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Register a new userSuperpixel Based Segmentation and Classification of Polyps in Wireless Capsule Endoscopy
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Added by
Omid Haji Maghsoudi
Publication date
2017
fields
Informatics Engineering
and research's language is
English
Authors
Omid Haji Maghsoudi
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Wireless Capsule Endoscopy (WCE) is a relatively new technology to record the entire GI trace, in vivo. The large amounts of frames captured during an examination cause difficulties for physicians to review all these frames. The need for reducing the reviewing time using some intelligent methods has been a challenge. Polyps are considered as growing tissues on the surface of intestinal tract not inside of an organ. Most polyps are not cancerous, but if one becomes larger than a centimeter, it can turn into cancer by great chance. The WCE frames provide the early stage possibility for detection of polyps. Here, the application of simple linear iterative clustering (SLIC) superpixel for segmentation of polyps in WCE frames is evaluated. Different SLIC superpixel numbers are examined to find the highest sensitivity for detection of polyps. The SLIC superpixel segmentation is promising to improve the results of previous studies. Finally, the superpixels were classified using a support vector machine (SVM) by extracting some texture and color features. The classification results showed a sensitivity of 91%.
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Wireless Capsule Endoscopy (WCE) is relatively a new technology to examine the entire GI trace. During an examination, it captures more than 55,000 frames. Reviewing all these images is time-consuming and prone to human error. It has been a challenge to develop intelligent methods assisting physicians to review the frames. The WCE frames are captured in 8-bit color depths which provides enough a color range to detect abnormalities. Here, superpixel based methods are proposed to segment five diseases including: bleeding, Crohns disease, Lymphangiectasia, Xanthoma, and Lymphoid hyperplasia. Two superpixels methods are compared to provide semantic segmentation of these prolific diseases: simple linear iterative clustering (SLIC) and quick shift (QS). The segmented superpixels were classified into two classes (normal and abnormal) by support vector machine (SVM) using texture and color features. For both superpixel methods, the accuracy, specificity, sensitivity, and precision (SLIC, QS) were around 92%, 93%, 93%, and 88%, respectively. However, SLIC was dramatically faster than QS.
Studying animal locomotion improves our understanding of motor control and aids in the treatment of motor impairment. Mice are a premier model of human disease and are the model system of choice for much of basic neuroscience. High frame rates (250 Hz) are needed to quantify the kinematics of these running rodents. Manual tracking, especially for multiple markers, becomes time-consuming and impossible. Therefore, an automated method is necessary. We propose a method to track the paws of the animal in the following manner: first, segmenting all the possible paws based on color; second, classifying the segmented objects using a support vector machine (SVM) and neural network (NN); third, classifying the objects using the kinematic features of the running animal, coupled with texture features from earlier frames; and finally, detecting and handling collisions to assure the correctness of labelled paws. The proposed method is validated in sixty 1,000 frame video sequences (4 seconds) captured by four cameras from five mice. The total sensitivity for tracking of the front and hind paw is 99.70% using the SVM classifier and 99.76% using the NN classifier. In addition, we show the feasibility of 3D reconstruction using the four camera system.
Deep learning in gastrointestinal endoscopy can assist to improve clinical performance and be helpful to assess lesions more accurately. To this extent, semantic segmentation methods that can perform automated real-time delineation of a region-of-interest, e.g., boundary identification of cancer or precancerous lesions, can benefit both diagnosis and interventions. However, accurate and real-time segmentation of endoscopic images is extremely challenging due to its high operator dependence and high-definition image quality. To utilize automated methods in clinical settings, it is crucial to design lightweight models with low latency such that they can be integrated with low-end endoscope hardware devices. In this work, we propose NanoNet, a novel architecture for the segmentation of video capsule endoscopy and colonoscopy images. Our proposed architecture allows real-time performance and has higher segmentation accuracy compared to other more complex ones. We use video capsule endoscopy and standard colonoscopy datasets with polyps, and a dataset consisting of endoscopy biopsies and surgical instruments, to evaluate the effectiveness of our approach. Our experiments demonstrate the increased performance of our architecture in terms of a trade-off between model complexity, speed, model parameters, and metric performances. Moreover, the resulting model size is relatively tiny, with only nearly 36,000 parameters compared to traditional deep learning approaches having millions of parameters.
Although wireless capsule endoscopy is the preferred modality for diagnosis and assessment of small bowel diseases, the poor camera resolution is a substantial limitation for both subjective and automated diagnostics. Enhanced-resolution endoscopy has shown to improve adenoma detection rate for conventional endoscopy and is likely to do the same for capsule endoscopy. In this work, we propose and quantitatively validate a novel framework to learn a mapping from low-to-high resolution endoscopic images. We combine conditional adversarial networks with a spatial attention block to improve the resolution by up to factors of 8x, 10x, 12x, respectively. Quantitative and qualitative studies performed demonstrate the superiority of EndoL2H over state-of-the-art deep super-resolution methods DBPN, RCAN and SRGAN. MOS tests performed by 30 gastroenterologists qualitatively assess and confirm the clinical relevance of the approach. EndoL2H is generally applicable to any endoscopic capsule system and has the potential to improve diagnosis and better harness computational approaches for polyp detection and characterization. Our code and trained models are available at https://github.com/CapsuleEndoscope/EndoL2H.
Current capsule endoscopes and next-generation robotic capsules for diagnosis and treatment of gastrointestinal diseases are complex cyber-physical platforms that must orchestrate complex software and hardware functions. The desired tasks for these systems include visual localization, depth estimation, 3D mapping, disease detection and segmentation, automated navigation, active control, path realization and optional therapeutic modules such as targeted drug delivery and biopsy sampling. Data-driven algorithms promise to enable many advanced functionalities for capsule endoscopes, but real-world data is challenging to obtain. Physically-realistic simulations providing synthetic data have emerged as a solution to the development of data-driven algorithms. In this work, we present a comprehensive simulation platform for capsule endoscopy operations and introduce VR-Caps, a virtual active capsule environment that simulates a range of normal and abnormal tissue conditions (e.g., inflated, dry, wet etc.) and varied organ types, capsule endoscope designs (e.g., mono, stereo, dual and 360{deg}camera), and the type, number, strength, and placement of internal and external magnetic sources that enable active locomotion. VR-Caps makes it possible to both independently or jointly develop, optimize, and test medical imaging and analysis software for the current and next-generation endoscopic capsule systems. To validate this approach, we train state-of-the-art deep neural networks to accomplish various medical image analysis tasks using simulated data from VR-Caps and evaluate the performance of these models on real medical data. Results demonstrate the usefulness and effectiveness of the proposed virtual platform in developing algorithms that quantify fractional coverage, camera trajectory, 3D map reconstruction, and disease classification.
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