Glomerulosclerosis identification in whole slide images using semantic segmentation.

BACKGROUND AND OBJECTIVE: Glomeruli identification, i.e., detection and characterization, is a key procedure in many nephropathology studies. In this paper, semantic segmentation based on convolutional neural networks (CNN) is proposed to detect glomeruli using Whole Slide Imaging (WSI) follows by a classification CNN to divide the glomeruli into normal and sclerosed. METHODS: Comparison between U-Net and SegNet CNNs is performed for pixel-level segmentation considering both a two and three class problem, that is, a) non-glomerular and glomerular structures and b) non-glomerular normal glomerular and sclerotic structures. The two class semantic segmentation result is then used for a CNN classification where glomerular regions are divided into normal and global sclerosed glomeruli. RESULTS: These methods were tested on a dataset composed of 47 WSIs belonging to human kidney sections stained with Periodic Acid Schiff (PAS). The best approach was the SegNet for two class segmentation follows by a fine-tuned AlexNet network to characterize the glomeruli. 98.16% of accuracy was obtained with this process of consecutive CNNs (SegNet-AlexNet) for segmentation and classification. CONCLUSION: The results obtained demonstrate that the sequential CNN segmentation-classification strategy achieves higher accuracy reducing misclassified cases and therefore being the methodology proposed for glomerulosclerosis detection.

Automatic quantification of IHC stain in breast TMA using colour analysis.

Immunohistochemical (IHC) biomarkers in breast tissue microarray (TMA) samples are used daily in pathology departments. In recent years, automatic methods to evaluate positive staining have been investigated since they may save time and reduce errors in the diagnosis. These errors are mostly due to subjective evaluation. The aim of this work is to develop a density tool able to automatically quantify the positive brown IHC stain in breast TMA for different biomarkers. To avoid the problem of colour variation and make a robust tool independent of the staining process, several colour standardization methods have been analysed. Four colour standardization methods have been compared against colour model segmentation. The standardization methods have been compared by means of NBS colour distance. The use of colour standardization helps to reduce noise due to stain and histological sample preparation. However, the most reliable and robust results have been obtained by combining the HSV and RGB colour models for segmentation with the HSB channels. The segmentation provides three outputs based on three saturation values for weak, medium and strong staining. Each output image can be combined according to the type of biomarker staining. The results with 12 biomarkers were evaluated and compared to the segmentation and density calculation done by expert pathologists. The Hausdorff distance, sensitivity and specificity have been used to quantitative validate the results. The tests carried out with 8000 TMA images provided an average of 95.94% accuracy applied to the total tissue cylinder area. Colour standardization was used only when the tissue core had blurring and fading stain and the expert could not evaluate them without a pre-processing.

New Trends of Emerging Technologies in Digital Pathology.

The future paradigm of pathology will be digital. Instead of conventional microscopy, a pathologist will perform a diagnosis through interacting with images on computer screens and performing quantitative analysis. The fourth generation of virtual slide telepathology systems, so-called virtual microscopy and whole-slide imaging (WSI), has allowed for the storage and fast dissemination of image data in pathology and other biomedical areas. These novel digital imaging modalities encompass high-resolution scanning of tissue slides and derived technologies, including automatic digitization and computational processing of whole microscopic slides. Moreover, automated image analysis with WSI can extract specific diagnostic features of diseases and quantify individual components of these features to support diagnoses and provide informative clinical measures of disease. Therefore, the challenge is to apply information technology and image analysis methods to exploit the new and emerging digital pathology technologies effectively in order to process and model all the data and information contained in WSI. The final objective is to support the complex workflow from specimen receipt to anatomic pathology report transmission, that is, to improve diagnosis both in terms of pathologists' efficiency and with new information. This article reviews the main concerns about and novel methods of digital pathology discussed at the latest workshop in the field carried out within the European project AIDPATH (Academia and Industry Collaboration for Digital Pathology).

Vascular patterns provide therapeutic targets in aggressive neuroblastic tumors.

Angiogenesis is essential for tumor growth and metastasis, nevertheless, in NB, results between different studies on angiogenesis have yielded contradictory results. An image analysis tool was developed to characterize the density, size and shape of total blood vessels and vascular segments in 458 primary neuroblastic tumors contained in tissue microarrays. The results were correlated with clinical and biological features of known prognostic value and with risk of progression to establish histological vascular patterns associated with different degrees of malignancy. Total blood vessels were larger, more abundant and more irregularly-shaped in tumors of patients with associated poor prognostic factors than in the favorable cohort. Tumor capillaries were less abundant and sinusoids more abundant in the patient cohort with unfavorable prognostic factors. Additionally, size of post-capillaries & metarterioles as well as higher sinusoid density can be included as predictive factors for survival. These patterns may therefore help to provide more accurate pre-treatment risk stratification, and could provide candidate targets for novel therapies.

Influence of Texture and Colour in Breast TMA Classification.

Breast cancer diagnosis is still done by observation of biopsies under the microscope. The development of automated methods for breast TMA classification would reduce diagnostic time. This paper is a step towards the solution for this problem and shows a complete study of breast TMA classification based on colour models and texture descriptors. The TMA images were divided into four classes: i) benign stromal tissue with cellularity, ii) adipose tissue, iii) benign and benign anomalous structures, and iv) ductal and lobular carcinomas. A relevant set of features was obtained on eight different colour models from first and second order Haralick statistical descriptors obtained from the intensity image, Fourier, Wavelets, Multiresolution Gabor, M-LBP and textons descriptors. Furthermore, four types of classification experiments were performed using six different classifiers: (1) classification per colour model individually, (2) classification by combination of colour models, (3) classification by combination of colour models and descriptors, and (4) classification by combination of colour models and descriptors with a previous feature set reduction. The best result shows an average of 99.05% accuracy and 98.34% positive predictive value. These results have been obtained by means of a bagging tree classifier with combination of six colour models and the use of 1719 non-correlated (correlation threshold of 97%) textural features based on Statistical, M-LBP, Gabor and Spatial textons descriptors.

A CAD System for the Acquisition and Classification of Breast TMA in Pathology.

Breast cancer is the most common type of cancer and the fifth leading cause of death in women over 40. Therefore, prompt diagnostic and treatment is essential. In this work a TMA Computer Aided Diagnosis (CAD) system has been implemented to provide support to pathologists in their daily work. For that purpose, the tool covers each and every process from the TMA core image acquisition to their individual classification. The first process includes: tissue core location, segmentation and rigid registration of digital microscopic images acquired at different magnifications (5x, 10x, 20x, 20x and 40x) from different devices. The classification process allows performing the core classification selecting different types of color models, texture descriptors and classifiers. Finally, the cores are classified into three categories: malignant, doubtful and benign.

Frequential versus spatial colour textons for breast TMA classification.

Advances in digital pathology are generating huge volumes of whole slide (WSI) and tissue microarray images (TMA) which are providing new insights into the causes of cancer. The challenge is to extract and process effectively all the information in order to characterize all the heterogeneous tissue-derived data. This study aims to identify an optimal set of features that best separates different classes in breast TMA. These classes are: stroma, adipose tissue, benign and benign anomalous structures and ductal and lobular carcinomas. To this end, we propose an exhaustive assessment on the utility of textons and colour for automatic classification of breast TMA. Frequential and spatial texton maps from eight different colour models were extracted and compared. Then, in a novel way, the TMA is characterized by the 1st and 2nd order Haralick statistical descriptors obtained from the texton maps with a total of 241 × 8 features for each original RGB image. Subsequently, a feature selection process is performed to remove redundant information and therefore to reduce the dimensionality of the feature vector. Three methods were evaluated: linear discriminant analysis, correlation and sequential forward search. Finally, an extended bank of classifiers composed of six techniques was compared, but only three of them could significantly improve accuracy rates: Fisher, Bagging Trees and AdaBoost. Our results reveal that the combination of different colour models applied to spatial texton maps provides the most efficient representation of the breast TMA. Specifically, we found that the best colour model combination is Hb, Luv and SCT for all classifiers and the classifier that performs best for all colour model combinations is the AdaBoost. On a database comprising 628 TMA images, classification yields an accuracy of 98.1% and a precision of 96.2% with a total of 316 features on spatial textons maps.

TMA vessel segmentation based on color and morphological features: application to angiogenesis research.

Given that angiogenesis and lymphangiogenesis are strongly related to prognosis in neoplastic and other pathologies and that many methods exist that provide different results, we aim to construct a morphometric tool allowing us to measure different aspects of the shape and size of vascular vessels in a complete and accurate way. The developed tool presented is based on vessel closing which is an essential property to properly characterize the size and the shape of vascular and lymphatic vessels. The method is fast and accurate improving existing tools for angiogenesis analysis. The tool also improves the accuracy of vascular density measurements, since the set of endothelial cells forming a vessel is considered as a single object.