Feasibility of automated 3-dimensional magnetic resonance imaging pancreas segmentation.

PurposeWith the advent of MR guided radiotherapy, internal organ motion can be imaged simultaneously during treatment. In this study, we evaluate the feasibility of pancreas MRI segmentation using state-of-the-art segmentation methods.Methods and materialT2 weighted HASTE and T1 weighted VIBE images were acquired on 3 patients and 2 healthy volunteers for a total of 12 imaging volumes. A novel dictionary learning (DL) method was used to segment the pancreas and compared to t mean-shift merging (MSM), distance regularized level set (DRLS), graph cuts (GC) and the segmentation results were compared to manual contours using Dice's index (DI), Hausdorff distance and shift of the-center-of-the-organ (SHIFT).ResultsAll VIBE images were successfully segmented by at least one of the auto-segmentation method with DI >0.83 and SHIFT ≤2 mm using the best automated segmentation method. The automated segmentation error of HASTE images was significantly greater. DL is statistically superior to the other methods in Dice's overlapping index. For the Hausdorff distance and SHIFT measurement, DRLS and DL performed slightly superior to the GC method, and substantially superior to MSM. DL required least human supervision and was faster to compute.ConclusionOur study demonstrated potential feasibility of automated segmentation of the pancreas on MRI images with minimal human supervision at the beginning of imaging acquisition. The achieved accuracy is promising for organ localization

Image-Based Flexible Endoscope Steering

Manually steering the tip of a flexible endoscope to navigate through an endoluminal path relies on the physician’s dexterity and experience. In this paper we present the realization of a robotic flexible endoscope steering system that uses the endoscopic images to control the tip orientation towards the direction of the lumen. Two image-based control algorithms are investigated, one is based on the optical flow and the other is based on the image intensity. Both are evaluated using simulations in which the endoscope was steered through the lumen. The RMS distance to the lumen center was less than 25% of the lumen width. An experimental setup was built using a standard flexible endoscope, and the image-based control algorithms were used to actuate the wheels of the endoscope for tip steering. Experiments were conducted in an anatomical model to simulate gastroscopy. The image intensity- based algorithm was capable of steering the endoscope tip through an endoluminal path from the mouth to the duodenum accurately. Compared to manual control, the robotically steered endoscope performed 68% better in terms of keeping the lumen centered in the image

Gait recognition and understanding based on hierarchical temporal memory using 3D gait semantic folding

Gait recognition and understanding systems have shown a wide-ranging application prospect. However, their use of unstructured data from image and video has affected their performance, e.g., they are easily influenced by multi-views, occlusion, clothes, and object carrying conditions. This paper addresses these problems using a realistic 3-dimensional (3D) human structural data and sequential pattern learning framework with top-down attention modulating mechanism based on Hierarchical Temporal Memory (HTM). First, an accurate 2-dimensional (2D) to 3D human body pose and shape semantic parameters estimation method is proposed, which exploits the advantages of an instance-level body parsing model and a virtual dressing method. Second, by using gait semantic folding, the estimated body parameters are encoded using a sparse 2D matrix to construct the structural gait semantic image. In order to achieve time-based gait recognition, an HTM Network is constructed to obtain the sequence-level gait sparse distribution representations (SL-GSDRs). A top-down attention mechanism is introduced to deal with various conditions including multi-views by refining the SL-GSDRs, according to prior knowledge. The proposed gait learning model not only aids gait recognition tasks to overcome the difficulties in real application scenarios but also provides the structured gait semantic images for visual cognition. Experimental analyses on CMU MoBo, CASIA B, TUM-IITKGP, and KY4D datasets show a significant performance gain in terms of accuracy and robustness

A manometric feature descriptor with linear-SVM to distinguish esophageal contraction vigor

n clinical, if a patient presents with nonmechanical obstructive dysphagia, esophageal chest pain, and gastro esophageal reflux symptoms, the physician will usually assess the esophageal dynamic function. High-resolution manometry (HRM) is a clinically commonly used technique for detection of esophageal dynamic function comprehensively and objectively. However, after the results of HRM are obtained, doctors still need to evaluate by a variety of parameters. This work is burdensome, and the process is complex. We conducted image processing of HRM to predict the esophageal contraction vigor for assisting the evaluation of esophageal dynamic function. Firstly, we used Feature-Extraction and Histogram of Gradients (FE-HOG) to analyses feature of proposal of swallow (PoS) to further extract higher-order features. Then we determine the classification of esophageal contraction vigor normal, weak and failed by using linear-SVM according to these features. Our data set includes 3000 training sets, 500 validation sets and 411 test sets. After verification our accuracy reaches 86.83%, which is higher than other common machine learning methods

Visualization Techniques for Tongue Analysis in Traditional Chinese Medicine

Visual inspection of the tongue has been an important diagnostic method of Traditional Chinese Medicine (TCM). Clinic data have shown significant connections between various viscera cancers and abnormalities in the tongue and the tongue coating. Visual inspection of the tongue is simple and inexpensive, but the current practice in TCM is mainly experience-based and the quality of the visual inspection varies between individuals. The computerized inspection method provides quantitative models to evaluate color, texture and surface features on the tongue. In this paper, we investigate visualization techniques and processes to allow interactive data analysis with the aim to merge computerized measurements with human expert's diagnostic variables based on five-scale diagnostic conditions: Healthy (H), History Cancers (HC), History of Polyps (HP), Polyps (P) and Colon Cancer (C)

PointNu-Net: Simultaneous Multi-tissue Histology Nuclei Segmentation and Classification in the Clinical Wild

Automatic nuclei segmentation and classification plays a vital role in digital pathology. However, previous works are mostly built on data with limited diversity and small sizes, making the results questionable or misleading in actual downstream tasks. In this paper, we aim to build a reliable and robust method capable of dealing with data from the 'the clinical wild'. Specifically, we study and design a new method to simultaneously detect, segment, and classify nuclei from Haematoxylin and Eosin (H&E) stained histopathology data, and evaluate our approach using the recent largest dataset: PanNuke. We address the detection and classification of each nuclei as a novel semantic keypoint estimation problem to determine the center point of each nuclei. Next, the corresponding class-agnostic masks for nuclei center points are obtained using dynamic instance segmentation. By decoupling two simultaneous challenging tasks, our method can benefit from class-aware detection and class-agnostic segmentation, thus leading to a significant performance boost. We demonstrate the superior performance of our proposed approach for nuclei segmentation and classification across 19 different tissue types, delivering new benchmark results.Comment: 10 pages,7 figures, journa

Medical Image Segmentation by Deep Convolutional Neural Networks

Medical image segmentation is a fundamental and critical step for medical image analysis. Due to the complexity and diversity of medical images, the segmentation of medical images continues to be a challenging problem. Recently, deep learning techniques, especially Convolution Neural Networks (CNNs) have received extensive research and achieve great success in many vision tasks. Specifically, with the advent of Fully Convolutional Networks (FCNs), automatic medical image segmentation based on FCNs is a promising research field. This thesis focuses on two medical image segmentation tasks: lung segmentation in chest X-ray images and nuclei segmentation in histopathological images. For the lung segmentation task, we investigate several FCNs that have been successful in semantic and medical image segmentation. We evaluate the performance of these different FCNs on three publicly available chest X-ray image datasets. For the nuclei segmentation task, since the challenges of this task are difficulty in segmenting the small, overlapping and touching nuclei, and limited ability of generalization to nuclei in different organs and tissue types, we propose a novel nuclei segmentation approach based on a two-stage learning framework and Deep Layer Aggregation (DLA). We convert the original binary segmentation task into a two-step task by adding nuclei-boundary prediction (3-classes) as an intermediate step. To solve our two-step task, we design a two-stage learning framework by stacking two U-Nets. The first stage estimates nuclei and their coarse boundaries while the second stage outputs the final fine-grained segmentation map. Furthermore, we also extend the U-Nets with DLA by iteratively merging features across different levels. We evaluate our proposed method on two public diverse nuclei datasets. The experimental results show that our proposed approach outperforms many standard segmentation architectures and recently proposed nuclei segmentation methods, and can be easily generalized across different cell types in various organs

Gland segmentation in gastric histology images: detection of intestinal metaplasia

Gastric cancer is one of the most frequent causes of cancer-related deaths worldwide. Gastric intestinal metaplasia (IM) of the mucosa of the stomach has been found to increase the risk of gastric cancer and is considered as one of the precancerous lesions. Therefore, early detection of IM may have a valuable role in histopathological risk assessment regarding the possibility of progression to cancer. Accurate segmentation and analysis of gastric glands from the histological images plays an important role in the diagnostic confirmation of IM. Thus, in this paper, we propose a framework for segmentation of gastric glands and detection of IM. More specifically, we propose the GAGL-Net for the segmentation of glands. Then, based on two features of the extracted glands we classify the tissues into normal and IM cases. The results showed that the proposed gland segmentation approach achieves an F1 score equal to 0.914. Furthermore, the proposed methodology shows great potential for the IM detection achieving an accuracy score equal to 96.6%. To evaluate the efficiency of the proposed methodology we used a publicly available dataset and we created the GAGL dataset consisting of 59 Whole Slide Images (WSI) including both IM and normal cases

Towards Developing Computer Vision Algorithms and Architectures for Real-world Applications

abstract: Computer vision technology automatically extracts high level, meaningful information from visual data such as images or videos, and the object recognition and detection algorithms are essential in most computer vision applications. In this dissertation, we focus on developing algorithms used for real life computer vision applications, presenting innovative algorithms for object segmentation and feature extraction for objects and actions recognition in video data, and sparse feature selection algorithms for medical image analysis, as well as automated feature extraction using convolutional neural network for blood cancer grading. To detect and classify objects in video, the objects have to be separated from the background, and then the discriminant features are extracted from the region of interest before feeding to a classifier. Effective object segmentation and feature extraction are often application specific, and posing major challenges for object detection and classification tasks. In this dissertation, we address effective object flow based ROI generation algorithm for segmenting moving objects in video data, which can be applied in surveillance and self driving vehicle areas. Optical flow can also be used as features in human action recognition algorithm, and we present using optical flow feature in pre-trained convolutional neural network to improve performance of human action recognition algorithms. Both algorithms outperform the state-of-the-arts at their time. Medical images and videos pose unique challenges for image understanding mainly due to the fact that the tissues and cells are often irregularly shaped, colored, and textured, and hand selecting most discriminant features is often difficult, thus an automated feature selection method is desired. Sparse learning is a technique to extract the most discriminant and representative features from raw visual data. However, sparse learning with \textit{L1} regularization only takes the sparsity in feature dimension into consideration; we improve the algorithm so it selects the type of features as well; less important or noisy feature types are entirely removed from the feature set. We demonstrate this algorithm to analyze the endoscopy images to detect unhealthy abnormalities in esophagus and stomach, such as ulcer and cancer. Besides sparsity constraint, other application specific constraints and prior knowledge may also need to be incorporated in the loss function in sparse learning to obtain the desired results. We demonstrate how to incorporate similar-inhibition constraint, gaze and attention prior in sparse dictionary selection for gastroscopic video summarization that enable intelligent key frame extraction from gastroscopic video data. With recent advancement in multi-layer neural networks, the automatic end-to-end feature learning becomes feasible. Convolutional neural network mimics the mammal visual cortex and can extract most discriminant features automatically from training samples. We present using convolutinal neural network with hierarchical classifier to grade the severity of Follicular Lymphoma, a type of blood cancer, and it reaches 91\% accuracy, on par with analysis by expert pathologists. Developing real world computer vision applications is more than just developing core vision algorithms to extract and understand information from visual data; it is also subject to many practical requirements and constraints, such as hardware and computing infrastructure, cost, robustness to lighting changes and deformation, ease of use and deployment, etc.The general processing pipeline and system architecture for the computer vision based applications share many similar design principles and architecture. We developed common processing components and a generic framework for computer vision application, and a versatile scale adaptive template matching algorithm for object detection. We demonstrate the design principle and best practices by developing and deploying a complete computer vision application in real life, building a multi-channel water level monitoring system, where the techniques and design methodology can be generalized to other real life applications. The general software engineering principles, such as modularity, abstraction, robust to requirement change, generality, etc., are all demonstrated in this research.Dissertation/ThesisDoctoral Dissertation Computer Science 201