Medical image segmentation has played an important role in medical analysis and widely developed for many clinical applications. Deep learning-based approaches have achieved high performance in semantic segmentation but they are limited to pixel-wise setting and imbalanced classes data problem. In this paper, we tackle those limitations by developing a new deep learning-based model which takes into account both higher feature level i.e. region inside contour, intermediate feature level i.e. offset curves around the contour and lower feature level i.e. contour. Our proposed Offset Curves (OsC) loss consists of three main fitting terms. The first fitting term focuses on pixel-wise level segmentation whereas the second fitting term acts as attention model which pays attention to the area around the boundaries (offset curves). The third terms plays a role as regularization term which takes the length of boundaries into account. We evaluate our proposed OsC loss on both 2D network and 3D network. Two common medical datasets, i.e. retina DRIVE and brain tumor BRATS 2018 datasets are used to benchmark our proposed loss performance. The experiments have shown that our proposed OsC loss function outperforms other mainstream loss functions such as Cross-Entropy, Dice, Focal on the most common segmentation networks Unet,more »
Narrow Band Active Contour Attention Model for Medical Segmentation
Medical image segmentation is one of the most challenging tasks in medical image analysis and widely developed for many clinical applications. While deep learning-based approaches have achieved impressive performance in semantic segmentation, they are limited to pixel-wise settings with imbalanced-class data problems and weak boundary object segmentation in medical images. In this paper, we tackle those limitations by developing a new two-branch deep network architecture which takes both higher level features and lower level features into account. The first branch extracts higher level feature as region information by a common encoder-decoder network structure such as Unet and FCN, whereas the second branch focuses on lower level features as support information around the boundary and processes in parallel to the first branch. Our key contribution is the second branch named Narrow Band Active Contour (NB-AC) attention model which treats the object contour as a hyperplane and all data inside a narrow band as support information that influences the position and orientation of the hyperplane. Our proposed NB-AC attention model incorporates the contour length with the region energy involving a fixed-width band around the curve or surface. The proposed network loss contains two fitting terms: (i) a high level feature (i.e., region) more »
- Award ID(s):
- 1946391
- Publication Date:
- NSF-PAR ID:
- 10321737
- Journal Name:
- Diagnostics
- Volume:
- 11
- Issue:
- 8
- ISSN:
- 2075-4418
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Accurate semantic image segmentation from medical imaging can enable intelligent vision-based assistance in robot-assisted minimally invasive surgery. The human body and surgical procedures are highly dynamic. While machine-vision presents a promising approach, sufficiently large training image sets for robust performance are either costly or unavailable. This work examines three novel generative adversarial network (GAN) methods of providing usable synthetic tool images using only surgical background images and a few real tool images. The best of these three novel approaches generates realistic tool textures while preserving local background content by incorporating both a style preservation and a content loss component into the proposed multi-level loss function. The approach is quantitatively evaluated, and results suggest that the synthetically generated training tool images enhance UNet tool segmentation performance. More specifically, with a random set of 100 cadaver and live endoscopic images from the University of Washington Sinus Dataset, the UNet trained with synthetically generated images using the presented method resulted in 35.7% and 30.6% improvement over using purely real images in mean Dice coefficient and Intersection over Union scores, respectively. This study is promising towards the use of more widely available and routine screening endoscopy to preoperatively generate synthetic training tool images formore »
-
Given earth imagery with spectral features on a terrain surface, this paper studies surface segmentation based on both explanatory features and surface topology. The problem is important in many spatial and spatiotemporal applications such as flood extent mapping in hydrology. The problem is uniquely challenging for several reasons: first, the size of earth imagery on a terrain surface is often much larger than the input of popular deep convolutional neural networks; second, there exists topological structure dependency between pixel classes on the surface, and such dependency can follow an unknown and non-linear distribution; third, there are often limited training labels. Existing methods for earth imagery segmentation often divide the imagery into patches and consider the elevation as an additional feature channel. These methods do not fully incorporate the spatial topological structural constraint within and across surface patches and thus often show poor results, especially when training labels are limited. Existing methods on semi-supervised and unsupervised learning for earth imagery often focus on learning representation without explicitly incorporating surface topology. In contrast, we propose a novel framework that explicitly models the topological skeleton of a terrain surface with a contour tree from computational topology, which is guided by the physical constraintmore »
-
Flooding is one of the leading threats of natural disasters to human life and property, especially in densely populated urban areas. Rapid and precise extraction of the flooded areas is key to supporting emergency-response planning and providing damage assessment in both spatial and temporal measurements. Unmanned Aerial Vehicles (UAV) technology has recently been recognized as an efficient photogrammetry data acquisition platform to quickly deliver high-resolution imagery because of its cost-effectiveness, ability to fly at lower altitudes, and ability to enter a hazardous area. Different image classification methods including SVM (Support Vector Machine) have been used for flood extent mapping. In recent years, there has been a significant improvement in remote sensing image classification using Convolutional Neural Networks (CNNs). CNNs have demonstrated excellent performance on various tasks including image classification, feature extraction, and segmentation. CNNs can learn features automatically from large datasets through the organization of multi-layers of neurons and have the ability to implement nonlinear decision functions. This study investigates the potential of CNN approaches to extract flooded areas from UAV imagery. A VGG-based fully convolutional network (FCN-16s) was used in this research. The model was fine-tuned and a k-fold cross-validation was applied to estimate the performance of the modelmore »
-
In recent years, deep neural networks have achieved state-of-the-art performance in a variety of recognition and segmentation tasks in medical imaging including brain tumor segmentation. We investigate that segmenting a brain tumor is facing to the imbalanced data problem where the number of pixels belonging to the background class (non tumor pixel) is much larger than the number of pixels belonging to the foreground class (tumor pixel). To address this problem, we propose a multitask network which is formed as a cascaded structure. Our model consists of two targets, i.e., (i) effectively differentiate the brain tumor regions and (ii) estimate the brain tumor mask. The first objective is performed by our proposed contextual brain tumor detection network, which plays a role of an attention gate and focuses on the region around brain tumor only while ignoring the far neighbor background which is less correlated to the tumor. Different from other existing object detection networks which process every pixel, our contextual brain tumor detection network only processes contextual regions around ground-truth instances and this strategy aims at producing meaningful regions proposals. The second objective is built upon a 3D atrous residual network and under an encode-decode network in order to effectivelymore »
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Publisher's Version of Record
- https://doi.org/10.3390/diagnostics11081393
