Segmentation has been a major task in neuroimaging. A large number of automated methods have been developed for segmenting healthy and diseased brain tissues. In recent years, deep learning techniques have attracted a lot of attention as a result of their high accuracy in different segmentation problems. We present a new deep learning based segmentation method, DeepMRSeg, that can be applied in a generic way to a variety of segmentation tasks. The proposed architecture combines recent advances in the field of biomedical image segmentation and computer vision. We use a modified UNet architecture that takes advantage of multiple convolution filter sizes to achieve multi-scale feature extraction adaptive to the desired segmentation task. Importantly, our method operates on minimally processed raw MRI scan. We validated our method on a wide range of segmentation tasks, including white matter lesion segmentation, segmentation of deep brain structures and hippocampus segmentation. We provide code and pre-trained models to allow researchers apply our method on their own datasets.
UNet architecture was introduced by @cite_1 . UNet has been an important advancement in the application of deep CNNs to the problem of biomedical image segmentation. CNNs have been initially used on classification problems by mapping input images to output class labels. However, in segmentation tasks, the desired output is an image, e.g. a binary segmentation map. UNet extended the CNN architecture by supplementing the usual contracting or encoding path with a symmetric expanding or decoding path, where pooling operators are replaced by upsampling operators. The encoding path allows the architecture to learn spatially relevant context information and the decoding path adds the precise localization back to the architecture, leading to a final segmentation image as output of the model.
@cite_1
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In this paper, we present UNet++, a new, more powerful architecture for medical image segmentation. Our architecture is essentially a deeply-supervised encoder-decoder network where the encoder and decoder sub-networks are connected through a series of nested, dense skip pathways. The re-designed skip pathways aim at reducing the semantic gap between the feature maps of the encoder and decoder sub-networks. We argue that the optimizer would deal with an easier learning task when the feature maps from the decoder and encoder networks are semantically similar. We have evaluated UNet++ in comparison with U-Net and wide U-Net architectures across multiple medical image segmentation tasks: nodule segmentation in the low-dose CT scans of chest, nuclei segmentation in the microscopy images, liver segmentation in abdominal CT scans, and polyp segmentation in colonoscopy videos. Our experiments demonstrate that UNet++ with deep supervision achieves an average IoU gain of 3.9 and 3.4 points over U-Net and wide U-Net, respectively. Convolutional neural networks (CNNs) have revolutionized medical image analysis over the past few years. The U-Net architecture is one of the most well-known CNN architectures for semantic segmentation and has achieved remarkable successes in many different medical image segmentation applications. The U-Net architecture consists of standard convolution layers, pooling layers, and upsampling layers. These convolution layers learn representative features of input images and construct segmentations based on the features. However, the features learned by standard convolution layers are not distinctive when the differences among different categories are subtle in terms of intensity, location, shape, and size. In this paper, we propose a novel CNN architecture, called Dense-Res-Inception Net (DRINet), which addresses this challenging problem. The proposed DRINet consists of three blocks, namely a convolutional block with dense connections, a deconvolutional block with residual inception modules, and an unpooling block. Our proposed architecture outperforms the U-Net in three different challenging applications, namely multi-class segmentation of cerebrospinal fluid on brain CT images, multi-organ segmentation on abdominal CT images, and multi-class brain tumor segmentation on MR images. State-of-the-art approaches for semantic image segmentation are built on Convolutional Neural Networks (CNNs). The typical segmentation architecture is composed of (a) a downsampling path responsible for extracting coarse semantic features, followed by (b) an upsampling path trained to recover the input image resolution at the output of the model and, optionally, (c) a post-processing module (e.g. Conditional Random Fields) to refine the model predictions. Recently, a new CNN architecture, Densely Connected Convolutional Networks (DenseNets), has shown excellent results on image classification tasks. The idea of DenseNets is based on the observation that if each layer is directly connected to every other layer in a feed-forward fashion then the network will be more accurate and easier to train. In this paper, we extend DenseNets to deal with the problem of semantic segmentation. We achieve state-of-the-art results on urban scene benchmark datasets such as CamVid and Gatech, without any further post-processing module nor pretraining. Moreover, due to smart construction of the model, our approach has much less parameters than currently published best entries for these datasets. Code to reproduce the experiments is available here : this https URL Recent advances in Convolutional Neural Networks (CNNs) have obtained promising results in difficult deep learning tasks. However, the success of a CNN depends on finding an architecture to fit a given problem. A hand-crafted architecture is a challenging, time-consuming process that requires expert knowledge and effort, due to a large number of architectural design choices. In this article, we present an efficient framework that automatically designs a high-performing CNN architecture for a given problem. In this framework, we introduce a new optimization objective function that combines the error rate and the information learnt by a set of feature maps using deconvolutional networks (deconvnet). The new objective function allows the hyperparameters of the CNN architecture to be optimized in a way that enhances the performance by guiding the CNN through better visualization of learnt features via deconvnet. The actual optimization of the objective function is carried out via the Nelder-Mead Method (NMM). Further, our new objective function results in much faster convergence towards a better architecture. The proposed framework has the ability to explore a CNN architecture’s numerous design choices in an efficient way and also allows effective, distributed execution and synchronization via web services. Empirically, we demonstrate that the CNN architecture designed with our approach outperforms several existing approaches in terms of its error rate. Our results are also competitive with state-of-the-art results on the MNIST dataset and perform reasonably against the state-of-the-art results on CIFAR-10 and CIFAR-100 datasets. Our approach has a significant role in increasing the depth, reducing the size of strides, and constraining some convolutional layers not followed by pooling layers in order to find a CNN architecture that produces a high recognition performance.