Evaluation Kidney Layer Segmentation on Whole Slide Imaging using Convolutional Neural Networks and Transformers

The segmentation of kidney layer structures, including cortex, outer stripe, inner stripe, and inner medulla within human kidney whole slide images (WSI) plays an essential role in automated image analysis in renal pathology. However, the current manual segmentation process proves labor-intensive and infeasible for handling the extensive digital pathology images encountered at a large scale. In response, the realm of digital renal pathology has seen the emergence of deep learning-based methodologies. However, very few, if any, deep learning based approaches have been applied to kidney layer structure segmentation. Addressing this gap, this paper assesses the feasibility of performing deep learning based approaches on kidney layer structure segmetnation. This study employs the representative convolutional neural network (CNN) and Transformer segmentation approaches, including Swin-Unet, Medical-Transformer, TransUNet, U-Net, PSPNet, and DeepLabv3+. We quantitatively evaluated six prevalent deep learning models on renal cortex layer segmentation using mice kidney WSIs. The empirical results stemming from our approach exhibit compelling advancements, as evidenced by a decent Mean Intersection over Union (mIoU) index. The results demonstrate that Transformer models generally outperform CNN-based models. By enabling a quantitative evaluation of renal cortical structures, deep learning approaches are promising to empower these medical professionals to make more informed kidney layer segmentation

Representations for Cognitive Vision : a Review of Appearance-Based, Spatio-Temporal, and Graph-Based Approaches

The emerging discipline of cognitive vision requires a proper representation of visual information including spatial and temporal relationships, scenes, events, semantics and context. This review article summarizes existing representational schemes in computer vision which might be useful for cognitive vision, a and discusses promising future research directions. The various approaches are categorized according to appearance-based, spatio-temporal, and graph-based representations for cognitive vision. While the representation of objects has been covered extensively in computer vision research, both from a reconstruction as well as from a recognition point of view, cognitive vision will also require new ideas how to represent scenes. We introduce new concepts for scene representations and discuss how these might be efficiently implemented in future cognitive vision systems

Automatic segmentation of the left ventricle cavity and myocardium in MRI data

A novel approach for the automatic segmentation has been developed to extract the epi-cardium and endo-cardium boundaries of the left ventricle (lv) of the heart. The developed segmentation scheme takes multi-slice and multi-phase magnetic resonance (MR) images of the heart, transversing the short-axis length from the base to the apex. Each image is taken at one instance in the heart's phase. The images are segmented using a diffusion-based filter followed by an unsupervised clustering technique and the resulting labels are checked to locate the (lv) cavity. From cardiac anatomy, the closest pool of blood to the lv cavity is the right ventricle cavity. The wall between these two blood-pools (interventricular septum) is measured to give an approximate thickness for the myocardium. This value is used when a radial search is performed on a gradient image to find appropriate robust segments of the epi-cardium boundary. The robust edge segments are then joined using a normal spline curve. Experimental results are presented with very encouraging qualitative and quantitative results and a comparison is made against the state-of-the art level-sets method

Image Segmentation by Edge Partitioning over a Nonsubmodular Markov Random Field

Edge weight-based segmentation methods, such as normalized cut or minimum cut, require a partition number specification for their energy formulation. The number of partitions plays an important role in the segmentation overall quality. However, finding a suitable partition number is a nontrivial problem, and the numbers are ordinarily manually assigned. This is an aspect of the general partition problem, where finding the partition number is an important and difficult issue. In this paper, the edge weights instead of the pixels are partitioned to segment the images. By partitioning the edge weights into two disjoints sets, that is, cut and connect, an image can be partitioned into all possible disjointed segments. The proposed energy function is independent of the number of segments. The energy is minimized by iterating the QPBO-α-expansion algorithm over the pairwise Markov random field and the mean estimation of the cut and connected edges. Experiments using the Berkeley database show that the proposed segmentation method can obtain equivalently accurate segmentation results without designating the segmentation numbers

Tumor Classification Using High-Order Gene Expression Profiles Based on Multilinear ICA

Motivation. Independent Components Analysis (ICA) maximizes the statistical independence of the representational components of a training gene expression profiles (GEP) ensemble, but it cannot distinguish relations between the different factors, or different modes, and it is not available to high-order GEP Data Mining. In order to generalize ICA, we introduce Multilinear-ICA and apply it to tumor classification using high order GEP. Firstly, we introduce the basis conceptions and operations of tensor and recommend Support Vector Machine (SVM) classifier and Multilinear-ICA. Secondly, the higher score genes of original high order GEP are selected by using t-statistics and tabulate tensors. Thirdly, the tensors are performed by Multilinear-ICA. Finally, the SVM is used to classify the tumor subtypes. Results. To show the validity of the proposed method, we apply it to tumor classification using high order GEP. Though we only use three datasets, the experimental results show that the method is effective and feasible. Through this survey, we hope to gain some insight into the problem of high order GEP tumor classification, in aid of further developing more effective tumor classification algorithms

Anomaly activity classification in the grocery stores

Nowadays, because of the growing number of robberies in shopping malls and grocery stores, automatic camera’s applications are vital necessities to detect anomalous actions. These events usually happen quickly and unexpectedly. Therefore, having a robust system which can classify anomalies in a real-time with minimum false alarms is required. Due to this needs, the main objective of this project is to classify anomalies which may happen in grocery stores. This objective is acquired by considering properties, such as; using one fixed camera in the store and the presence of at least one person in the camera view. The actions of human upper body are used to determine the anomalies. Articulated motion model is used as the basis of the anomalies classification design. In the design, the process starts with feature extraction and followed by target model establishment, tracking and action classification. The features such as color and image gradient built the template as the target model. Then, the models of different upper body parts are tracked during consecutive frames by the tracking method which is sum of square differences (SSD) combined with the Kalman filter as the predictor. The spatio-temporal information as the trajectory of limbs gained by tracking part is sent to proposed classification part. For classification, three different scenarios are studied: attacking cash machine, cashier’s attacking and making the store messy. In implementing these scenarios, some events were introduced. These events are; basic (static) events which are the static objects in the scene, spatial events which are those actions depend on coordinates of body parts and spatio-temporal events in which these actions are tracked in consecutive frames. At last, if one of the scenarios happens, an anomalous action will be detected. The results show the robustness of the proposed methods which have the minimum false positive error of 7% for the cash machine attack and minimum false negative error of 19% for the cashier’s attacking scenario