Automated gleason grading on prostate biopsy slides by statistical representations of homology profile

Computational pathology: A survey review and the way forward

Computational Pathology (CPath) is an interdisciplinary science that augments developments of computational approaches to analyze and model medical histopathology images. The main objective for CPath is to develop infrastructure and workflows of digital diagnostics as an assistive CAD system for clinical pathology, facilitating transformational changes in the diagnosis and treatment of cancer that are mainly address by CPath tools. With evergrowing developments in deep learning and computer vision algorithms, and the ease of the data flow from digital pathology, currently CPath is witnessing a paradigm shift. Despite the sheer volume of engineering and scientific works being introduced for cancer image analysis, there is still a considerable gap of adopting and integrating these algorithms in clinical practice. This raises a significant question regarding the direction and trends that are undertaken in CPath. In this article we provide a comprehensive review of more than 800 papers to address the challenges faced in problem design all-the-way to the application and implementation viewpoints. We have catalogued each paper into a model-card by examining the key works and challenges faced to layout the current landscape in CPath. We hope this helps the community to locate relevant works and facilitate understanding of the field's future directions. In a nutshell, we oversee the CPath developments in cycle of stages which are required to be cohesively linked together to address the challenges associated with such multidisciplinary science. We overview this cycle from different perspectives of data-centric, model-centric, and application-centric problems. We finally sketch remaining challenges and provide directions for future technical developments and clinical integration of CPath. For updated information on this survey review paper and accessing to the original model cards repository, please refer to GitHub. Updated version of this draft can also be found from arXiv.

An Artificial Intelligent System for Prostate Cancer Diagnosis in Whole Slide Images

In recent years a significant demand to develop computer-assisted diagnostic tools to assess prostate cancer using whole slide images has been observed. In this study we develop and validate a machine learning system for cancer assessment, inclusive of detection of perineural invasion and measurement of cancer portion to meet clinical reporting needs. The system analyses the whole slide image in three consecutive stages: tissue detection, classification, and slide level analysis. The whole slide image is divided into smaller regions (patches). The tissue detection stage relies upon traditional machine learning to identify WSI patches containing tissue, which are then further assessed at the classification stage where deep learning algorithms are employed to detect and classify cancer tissue. At the slide level analysis stage, entire slide level information is generated by aggregating all the patch level information of the slide. A total of 2340 haematoxylin and eosin stained slides were used to train and validate the system. A medical team consisting of 11 board certified pathologists with prostatic pathology subspeciality competences working independently in 4 different medical centres performed the annotations. Pixel-level annotation based on an agreed set of 10 annotation terms, determined based on medical relevance and prevalence, was created by the team. The system achieved an accuracy of 99.53% in tissue detection, with sensitivity and specificity respectively of 99.78% and 99.12%. The system achieved an accuracy of 92.80% in classifying tissue terms, with sensitivity and specificity respectively 92.61% and 99.25%, when 5x magnification level was used. For 10x magnification, these values were respectively 91.04%, 90.49%, and 99.07%. For 20x magnification they were 84.71%, 83.95%, 90.13%.

Advancing Precision Medicine: Algebraic Topology and Differential Geometry in Radiology and Computational Pathology

Precision medicine aims to provide personalized care based on individual patient characteristics, rather than guideline-directed therapies for groups of diseases or patient demographics. Images-both radiology- and pathology-derived-are a major source of information on presence, type, and status of disease. Exploring the mathematical relationship of pixels in medical imaging ("radiomics") and cellular-scale structures in digital pathology slides ("pathomics") offers powerful tools for extracting both qualitative and, increasingly, quantitative data. These analytical approaches, however, may be significantly enhanced by applying additional methods arising from fields of mathematics such as differential geometry and algebraic topology that remain underexplored in this context. Geometry's strength lies in its ability to provide precise local measurements, such as curvature, that can be crucial for identifying abnormalities at multiple spatial levels. These measurements can augment the quantitative features extracted in conventional radiomics, leading to more nuanced diagnostics. By contrast, topology serves as a robust shape descriptor, capturing essential features such as connected components and holes. The field of topological data analysis was initially founded to explore the shape of data, with functional network connectivity in the brain being a prominent example. Increasingly, its tools are now being used to explore organizational patterns of physical structures in medical images and digitized pathology slides. By leveraging tools from both differential geometry and algebraic topology, researchers and clinicians may be able to obtain a more comprehensive, multi-layered understanding of medical images and contribute to precision medicine's armamentarium.

A quantitative evaluation method utilizing the homology concept to assess the state of chromatin within the nucleus of lung cancer

Homology is a mathematical tool to quantify "the contact degree", which can be expressed in terms of Betti numbers. The Betti numbers used in this study consisted of two numbers, b0 (a zero-dimensional Betti number) and b1 (a one-dimensional Betti number). We developed a chromatin homology profile (CHP) method to quantify the chromatin contact degree based on this mathematical tool. Using the CHP method we analyzed the number of holes (surrounded areas = b1 value) formed by the chromatin contact and calculated the maximum value of b1 (b1MAX), the value of b1 exceeding 5 for the first time or Homology Value (HV), and the chromatin density (b1MAX/ns2). We attempted to detect differences in chromatin patterns and differentiate histological types of lung cancer from respiratory cytology using these three features. The HV of cancer cells was significantly lower than that of non-cancerous cells. Furthermore, b1MAX and b1MAX/ns2 showed significant differences between small cell and non-small cell carcinomas and between adenocarcinomas and squamous cell carcinomas, respectively. We quantitatively analyzed the chromatin patterns using homology and showed that the CHP method may be a useful tool for differentiating histological types of lung cancer in respiratory cytology.

A novel pipeline for computerized mouse spermatogenesis staging

MOTIVATION

Differentiating 12 stages of the mouse seminiferous epithelial cycle is vital towards understanding the dynamic spermatogenesis process. However, it is challenging since two adjacent spermatogenic stages are morphologically similar. Distinguishing Stages I-III from Stages IV-V is important for histologists to understand sperm development in wildtype mice and spermatogenic defects in infertile mice. To achieve this, we propose a novel pipeline for computerized spermatogenesis staging (CSS).

RESULTS

The CSS pipeline comprises four parts: (i) A seminiferous tubule segmentation model is developed to extract every single tubule; (ii) A multi-scale learning (MSL) model is developed to integrate local and global information of a seminiferous tubule to distinguish Stages I-V from Stages VI-XII; (iii) a multi-task learning (MTL) model is developed to segment the multiple testicular cells for Stages I-V without an exhaustive requirement for manual annotation; (iv) A set of 204D image-derived features is developed to discriminate Stages I-III from Stages IV-V by capturing cell-level and image-level representation. Experimental results suggest that the proposed MSL and MTL models outperform classic single-scale and single-task models when manual annotation is limited. In addition, the proposed image-derived features are discriminative between Stages I-III and Stages IV-V. In conclusion, the CSS pipeline can not only provide histologists with a solution to facilitate quantitative analysis for spermatogenesis stage identification but also help them to uncover novel computerized image-derived biomarkers.

AVAILABILITY AND IMPLEMENTATION

https://github.com/jydada/CSS.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Histopathological Tissue Segmentation of Lung Cancer with Bilinear CNN and Soft Attention

Automatic tissue segmentation in whole-slide images (WSIs) is a critical task in hematoxylin and eosin- (H&E-) stained histopathological images for accurate diagnosis and risk stratification of lung cancer. Patch classification and stitching the classification results can fast conduct tissue segmentation of WSIs. However, due to the tumour heterogeneity, large intraclass variability and small interclass variability make the classification task challenging. In this paper, we propose a novel bilinear convolutional neural network- (Bilinear-CNN-) based model with a bilinear convolutional module and a soft attention module to tackle this problem. This method investigates the intraclass semantic correspondence and focuses on the more distinguishable features that make feature output variations relatively large between interclass. The performance of the Bilinear-CNN-based model is compared with other state-of-the-art methods on the histopathological classification dataset, which consists of 107.7 k patches of lung cancer. We further evaluate our proposed algorithm on an additional dataset from colorectal cancer. Extensive experiments show that the performance of our proposed method is superior to that of previous state-of-the-art ones and the interpretability of our proposed method is demonstrated by Grad-CAM.

Development of “Mathematical Technology for Cytopathology,” an Image Analysis Algorithm for Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer-related death worldwide. The accuracy of a PDAC diagnosis based on endoscopic ultrasonography-guided fine-needle aspiration cytology can be strengthened by performing a rapid on-site evaluation (ROSE). However, ROSE can only be performed in a limited number of facilities, due to a relative lack of available resources or cytologists with sufficient training. Therefore, we developed the Mathematical Technology for Cytopathology (MTC) algorithm, which does not require teaching data or large-scale computing. We applied the MTC algorithm to support the cytological diagnosis of pancreatic cancer tissues, by converting medical images into structured data, which rendered them suitable for artificial intelligence (AI) analysis. Using this approach, we successfully clarified ambiguous cell boundaries by solving a reaction–diffusion system and quantitating the cell nucleus status. A diffusion coefficient (D) of 150 showed the highest accuracy (i.e., 74%), based on a univariate analysis. A multivariate analysis was performed using 120 combinations of evaluation indices, and the highest accuracies for each D value studied (50, 100, and 150) were all ≥70%. Thus, our findings indicate that MTC can help distinguish between adenocarcinoma and benign pancreatic tissues, and imply its potential for facilitating rapid progress in clinical diagnostic applications.

[Automated grading of glioma based on density and atypia analysis in whole slide images]

Glioma is the most common malignant brain tumor and classification of low grade glioma (LGG) and high grade glioma (HGG) is an important reference of making decisions on patient treatment options and prognosis. This work is largely done manually by pathologist based on an examination of whole slide image (WSI), which is arduous and heavily dependent on doctors' experience. In the World Health Organization (WHO) criteria, grade of glioma is closely related to hypercellularity, nuclear atypia and necrosis. Inspired by this, this paper designed and extracted cell density and atypia features to classify LGG and HGG. First, regions of interest (ROI) were located by analyzing cell density and global density features were extracted as well. Second, local density and atypia features were extracted in ROI. Third, balanced support vector machine (SVM) classifier was trained and tested using 10 selected features. The area under the curve (AUC) and accuracy (ACC) of 5-fold cross validation were 0.92 ± 0.01 and 0.82 ± 0.01 respectively. The results demonstrate that the proposed method of locating ROI is effective and the designed features of density and atypia can be used to predict glioma grade accurately, which can provide reliable basis for clinical diagnosis.

GestAltNet: aggregation and attention to improve deep learning of gestational age from placental whole-slide images

The placenta is the first organ to form and performs the functions of the lung, gut, kidney, and endocrine systems. Abnormalities in the placenta cause or reflect most abnormalities in gestation and can have life-long consequences for the mother and infant. Placental villi undergo a complex but reproducible sequence of maturation across the third-trimester. Abnormalities of villous maturation are a feature of gestational diabetes and preeclampsia, among others, but there is significant interobserver variability in their diagnosis. Machine learning has emerged as a powerful tool for research in pathology. To capture the volume of data and manage heterogeneity within the placenta, we developed GestaltNet, which emulates human attention to high-yield areas and aggregation across regions. We used this network to estimate the gestational age (GA) of scanned placental slides and compared it to a baseline model lacking the attention and aggregation functions. In the test set, GestaltNet showed a higher r2 (0.9444 vs. 0.9220) than the baseline model. The mean absolute error (MAE) between the estimated and actual GA was also better in the GestaltNet (1.0847 weeks vs. 1.4505 weeks). On whole-slide images, we found the attention sub-network discriminates areas of terminal villi from other placental structures. Using this behavior, we estimated GA for 36 whole slides not previously seen by the model. In this task, similar to that faced by human pathologists, the model showed an r2 of 0.8859 with an MAE of 1.3671 weeks. We show that villous maturation is machine-recognizable. Machine-estimated GA could be useful when GA is unknown or to study abnormalities of villous maturation, including those in gestational diabetes or preeclampsia. GestaltNet points toward a future of genuinely whole-slide digital pathology by incorporating human-like behaviors of attention and aggregation.

Homology-Based Image Processing for Automatic Classification of Histopathological Images of Lung Tissue

Simple Summary

The purpose of this study was to develop a computer-aided diagnosis (CAD) system for automatic classification of histopathological images of lung tissues. Homology-based image processing (HI) was proposed for CAD. For developing and validating CAD with HI, two datasets of histopathological images of lung tissues were used. The private dataset consists of 94 histopathological images that were obtained for the following five categories: normal, emphysema, atypical adenomatous hyperplasia, lepidic pattern of adenocarcinoma, and invasive adenocarcinoma. The public dataset consists of 15,000 histopathological images that were obtained for the following three categories: lung adenocarcinoma, lung squamous cell carcinoma, and benign lung tissue. For the two datasets, our results show that HI was more useful than conventional texture analysis for the CAD system.

Abstract

The purpose of this study was to develop a computer-aided diagnosis (CAD) system for automatic classification of histopathological images of lung tissues. Two datasets (private and public datasets) were obtained and used for developing and validating CAD. The private dataset consists of 94 histopathological images that were obtained for the following five categories: normal, emphysema, atypical adenomatous hyperplasia, lepidic pattern of adenocarcinoma, and invasive adenocarcinoma. The public dataset consists of 15,000 histopathological images that were obtained for the following three categories: lung adenocarcinoma, lung squamous cell carcinoma, and benign lung tissue. These images were automatically classified using machine learning and two types of image feature extraction: conventional texture analysis (TA) and homology-based image processing (HI). Multiscale analysis was used in the image feature extraction, after which automatic classification was performed using the image features and eight machine learning algorithms. The multicategory accuracy of our CAD system was evaluated in the two datasets. In both the public and private datasets, the CAD system with HI was better than that with TA. It was possible to build an accurate CAD system for lung tissues. HI was more useful for the CAD systems than TA.