scholarly journals Match Feature U-Net: Dynamic Receptive Field Networks for Biomedical Image Segmentation

Symmetry ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 1230
Author(s):  
Xiaofei Qin ◽  
Chengzi Wu ◽  
Hang Chang ◽  
Hao Lu ◽  
Xuedian Zhang
Keyword(s):  
Image Segmentation ◽  
Receptive Field ◽  
Medical Image ◽  
Medical Image Analysis ◽  
Medical Image Segmentation ◽  
Training Data ◽  
Cell Segmentation ◽  
Biomedical Image ◽  
Nuclei Segmentation ◽  
Kernel Convolution

Medical image segmentation is a fundamental task in medical image analysis. Dynamic receptive field is very helpful for accurate medical image segmentation, which needs to be further studied and utilized. In this paper, we propose Match Feature U-Net, a novel, symmetric encoder– decoder architecture with dynamic receptive field for medical image segmentation. We modify the Selective Kernel convolution (a module proposed in Selective Kernel Networks) by inserting a newly proposed Match operation, which makes similar features in different convolution branches have corresponding positions, and then we replace the U-Net’s convolution with the redesigned Selective Kernel convolution. This network is a combination of U-Net and improved Selective Kernel convolution. It inherits the advantages of simple structure and low parameter complexity of U-Net, and enhances the efficiency of dynamic receptive field in Selective Kernel convolution, making it an ideal model for medical image segmentation tasks which often have small training data and large changes in targets size. Compared with state-of-the-art segmentation methods, the number of parameters in Match Feature U-Net (2.65 M) is 34% of U-Net (7.76 M), 29% of UNet++ (9.04 M), and 9.1% of CE-Net (29 M). We evaluated the proposed architecture in four medical image segmentation tasks: nuclei segmentation in microscopy images, breast cancer cell segmentation, gland segmentation in colon histology images, and disc/cup segmentation. Our experimental results show that Match Feature U-Net achieves an average Mean Intersection over Union (MIoU) gain of 1.8, 1.45, and 2.82 points over U-Net, UNet++, and CE-Net, respectively.

scholarly journals A General System for Automatic Biomedical Image Segmentation Using Intensity Neighborhoods

2011 ◽  
Vol 2011 ◽  
pp. 1-12 ◽  
Author(s):  
Cheng Chen ◽  
John A. Ozolek ◽  
Wei Wang ◽  
Gustavo K. Rohde
Keyword(s):  
Image Segmentation ◽  
Learning Strategy ◽  
General System ◽  
Training Data ◽  
Tissue Segmentation ◽  
Biomedical Image ◽  
Nuclei Segmentation ◽  
Segmentation Methods ◽  
Microscopy Images ◽  
Better Than

Image segmentation is important with applications to several problems in biology and medicine. While extensively researched, generally, current segmentation methods perform adequately in the applications for which they were designed, but often require extensive modifications or calibrations before being used in a different application. We describe an approach that, with few modifications, can be used in a variety of image segmentation problems. The approach is based on a supervised learning strategy that utilizes intensity neighborhoods to assign each pixel in a test image its correct class based on training data. We describe methods for modeling rotations and variations in scales as well as a subset selection for training the classifiers. We show that the performance of our approach in tissue segmentation tasks in magnetic resonance and histopathology microscopy images, as well as nuclei segmentation from fluorescence microscopy images, is similar to or better than several algorithms specifically designed for each of these applications.

scholarly journals 3D Dense Separated Convolution Module for Volumetric Medical Image Analysis

2020 ◽  
Vol 10 (2) ◽  
pp. 485 ◽  
Author(s):  
Lei Qu ◽  
Changfeng Wu ◽  
Liang Zou
Keyword(s):  
Image Analysis ◽  
Medical Image ◽  
Medical Image Analysis ◽  
Training Data ◽  
Biomedical Image ◽  
Challenging Tasks ◽  
Model Size ◽  
Context Mining ◽  
Representational Power ◽  
3D Dsc

With the thriving of deep learning, 3D convolutional neural networks have become a popular choice in volumetric image analysis due to their impressive 3D context mining ability. However, the 3D convolutional kernels will introduce a significant increase in the amount of trainable parameters. Considering the training data are often limited in biomedical tasks, a trade-off has to be made between model size and its representational power. To address this concern, in this paper, we propose a novel 3D Dense Separated Convolution (3D-DSC) module to replace the original 3D convolutional kernels. The 3D-DSC module is constructed by a series of densely connected 1D filters. The decomposition of 3D kernel into 1D filters reduces the risk of overfitting by removing the redundancy of 3D kernels in a topologically constrained manner, while providing the infrastructure for deepening the network. By further introducing nonlinear layers and dense connections between 1D filters, the network’s representational power can be significantly improved while maintaining a compact architecture. We demonstrate the superiority of 3D-DSC on volumetric medical image classification and segmentation, which are two challenging tasks often encountered in biomedical image computing.

scholarly journals THE LAYERED NET SURFACE PROBLEMS IN DISCRETE GEOMETRY AND MEDICAL IMAGE SEGMENTATION

2007 ◽  
Vol 17 (03) ◽  
pp. 261-296 ◽  
Author(s):  
XIAODONG WU ◽  
DANNY Z. CHEN ◽  
KANG LI ◽  
MILAN SONKA
Keyword(s):  
Image Segmentation ◽  
Polynomial Time ◽  
Medical Image ◽  
Medical Image Analysis ◽  
Simultaneous Detection ◽  
Exact Algorithms ◽  
Medical Image Segmentation ◽  
Efficient Detection ◽  
Column Graph ◽  
Voxel Grid

Efficient detection of multiple inter-related surfaces representing the boundaries of objects of interest in d-D images (d ≥ 3) is important and remains challenging in many medical image analysis applications. In this paper, we study several layered net surface (LNS) problems captured by an interesting type of geometric graphs called ordered multi-column graphs in the d-D discrete space (d ≥ 3 is any constant integer). The LNS problems model the simultaneous detection of multiple mutually related surfaces in three or higher dimensional medical images. Although we prove that the d-D LNS problem (d ≥ 3) on a general ordered multi-column graph is NP-hard, the (special) ordered multi-column graphs that model medical image segmentation have the self-closure structures and thus admit polynomial time exact algorithms for solving the LNS problems. Our techniques also solve the related net surface volume (NSV) problems of computing well-shaped geometric regions of an optimal total volume in a d-D weighted voxel grid. The NSV problems find applications in medical image segmentation and data mining. Our techniques yield the first polynomial time exact algorithms for several high dimensional medical image segmentation problems. Experiments and comparisons based on real medical data showed that our LNS algorithms and software are computationally efficient and produce highly accurate and consistent segmentation results.

scholarly journals Digital Medical Image Segmentation Using Fuzzy C-Means Clustering

2020 ◽  
Vol 4 (1) ◽  
pp. 51 ◽  
Author(s):  
Bakhtyar Ahmed Mohammed ◽  
Muzhir Shaban Al-Ani
Keyword(s):  
Image Segmentation ◽  
Medical Image ◽  
Medical Image Analysis ◽  
Brain Mri ◽  
Accurate Method ◽  
Medical Image Segmentation ◽  
Fuzzy C Means ◽  
Fcm Clustering ◽  
The Brain ◽  
Digital Medical Image

In the modern globe, digital medical image processing is a major branch to study in the fields of medical and information technology. Every medical field relies on digital medical imaging in diagnosis for most of their cases. One of the major components of medical image analysis is medical image segmentation. Medical image segmentation participates in the diagnosis process, and it aids the processes of other medical image components to increase the accuracy. In unsupervised methods, fuzzy c-means (FCM) clustering is the most accurate method for image segmentation, and it can be smooth and bear desirable outcomes. The intention of this study is to establish a strong systematic way to segment complicate medical image cases depend on the proposed method to share in the decision-making process. This study mentions medical image modalities and illustrates the steps of the FCM clustering method mathematically with example. It segments magnetic resonance imaging (MRI) of the brain to separate tumor inside the brain MRI according to four statuses.

scholarly journals Generative Adversarial Networks for Pre-training of Medical Image Segmentation Networks

2020 ◽  
Author(s):  
Kun Chen ◽  
Manning Wang ◽  
Zhijian Song
Keyword(s):  
Neural Networks ◽  
Image Segmentation ◽  
Medical Image ◽  
Deep Neural Networks ◽  
Data Augmentation ◽  
Medical Image Segmentation ◽  
Training Data ◽  
Generative Adversarial Networks ◽  
Adversarial Networks ◽  
Synthetic Images

Abstract Background: Deep neural networks have been widely used in medical image segmentation and have achieved state-of-the-art performance in many tasks. However, different from the segmentation of natural images or video frames, the manual segmentation of anatomical structures in medical images needs high expertise so the scale of labeled training data is very small, which is a major obstacle for the improvement of deep neural networks performance in medical image segmentation. Methods: In this paper, we proposed a new end-to-end generation-segmentation framework by integrating Generative Adversarial Networks (GAN) and a segmentation network and train them simultaneously. The novelty is that during the training of the GAN, the intermediate synthetic images generated by the generator of the GAN are used to pre-train the segmentation network. As the advances of the training of the GAN, the synthetic images evolve gradually from being very coarse to containing more realistic textures, and these images help train the segmentation network gradually. After the training of GAN, the segmentation network is then fine-tuned by training with the real labeled images. Results: We evaluated the proposed framework on four different datasets, including 2D cardiac dataset and lung dataset, 3D prostate dataset and liver dataset. Compared with original U-net and CE-Net, our framework can achieve better segmentation performance. Our framework also can get better segmentation results than U-net on small datasets. In addition, our framework is more effective than the usual data augmentation methods. Conclusions: The proposed framework can be used as a pre-train method of segmentation network, which helps to get a better segmentation result. Our method can solve the shortcomings of current data augmentation methods to some extent.

scholarly journals CMM-Net: Contextual Multi-Scale Multi-Level Network for Efficient Biomedical Image Segmentation

2021 ◽  
Author(s):  
Mohammed Al-masni ◽  
Dong-Hyun Kim
Keyword(s):  
Image Segmentation ◽  
Blood Vessels ◽  
Medical Image ◽  
Spatial Scales ◽  
Medical Image Analysis ◽  
Skin Lesions ◽  
Medical Image Segmentation ◽  
Multi Scale ◽  
Retinal Blood Vessels ◽  
Multi Level

Abstract Medical image segmentation of tissue abnormalities, key organs, or blood vascular system is of great significance for any computerized diagnostic system. However, automatic segmentation in medical image analysis is a challenging task since it requires sophisticated knowledge of the target organ anatomy. This paper develops an end-to-end deep learning segmentation method called Contextual Multi-Scale Multi-Level Network (CMM-Net). The main idea is to fuse the global contextual features of multiple spatial scales at every contracting convolutional network level in the U-Net. Also, we re-exploit the dilated convolution module that enables an expansion of the receptive field with different rates depending on the size of feature maps throughout the networks. In addition, an augmented testing scheme referred to as Inversion Recovery (IR) which uses logical “OR” and “AND” operators is developed. The proposed segmentation network is evaluated on three medical imaging datasets, namely ISIC 2017 for skin lesions segmentation from dermoscopy images, DRIVE for retinal blood vessels segmentation from fundus images, and BraTS 2018 for brain gliomas segmentation from MR scans. The experimental results showed superior state-of-the-art performance with overall dice similarity coefficients of 85.78%, 80.27%, and 88.96% on the segmentation of skin lesions, retinal blood vessels, and brain tumors, respectively. The proposed CMM-Net is inherently general and could be efficiently applied as a robust tool for various medical image segmentations.

scholarly journals Optic Disc Segmentation Using Attention-Based U-Net and the Improved Cross-Entropy Convolutional Neural Network

Entropy ◽  
2020 ◽  
Vol 22 (8) ◽  
pp. 844
Author(s):  
Baixin Jin ◽  
Pingping Liu ◽  
Peng Wang ◽  
Lida Shi ◽  
Jing Zhao
Keyword(s):  
Image Processing ◽  
Image Segmentation ◽  
Deep Learning ◽  
Optic Disc ◽  
Medical Image ◽  
Medical Image Analysis ◽  
Medical Image Segmentation ◽  
Attention Mechanism ◽  
Cross Entropy ◽  
Segmentation Task

Medical image segmentation is an important part of medical image analysis. With the rapid development of convolutional neural networks in image processing, deep learning methods have achieved great success in the field of medical image processing. Deep learning is also used in the field of auxiliary diagnosis of glaucoma, and the effective segmentation of the optic disc area plays an important assistant role in the diagnosis of doctors in the clinical diagnosis of glaucoma. Previously, many U-Net-based optic disc segmentation methods have been proposed. However, the channel dependence of different levels of features is ignored. The performance of fundus image segmentation in small areas is not satisfactory. In this paper, we propose a new aggregation channel attention network to make full use of the influence of context information on semantic segmentation. Different from the existing attention mechanism, we exploit channel dependencies and integrate information of different scales into the attention mechanism. At the same time, we improved the basic classification framework based on cross entropy, combined the dice coefficient and cross entropy, and balanced the contribution of dice coefficients and cross entropy loss to the segmentation task, which enhanced the performance of the network in small area segmentation. The network retains more image features, restores the significant features more accurately, and further improves the segmentation performance of medical images. We apply it to the fundus optic disc segmentation task. We demonstrate the segmentation performance of the model on the Messidor dataset and the RIM-ONE dataset, and evaluate the proposed architecture. Experimental results show that our network architecture improves the prediction performance of the base architectures under different datasets while maintaining the computational efficiency. The results render that the proposed technologies improve the segmentation with 0.0469 overlapping error on Messidor.

Medical Image Segmentation based on U-Net: A Review

2020 ◽  
Vol 64 (2) ◽  
pp. 20508-1-20508-12 ◽  
Author(s):  
Getao Du ◽  
Xu Cao ◽  
Jimin Liang ◽  
Xueli Chen ◽  
Yonghua Zhan
Keyword(s):  
Neural Network ◽  
Image Analysis ◽  
Image Segmentation ◽  
Deep Learning ◽  
Medical Imaging ◽  
Medical Image ◽  
Medical Images ◽  
Medical Image Analysis ◽  
Medical Image Segmentation ◽  
Imaging Systems

Abstract Medical image analysis is performed by analyzing images obtained by medical imaging systems to solve clinical problems. The purpose is to extract effective information and improve the level of clinical diagnosis. In recent years, automatic segmentation based on deep learning (DL) methods has been widely used, where a neural network can automatically learn image features, which is in sharp contrast with the traditional manual learning method. U-net is one of the most important semantic segmentation frameworks for a convolutional neural network (CNN). It is widely used in the medical image analysis domain for lesion segmentation, anatomical segmentation, and classification. The advantage of this network framework is that it can not only accurately segment the desired feature target and effectively process and objectively evaluate medical images but also help to improve accuracy in the diagnosis by medical images. Therefore, this article presents a literature review of medical image segmentation based on U-net, focusing on the successful segmentation experience of U-net for different lesion regions in six medical imaging systems. Along with the latest advances in DL, this article introduces the method of combining the original U-net architecture with deep learning and a method for improving the U-net network.

Sign in / Sign up

Export Citation Format

Share Document