Texture Analysis of Abnormal Cell Images for Predicting the Continuum of Colorectal Cancer

Applications of discriminative and deep learning feature extraction methods for whole slide image analysis: A survey

Digital pathology technologies, including whole slide imaging (WSI), have significantly improved modern clinical practices by facilitating storing, viewing, processing, and sharing digital scans of tissue glass slides. Researchers have proposed various artificial intelligence (AI) solutions for digital pathology applications, such as automated image analysis, to extract diagnostic information from WSI for improving pathology productivity, accuracy, and reproducibility. Feature extraction methods play a crucial role in transforming raw image data into meaningful representations for analysis, facilitating the characterization of tissue structures, cellular properties, and pathological patterns. These features have diverse applications in several digital pathology applications, such as cancer prognosis and diagnosis. Deep learning-based feature extraction methods have emerged as a promising approach to accurately represent WSI contents and have demonstrated superior performance in histology-related tasks. In this survey, we provide a comprehensive overview of feature extraction methods, including both manual and deep learning-based techniques, for the analysis of WSIs. We review relevant literature, analyze the discriminative and geometric features of WSIs (i.e., features suited to support the diagnostic process and extracted by "engineered" methods as opposed to AI), and explore predictive modeling techniques using AI and deep learning. This survey examines the advances, challenges, and opportunities in this rapidly evolving field, emphasizing the potential for accurate diagnosis, prognosis, and decision-making in digital pathology.

Accurate recognition of colorectal cancer with semi-supervised deep learning on pathological images

Machine-assisted pathological recognition has been focused on supervised learning (SL) that suffers from a significant annotation bottleneck. We propose a semi-supervised learning (SSL) method based on the mean teacher architecture using 13,111 whole slide images of colorectal cancer from 8803 subjects from 13 independent centers. SSL (~3150 labeled, ~40,950 unlabeled; ~6300 labeled, ~37,800 unlabeled patches) performs significantly better than the SL. No significant difference is found between SSL (~6300 labeled, ~37,800 unlabeled) and SL (~44,100 labeled) at patch-level diagnoses (area under the curve (AUC): 0.980 ± 0.014 vs. 0.987 ± 0.008, P value = 0.134) and patient-level diagnoses (AUC: 0.974 ± 0.013 vs. 0.980 ± 0.010, P value = 0.117), which is close to human pathologists (average AUC: 0.969). The evaluation on 15,000 lung and 294,912 lymph node images also confirm SSL can achieve similar performance as that of SL with massive annotations. SSL dramatically reduces the annotations, which has great potential to effectively build expert-level pathological artificial intelligence platforms in practice.

Improved window adaptive gray level co-occurrence matrix for extraction and analysis of texture characteristics of pulmonary nodules

BACKGROUND AND OBJECTIVE

Identifying benign and malignant pulmonary nodules is essential for the early diagnosis of lung cancer and targeted surgical resection. This study aimed to differentiate benign from malignant pulmonary nodules based on computed tomography (CT) plain scan texture analysis technique.

METHODS

A total of 47 pulmonary nodules use the improved window adaptive gray level co-occurrence matrix (GLCM) algorithm to extract the texture characteristics of the area of interest. The Fisher coefficient (Fisher), classification error probability joint average correlation coefficient (POE+ACC), mutual information (MI), and the combination of above three methods joint (FPM) were used to select the best texture parameters set. After that, the analysis of the screened texture parameters was adopted. The B11 module provides four analytical methods, including raw data analysis (RDA), principal component analysis (PCA), linear discriminant analysis (LDA), and nonlinear discriminant analysis (NDA). The results were expressed in the form of misclassification rate (MCR). Region of curve (ROC) analysis was also performed on the selected optimal texture parameters.

RESULTS

The MCR of all the three texture feature extraction methods, Fisher, POE+ACC, and MI, were lower in differentiating benign from malignant pulmonary nodules. FPM method could further reduce the MCR. The NDA analysis had the lowest MCR for both of these three feature extraction methods. The MCR can be further reduced to 2.13% by the combination of NDA and FPM. The ROC curve showed that Perc.01% parameter had the highest AUC value and the most discriminative efficacy.

CONCLUSION

The lowest MCR values were calculated by the FPM dimensionality reduction method and the NDA analysis method. The improved GLCM algorithm has a discriminative role in CT texture analysis of benign and malignant pulmonary nodules.

Accurate diagnosis of colorectal cancer based on histopathology images using artificial intelligence

BACKGROUND

Accurate and robust pathological image analysis for colorectal cancer (CRC) diagnosis is time-consuming and knowledge-intensive, but is essential for CRC patients' treatment. The current heavy workload of pathologists in clinics/hospitals may easily lead to unconscious misdiagnosis of CRC based on daily image analyses.

METHODS

Based on a state-of-the-art transfer-learned deep convolutional neural network in artificial intelligence (AI), we proposed a novel patch aggregation strategy for clinic CRC diagnosis using weakly labeled pathological whole-slide image (WSI) patches. This approach was trained and validated using an unprecedented and enormously large number of 170,099 patches, > 14,680 WSIs, from > 9631 subjects that covered diverse and representative clinical cases from multi-independent-sources across China, the USA, and Germany.

RESULTS

Our innovative AI tool consistently and nearly perfectly agreed with (average Kappa statistic 0.896) and even often better than most of the experienced expert pathologists when tested in diagnosing CRC WSIs from multicenters. The average area under the receiver operating characteristics curve (AUC) of AI was greater than that of the pathologists (0.988 vs 0.970) and achieved the best performance among the application of other AI methods to CRC diagnosis. Our AI-generated heatmap highlights the image regions of cancer tissue/cells.

CONCLUSIONS

This first-ever generalizable AI system can handle large amounts of WSIs consistently and robustly without potential bias due to fatigue commonly experienced by clinical pathologists. It will drastically alleviate the heavy clinical burden of daily pathology diagnosis and improve the treatment for CRC patients. This tool is generalizable to other cancer diagnosis based on image recognition.

Segmentation and Grade Prediction of Colon Cancer Digital Pathology Images Across Multiple Institutions

Distinguishing benign from malignant disease is a primary challenge for colon histopathologists. Current clinical methods rely on qualitative visual analysis of features such as glandular architecture and size that exist on a continuum from benign to malignant. Consequently, discordance between histopathologists is common. To provide more reliable analysis of colon specimens, we propose an end-to-end computational pathology pipeline that encompasses gland segmentation, cancer detection, and then further breaking down the malignant samples into different cancer grades. We propose a multi-step gland segmentation method, which models tissue components as ellipsoids. For cancer detection/grading, we encode cellular morphology, spatial architectural patterns of glands, and texture by extracting multi-scale features: (i) Gland-based: extracted from individual glands, (ii) local-patch-based: computed from randomly-selected image patches, and (iii) image-based: extracted from images, and employ a hierarchical ensemble-classification method. Using two datasets (Rawalpindi Medical College (RMC), n = 174 and gland segmentation (GlaS), n = 165) with three cancer grades, our method reliably delineated gland regions (RMC = 87.5%, GlaS = 88.4%), detected the presence of malignancy (RMC = 97.6%, GlaS = 98.3%), and predicted tumor grade (RMC = 98.6%, GlaS = 98.6%). Training the model using one dataset and testing it on the other showed strong concordance in cancer detection (Train RMC – Test GlaS = 94.5%, Train GlaS – Test RMC = 93.7%) and grading (Train RMC – Test GlaS = 95%, Train GlaS – Test RMC = 95%) suggesting that the model will be applicable across institutions. With further prospective validation, the techniques demonstrated here may provide a reproducible and easily accessible method to standardize analysis of colon cancer specimens.

On Structural Entropy and Spatial Filling Factor Analysis of Colonoscopy Pictures

Colonoscopy is the standard device for diagnosing colorectal cancer, which develops from little lesions on the bowel wall called polyps. The Rényi entropies-based structural entropy and spatial filling factor are two scale- and resolution-independent quantities that characterize the shape of a probability distribution with the help of characteristic curves of the structural entropy–spatial filling factor map. This alternative definition of structural entropy is easy to calculate, independent of the image resolution, and does not require the calculation of neighbor statistics, unlike the other graph-based structural entropies.The distant goal of this study was to help computer aided diagnosis in finding colorectal polyps by making the Rényi entropy based structural entropy more understood. The direct goal was to determine characteristic curves that can differentiate between polyps and other structure on the picture. After analyzing the distribution of colonoscopy picture color channels, the typical structures were modeled with simple geometrical functions and the structural entropy–spatial filling factor characteristic curves were determined for these model structures for various parameter sets. A colonoscopy image analying method, i.e., the line- or column-wise scanning of the picture, was also tested, with satisfactory matching of the characteristic curve and the image.

Radiomics Evaluation of Histological Heterogeneity Using Multiscale Textures Derived From 3D Wavelet Transformation of Multispectral Images

Purpose

Colorectal cancer (CRC) is markedly heterogeneous and develops progressively toward malignancy through several stages which include stroma (ST), benign hyperplasia (BH), intraepithelial neoplasia (IN) or precursor cancerous lesion, and carcinoma (CA). Identification of the malignancy stage of CRC pathology tissues (PT) allows the most appropriate therapeutic intervention.

Methods

This study investigates multiscale texture features extracted from CRC pathology sections using 3D wavelet transform (3D-WT) filter. Multiscale features were extracted from digital whole slide images of 39 patients that were segmented in a pre-processing step using an active contour model. The capacity for multiscale texture to compare and classify between PTs was investigated using ANOVA significance test and random forest classifier models, respectively.

Results

12 significant features derived from the multiscale texture (i.e., variance, entropy, and energy) were found to discriminate between CRC grades at a significance value of p < 0.01 after correction. Combining multiscale texture features lead to a better predictive capacity compared to prediction models based on individual scale features with an average (±SD) classification accuracy of 93.33 (±3.52)%, sensitivity of 88.33 (± 4.12)%, and specificity of 96.89 (± 3.88)%. Entropy was found to be the best classifier feature across all the PT grades with an average of the area under the curve (AUC) value of 91.17, 94.21, 97.70, 100% for ST, BH, IN, and CA, respectively.

Conclusion

Our results suggest that multiscale texture features based on 3D-WT are sensitive enough to discriminate between CRC grades with the entropy feature, the best predictor of pathology grade.