with respect to several deficits caused by image acquisition systems and produces objective and reproducible results. Thanks to its flexibility, MIAQuant_Learn represents an important tool to be exploited in basic research where needs are constantly changing.

Digital image analysis in breast pathology-from image processing techniques to artificial intelligence

Breast cancer is the most common malignant disease in women worldwide. In recent decades, earlier diagnosis and better adjuvant therapy have substantially improved patient outcome. Diagnosis by histopathology has proven to be instrumental to guide breast cancer treatment, but new challenges have emerged as our increasing understanding of cancer over the years has revealed its complex nature. As patient demand for personalized breast cancer therapy grows, we face an urgent need for more precise biomarker assessment and more accurate histopathologic breast cancer diagnosis to make better therapy decisions. The digitization of pathology data has opened the door to faster, more reproducible, and more precise diagnoses through computerized image analysis. Software to assist diagnostic breast pathology through image processing techniques have been around for years. But recent breakthroughs in artificial intelligence (AI) promise to fundamentally change the way we detect and treat breast cancer in the near future. Machine learning, a subfield of AI that applies statistical methods to learn from data, has seen an explosion of interest in recent years because of its ability to recognize patterns in data with less need for human instruction. One technique in particular, known as deep learning, has produced groundbreaking results in many important problems including image classification and speech recognition. In this review, we will cover the use of AI and deep learning in diagnostic breast pathology, and other recent developments in digital image analysis.

Radiogenomics analysis identifies correlations of digital mammography with clinical molecular signatures in breast cancer

In breast cancer, well-known gene expression subtypes have been related to a specific clinical outcome. However, their impact on the breast tissue phenotype has been poorly studied. Here, we investigate the association of imaging data of tumors to gene expression signatures from 71 patients with breast cancer that underwent pre-treatment digital mammograms and tumor biopsies. From digital mammograms, a semi-automated radiogenomics analysis generated 1,078 features describing the shape, signal distribution, and texture of tumors along their contralateral image used as control. From tumor biopsy, we estimated the OncotypeDX and PAM50 recurrence scores using gene expression microarrays. Then, we used multivariate analysis under stringent cross-validation to train models predicting recurrence scores. Few univariate features reached Spearman correlation coefficients above 0.4. Nevertheless, multivariate analysis yielded significantly correlated models for both signatures (correlation of OncotypeDX = 0.49 ± 0.07 and PAM50 = 0.32 ± 0.10 in stringent cross-validation and OncotypeDX = 0.83 and PAM50 = 0.78 for a unique model). Equivalent models trained from the unaffected contralateral breast were not correlated suggesting that the image signatures were tumor-specific and that overfitting was not a considerable issue. We also noted that models were improved by combining clinical information (triple negative status and progesterone receptor). The models used mostly wavelets and fractal features suggesting their importance to capture tumor information. Our results suggest that molecular-based recurrence risk and breast cancer subtypes have observable radiographic phenotypes. To our knowledge, this is the first study associating mammographic information to gene expression recurrence signatures.

Label-free cell nuclear imaging by Grüneisen relaxation photoacoustic microscopy

Photoacoustic microscopy (PAM) with ultraviolet (UV) laser illumination has recently been demonstrated as a promising tool that provides fast, label-free, and multilayered histologic imaging of human breast tissue. Thus far, the axial resolution has been determined ultrasonically. To enable optically defined axial resolution, we exploit the Grüneisen relaxation (GR) effect. By imaging mouse brain slices, we show that GRUV-PAM reveals detailed information about three-dimensional cell nuclear distributions and internal structures, which are important diagnostic features for cancers. Due to the nonlinear effect, GRUV-PAM also provides better contrast in images of cell nuclei.

Inferring cell state by quantitative motility analysis reveals a dynamic state system and broken detailed balance

Cell populations display heterogeneous and dynamic phenotypic states at multiple scales. Similar to molecular features commonly used to explore cell heterogeneity, cell behavior is a rich phenotypic space that may allow for identification of relevant cell states. Inference of cell state from cell behavior across a time course may enable the investigation of dynamics of transitions between heterogeneous cell states, a task difficult to perform with destructive molecular observations. Cell motility is one such easily observed cell behavior with known biomedical relevance. To investigate heterogenous cell states and their dynamics through the lens of cell behavior, we developed Heteromotility, a software tool to extract quantitative motility features from timelapse cell images. In mouse embryonic fibroblasts (MEFs), myoblasts, and muscle stem cells (MuSCs), Heteromotility analysis identifies multiple motility phenotypes within the population. In all three systems, the motility state identity of individual cells is dynamic. Quantification of state transitions reveals that MuSCs undergoing activation transition through progressive motility states toward the myoblast phenotype. Transition rates during MuSC activation suggest non-linear kinetics. By probability flux analysis, we find that this MuSC motility state system breaks detailed balance, while the MEF and myoblast systems do not. Balanced behavior state transitions can be captured by equilibrium formalisms, while unbalanced switching between states violates equilibrium conditions and would require an external driving force. Our data indicate that the system regulating cell behavior can be decomposed into a set of attractor states which depend on the identity of the cell, together with a set of transitions between states. These results support a conceptual view of cell populations as dynamical systems, responding to inputs from signaling pathways and generating outputs in the form of state transitions and observable motile behaviors.

A novel overlapped nuclei splitting algorithm for histopathological images

BACKGROUND AND OBJECTIVE

Nuclei segmentation is a common process for quantitative analysis of histopathological images. However, this process generally results in overlapping of nuclei due to the nature of images, the sample preparation and staining, and image acquisition processes as well as insufficiency of 2D histopathological images to represent 3D characteristics of tissues. We present a novel algorithm to split overlapped nuclei.

METHODS

The histopathological images are initially segmented by K-Means segmentation algorithm. Then, nuclei cluster are converted to binary image. The overlapping is detected by applying threshold area value to nuclei in the binary image. The splitting algorithm is applied to the overlapped nuclei. In first stage of splitting, circles are drawn on overlapped nuclei. The radius of the circles is calculated by using circle area formula, and each pixel's coordinates of overlapped nuclei are selected as center coordinates for each circle. The pixels in the circle that contains maximum number of intersected pixels in both the circle and the overlapped nuclei are removed from the overlapped nuclei, and the filled circle labeled as a nucleus.

RESULTS

The algorithm has been tested on histopathological images of healthy and damaged kidney tissues and compared with the results provided by an expert and three related studies. The results demonstrated that the proposed splitting algorithm can segment the overlapping nuclei with accuracy of 84%.

CONCLUSIONS

The study presents a novel algorithm splitting the overlapped nuclei in histopathological images and provides more accurate cell counting in histopathological analysis. Furthermore, the proposed splitting algorithm has the potential to be used in different fields to split any overlapped circular patterns.

Automatic cellularity assessment from post-treated breast surgical specimens

Neoadjuvant treatment (NAT) of breast cancer (BCa) is an option for patients with the locally advanced disease. It has been compared with standard adjuvant therapy with the aim of improving prognosis and surgical outcome. Moreover, the response of the tumor to the therapy provides useful information for patient management. The pathological examination of the tissue sections after surgery is the gold-standard to estimate the residual tumor and the assessment of cellularity is an important component of tumor burden assessment. In the current clinical practice, tumor cellularity is manually estimated by pathologists on hematoxylin and eosin (H&E) stained slides, the quality, and reliability of which might be impaired by inter-observer variability which potentially affects prognostic power assessment in NAT trials. This procedure is also qualitative and time-consuming. In this paper, we describe a method of automatically assessing cellularity. A pipeline to automatically segment nuclei figures and estimate residual cancer cellularity from within patches and whole slide images (WSIs) of BCa was developed. We have compared the performance of our proposed pipeline in estimating residual cancer cellularity with that of two expert pathologists. We found an intra-class agreement coefficient (ICC) of 0.89 (95% CI of [0.70, 0.95]) between pathologists, 0.74 (95% CI of [0.70, 0.77]) between pathologist #1 and proposed method, and 0.75 (95% CI of [0.71, 0.79]) between pathologist #2 and proposed method. We have also successfully applied our proposed technique on a WSI to locate areas with high concentration of residual cancer. The main advantage of our approach is that it is fully automatic and can be used to find areas with high cellularity in WSIs. This provides a first step in developing an automatic technique for post-NAT tumor response assessment from pathology slides. © 2017 International Society for Advancement of Cytometry.

Grading of invasive breast carcinoma through Grassmannian VLAD encoding

In this paper we address the problem of automated grading of invasive breast carcinoma through the encoding of histological images as VLAD (Vector of Locally Aggregated Descriptors) representations on the Grassmann manifold. The proposed method considers each image as a set of multidimensional spatially-evolving signals that can be efficiently modeled through a higher-order linear dynamical systems analysis. Subsequently, each H&E (Hematoxylin and Eosin) stained breast cancer histological image is represented as a cloud of points on the Grassmann manifold, while a vector representation approach is applied aiming to aggregate the Grassmannian points based on a locality criterion on the manifold. To evaluate the efficiency of the proposed methodology, two datasets with different characteristics were used. More specifically, we created a new medium-sized dataset consisting of 300 annotated images (collected from 21 patients) of grades 1, 2 and 3, while we also provide experimental results using a large dataset, namely BreaKHis, containing 7,909 breast cancer histological images, collected from 82 patients, of both benign and malignant cases. Experimental results have shown that the proposed method outperforms a number of state of the art approaches providing average classification rates of 95.8% and 91.38% with our dataset and the BreaKHis dataset, respectively.

A structured latent model for ovarian carcinoma subtyping from histopathology slides

Accurate subtyping of ovarian carcinomas is an increasingly critical and often challenging diagnostic process. This work focuses on the development of an automatic classification model for ovarian carcinoma subtyping. Specifically, we present a novel clinically inspired contextual model for histopathology image subtyping of ovarian carcinomas. A whole slide image is modelled using a collection of tissue patches extracted at multiple magnifications. An efficient and effective feature learning strategy is used for feature representation of a tissue patch. The locations of salient, discriminative tissue regions are treated as latent variables allowing the model to explicitly ignore portions of the large tissue section that are unimportant for classification. These latent variables are considered in a structured formulation to model the contextual information represented from the multi-magnification analysis of tissues. A novel, structured latent support vector machine formulation is defined and used to combine information from multiple magnifications while simultaneously operating within the latent variable framework. The structural and contextual nature of our method addresses the challenges of intra-class variation and pathologists' workload, which are prevalent in histopathology image classification. Extensive experiments on a dataset of 133 patients demonstrate the efficacy and accuracy of the proposed method against state-of-the-art approaches for histopathology image classification. We achieve an average multi-class classification accuracy of 90%, outperforming existing works while obtaining substantial agreement with six clinicians tested on the same dataset.

Two-phase deep convolutional neural network for reducing class skewness in histopathological images based breast cancer detection

Different types of breast cancer are affecting lives of women across the world. Common types include Ductal carcinoma in situ (DCIS), Invasive ductal carcinoma (IDC), Tubular carcinoma, Medullary carcinoma, and Invasive lobular carcinoma (ILC). While detecting cancer, one important factor is mitotic count - showing how rapidly the cells are dividing. But the class imbalance problem, due to the small number of mitotic nuclei in comparison to the overwhelming number of non-mitotic nuclei, affects the performance of classification models. This work presents a two-phase model to mitigate the class biasness issue while classifying mitotic and non-mitotic nuclei in breast cancer histopathology images through a deep convolutional neural network (CNN). First, nuclei are segmented out using blue ratio and global binary thresholding. In Phase-1 a CNN is then trained on the segmented out 80×80 pixel patches based on a standard dataset. Hard non-mitotic examples are identified and augmented; mitotic examples are oversampled by rotation and flipping; whereas non-mitotic examples are undersampled by blue ratio histogram based k-means clustering. Based on this information from Phase-1, the dataset is modified for Phase-2 in order to reduce the effects of class imbalance. The proposed CNN architecture and data balancing technique yielded an F-measure of 0.79, and outperformed all the methods relying on specific handcrafted features, as well as those using a combination of handcrafted and CNN-generated features.

Computer-aided prognosis on breast cancer with hematoxylin and eosin histopathology images: A review

With the advance of digital pathology, image analysis has begun to show its advantages in information analysis of hematoxylin and eosin histopathology images. Generally, histological features in hematoxylin and eosin images are measured to evaluate tumor grade and prognosis for breast cancer. This review summarized recent works in image analysis of hematoxylin and eosin histopathology images for breast cancer prognosis. First, prognostic factors for breast cancer based on hematoxylin and eosin histopathology images were summarized. Then, usual procedures of image analysis for breast cancer prognosis were systematically reviewed, including image acquisition, image preprocessing, image detection and segmentation, and feature extraction. Finally, the prognostic value of image features and image feature–based prognostic models was evaluated. Moreover, we discussed the issues of current analysis, and some directions for future research.

Evaluation of nucleus segmentation in digital pathology images through large scale image synthesis

Digital histopathology images with more than 1 Gigapixel are drawing more and more attention in clinical, biomedical research, and computer vision fields. Among the multiple observable features spanning multiple scales in the pathology images, the nuclear morphology is one of the central criteria for diagnosis and grading. As a result it is also the mostly studied target in image computing. Large amount of research papers have devoted to the problem of extracting nuclei from digital pathology images, which is the foundation of any further correlation study. However, the validation and evaluation of nucleus extraction have yet been formulated rigorously and systematically. Some researches report a human verified segmentation with thousands of nuclei, whereas a single whole slide image may contain up to million. The main obstacle lies in the difficulty of obtaining such a large number of validated nuclei, which is essentially an impossible task for pathologist. We propose a systematic validation and evaluation approach based on large scale image synthesis. This could facilitate a more quantitatively validated study for current and future histopathology image analysis field.

Computer-based image analysis in breast pathology

Whole slide imaging (WSI) has the potential to be utilized in telepathology, teleconsultation, quality assurance, clinical education, and digital image analysis to aid pathologists. In this paper, the potential added benefits of computer-assisted image analysis in breast pathology are reviewed and discussed. One of the major advantages of WSI systems is the possibility of doing computer-based image analysis on the digital slides. The purpose of computer-assisted analysis of breast virtual slides can be (i) segmentation of desired regions or objects such as diagnostically relevant areas, epithelial nuclei, lymphocyte cells, tubules, and mitotic figures, (ii) classification of breast slides based on breast cancer (BCa) grades, the invasive potential of tumors, or cancer subtypes, (iii) prognosis of BCa, or (iv) immunohistochemical quantification. While encouraging results have been achieved in this area, further progress is still required to make computer-based image analysis of breast virtual slides acceptable for clinical practice.