A digital pathology workflow for the segmentation and classification of gastric glands: Study of gastric atrophy and intestinal metaplasia cases.

Gastric cancer is one of the most frequent causes of cancer-related deaths worldwide. Gastric atrophy (GA) and gastric intestinal metaplasia (IM) of the mucosa of the stomach have been found to increase the risk of gastric cancer and are considered precancerous lesions. Therefore, the early detection of GA and IM may have a valuable role in histopathological risk assessment. However, GA and IM are difficult to confirm endoscopically and, following the Sydney protocol, their diagnosis depends on the analysis of glandular morphology and on the identification of at least one well-defined goblet cell in a set of hematoxylin and eosin (H&E) -stained biopsy samples. To this end, the precise segmentation and classification of glands from the histological images plays an important role in the diagnostic confirmation of GA and IM. In this paper, we propose a digital pathology end-to-end workflow for gastric gland segmentation and classification for the analysis of gastric tissues. The proposed GAGL-VTNet, initially, extracts both global and local features combining multi-scale feature maps for the segmentation of glands and, subsequently, it adopts a vision transformer that exploits the visual dependences of the segmented glands towards their classification. For the analysis of gastric tissues, segmentation of mucosa is performed through an unsupervised model combining energy minimization and a U-Net model. Then, features of the segmented glands and mucosa are extracted and analyzed. To evaluate the efficiency of the proposed methodology we created the GAGL dataset consisting of 85 WSI, collected from 20 patients. The results demonstrate the existence of significant differences of the extracted features between normal, GA and IM cases. The proposed approach for gland and mucosa segmentation achieves an object dice score equal to 0.908 and 0.967 respectively, while for the classification of glands it achieves an F1 score equal to 0.94 showing great potential for the automated quantification and analysis of gastric biopsies.

Pedestrian Detection Using Integrated Aggregate Channel Features and Multitask Cascaded Convolutional Neural-Network-Based Face Detectors.

Pedestrian detection is a challenging task, mainly owing to the numerous appearances of human bodies. Modern detectors extract representative features via the deep neural network; however, they usually require a large training set and high-performance GPUs. For these cases, we propose a novel human detection approach that integrates a pretrained face detector based on multitask cascaded convolutional neural networks and a traditional pedestrian detector based on aggregate channel features via a score combination module. The proposed detector is a promising approach that can be used to handle pedestrian detection with limited datasets and computational resources. The proposed detector is investigated comprehensively in terms of parameter choices to optimize its performance. The robustness of the proposed detector in terms of the training set, test set, and threshold is observed via tests and cross dataset validations on various pedestrian datasets, including the INRIA, part of the ETHZ, and the Caltech and Citypersons datasets. Experiments have proved that this integrated detector yields a significant increase in recall and a decrease in the log average miss rate compared with sole use of the traditional pedestrian detector. At the same time, the proposed method achieves a comparable performance to FRCNN on the INRIA test set compared with sole use of the Aggregated Channel Features detector.

Tertiary lymphoid structures (TLS) identification and density assessment on H&E-stained digital slides of lung cancer.

Tertiary lymphoid structures (TLS) are ectopic aggregates of lymphoid cells in inflamed, infected, or tumoral tissues that are easily recognized on an H&E histology slide as discrete entities, distinct from lymphocytes. TLS are associated with improved cancer prognosis but there is no standardised method available to quantify their presence. Previous studies have used immunohistochemistry to determine the presence of specific cells as a marker of the TLS. This has now been proven to be an underestimate of the true number of TLS. Thus, we propose a methodology for the automated identification and quantification of TLS, based on H&E slides. We subsequently determined the mathematical criteria defining a TLS. TLS regions were identified through a deep convolutional neural network and segmentation of lymphocytes was performed through an ellipsoidal model. This methodology had a 92.87% specificity at 95% sensitivity, 88.79% specificity at 98% sensitivity and 84.32% specificity at 99% sensitivity level based on 144 TLS annotated H&E slides implying that the automated approach was able to reproduce the histopathologists' assessment with great accuracy. We showed that the minimum number of lymphocytes within TLS is 45 and the minimum TLS area is 6,245µm2. Furthermore, we have shown that the density of the lymphocytes is more than 3 times those outside of the TLS. The mean density and standard deviation of lymphocytes within a TLS area are 0.0128/µm2 and 0.0026/µm2 respectively compared to 0.004/µm2 and 0.001/µm2 in non-TLS regions. The proposed methodology shows great potential for automated identification and quantification of the TLS density on digital H&E slides.

A Review on Early Forest Fire Detection Systems Using Optical Remote Sensing.

The environmental challenges the world faces nowadays have never been greater or more complex. Global areas covered by forests and urban woodlands are threatened by natural disasters that have increased dramatically during the last decades, in terms of both frequency and magnitude. Large-scale forest fires are one of the most harmful natural hazards affecting climate change and life around the world. Thus, to minimize their impacts on people and nature, the adoption of well-planned and closely coordinated effective prevention, early warning, and response approaches are necessary. This paper presents an overview of the optical remote sensing technologies used in early fire warning systems and provides an extensive survey on both flame and smoke detection algorithms employed by each technology. Three types of systems are identified, namely terrestrial, airborne, and spaceborne-based systems, while various models aiming to detect fire occurrences with high accuracy in challenging environments are studied. Finally, the strengths and weaknesses of fire detection systems based on optical remote sensing are discussed aiming to contribute to future research projects for the development of early warning fire systems.

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.