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Journal ArticleDOI

3D deeply supervised network for automated segmentation of volumetric medical images.

01 Oct 2017-Medical Image Analysis (Elsevier)-Vol. 41, Iss: 41, pp 40-54
TL;DR: The proposed 3D DSN is capable of conducting volume‐to‐volume learning and inference, which can eliminate redundant computations and alleviate the risk of over‐fitting on limited training data, and the3D deep supervision mechanism can effectively cope with the optimization problem of gradients vanishing or exploding when training a 3D deep model.
About: This article is published in Medical Image Analysis.The article was published on 2017-10-01. It has received 507 citations till now. The article focuses on the topics: Scale-space segmentation & Image segmentation.
Citations
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Journal ArticleDOI
TL;DR: UNet++ as mentioned in this paper proposes an efficient ensemble of U-Nets of varying depths, which partially share an encoder and co-learn simultaneously using deep supervision, leading to a highly flexible feature fusion scheme.
Abstract: The state-of-the-art models for medical image segmentation are variants of U-Net and fully convolutional networks (FCN). Despite their success, these models have two limitations: (1) their optimal depth is apriori unknown, requiring extensive architecture search or inefficient ensemble of models of varying depths; and (2) their skip connections impose an unnecessarily restrictive fusion scheme, forcing aggregation only at the same-scale feature maps of the encoder and decoder sub-networks. To overcome these two limitations, we propose UNet++, a new neural architecture for semantic and instance segmentation, by (1) alleviating the unknown network depth with an efficient ensemble of U-Nets of varying depths, which partially share an encoder and co-learn simultaneously using deep supervision; (2) redesigning skip connections to aggregate features of varying semantic scales at the decoder sub-networks, leading to a highly flexible feature fusion scheme; and (3) devising a pruning scheme to accelerate the inference speed of UNet++. We have evaluated UNet++ using six different medical image segmentation datasets, covering multiple imaging modalities such as computed tomography (CT), magnetic resonance imaging (MRI), and electron microscopy (EM), and demonstrating that (1) UNet++ consistently outperforms the baseline models for the task of semantic segmentation across different datasets and backbone architectures; (2) UNet++ enhances segmentation quality of varying-size objects—an improvement over the fixed-depth U-Net; (3) Mask RCNN++ (Mask R-CNN with UNet++ design) outperforms the original Mask R-CNN for the task of instance segmentation; and (4) pruned UNet++ models achieve significant speedup while showing only modest performance degradation. Our implementation and pre-trained models are available at https://github.com/MrGiovanni/UNetPlusPlus .

1,487 citations

Journal ArticleDOI
TL;DR: A critical appraisal of popular methods that have employed deep learning techniques for medical image segmentation is presented and the most common challenges incurred are summarized and suggest possible solutions.
Abstract: Deep learning-based image segmentation is by now firmly established as a robust tool in image segmentation. It has been widely used to separate homogeneous areas as the first and critical component of diagnosis and treatment pipeline. In this article, we present a critical appraisal of popular methods that have employed deep-learning techniques for medical image segmentation. Moreover, we summarize the most common challenges incurred and suggest possible solutions.

794 citations


Cites background or methods from "3D deeply supervised network for au..."

  • ...This system has achieved 0.823 Dice score for lesion segmentation in CT images and 0.85 in MRI images....

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  • ...They even further expanded the idea by applying different modalities (i.e., brain MRI, breast MRI, and cardiac CTA) for each segmentation task....

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  • ...The auxiliary losses together with the original loss of the hidden layer are combined to strengthening the gradient [23, 86, 87]....

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  • ...The fact that the ROI in medical images usually distributed over multiple adjacent slices (e.g., in CT or MRI), results in having correlations in successive slices....

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  • ...One of the earlier solutions for this issue is to apply pooling layers which can reduce the dimensionality of the parameters [23]....

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Posted Content
TL;DR: A Recurrent Convolutional Neural Network (RCNN) based on U-Net as well as a Recurrent Residual convolutional neural Network (RRCNN), which are named RU-Net and R2U-Net respectively are proposed, which show superior performance on segmentation tasks compared to equivalent models including U-nets and residual U- net.
Abstract: Deep learning (DL) based semantic segmentation methods have been providing state-of-the-art performance in the last few years. More specifically, these techniques have been successfully applied to medical image classification, segmentation, and detection tasks. One deep learning technique, U-Net, has become one of the most popular for these applications. In this paper, we propose a Recurrent Convolutional Neural Network (RCNN) based on U-Net as well as a Recurrent Residual Convolutional Neural Network (RRCNN) based on U-Net models, which are named RU-Net and R2U-Net respectively. The proposed models utilize the power of U-Net, Residual Network, as well as RCNN. There are several advantages of these proposed architectures for segmentation tasks. First, a residual unit helps when training deep architecture. Second, feature accumulation with recurrent residual convolutional layers ensures better feature representation for segmentation tasks. Third, it allows us to design better U-Net architecture with same number of network parameters with better performance for medical image segmentation. The proposed models are tested on three benchmark datasets such as blood vessel segmentation in retina images, skin cancer segmentation, and lung lesion segmentation. The experimental results show superior performance on segmentation tasks compared to equivalent models including U-Net and residual U-Net (ResU-Net).

700 citations


Cites methods from "3D deeply supervised network for au..."

  • ...Furthermore, a 3D deeply supervised approach for automated segmentation of volumetric medical images was presented in [36]....

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Journal ArticleDOI
TL;DR: This paper provides a comprehensive survey on the application of DL, RL, and deep RL techniques in mining biological data and compares the performances of DL techniques when applied to different data sets across various application domains.
Abstract: Rapid advances in hardware-based technologies during the past decades have opened up new possibilities for life scientists to gather multimodal data in various application domains, such as omics , bioimaging , medical imaging , and (brain/body)–machine interfaces . These have generated novel opportunities for development of dedicated data-intensive machine learning techniques. In particular, recent research in deep learning (DL), reinforcement learning (RL), and their combination (deep RL) promise to revolutionize the future of artificial intelligence. The growth in computational power accompanied by faster and increased data storage, and declining computing costs have already allowed scientists in various fields to apply these techniques on data sets that were previously intractable owing to their size and complexity. This paper provides a comprehensive survey on the application of DL, RL, and deep RL techniques in mining biological data. In addition, we compare the performances of DL techniques when applied to different data sets across various application domains. Finally, we outline open issues in this challenging research area and discuss future development perspectives.

622 citations


Cites methods from "3D deeply supervised network for au..."

  • ...the DBN [145], and blood pool (BP) and myocardium (MC) using the CNN [157]....

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Journal ArticleDOI
TL;DR: A novel deep learning-based interactive segmentation framework by incorporating CNNs into a bounding box and scribble-based segmentation pipeline and proposing a weighted loss function considering network and interaction-based uncertainty for the fine tuning is proposed.
Abstract: Convolutional neural networks (CNNs) have achieved state-of-the-art performance for automatic medical image segmentation. However, they have not demonstrated sufficiently accurate and robust results for clinical use. In addition, they are limited by the lack of image-specific adaptation and the lack of generalizability to previously unseen object classes (a.k.a. zero-shot learning). To address these problems, we propose a novel deep learning-based interactive segmentation framework by incorporating CNNs into a bounding box and scribble-based segmentation pipeline. We propose image-specific fine tuning to make a CNN model adaptive to a specific test image, which can be either unsupervised (without additional user interactions) or supervised (with additional scribbles). We also propose a weighted loss function considering network and interaction-based uncertainty for the fine tuning. We applied this framework to two applications: 2-D segmentation of multiple organs from fetal magnetic resonance (MR) slices, where only two types of these organs were annotated for training and 3-D segmentation of brain tumor core (excluding edema) and whole brain tumor (including edema) from different MR sequences, where only the tumor core in one MR sequence was annotated for training. Experimental results show that: 1) our model is more robust to segment previously unseen objects than state-of-the-art CNNs; 2) image-specific fine tuning with the proposed weighted loss function significantly improves segmentation accuracy; and 3) our method leads to accurate results with fewer user interactions and less user time than traditional interactive segmentation methods.

582 citations


Additional excerpts

  • ...For 3D volumes, patch-based CNNs have been proposed for segmentation of the brain tumor [7] and pancreas [14], and more powerful end-to-end 3D CNNs include V-Net [15], HighRes3DNet [8], and 3D deeply supervised network [16]....

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References
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TL;DR: In this article, the authors proposed a residual learning framework to ease the training of networks that are substantially deeper than those used previously, which won the 1st place on the ILSVRC 2015 classification task.
Abstract: Deeper neural networks are more difficult to train. We present a residual learning framework to ease the training of networks that are substantially deeper than those used previously. We explicitly reformulate the layers as learning residual functions with reference to the layer inputs, instead of learning unreferenced functions. We provide comprehensive empirical evidence showing that these residual networks are easier to optimize, and can gain accuracy from considerably increased depth. On the ImageNet dataset we evaluate residual nets with a depth of up to 152 layers—8× deeper than VGG nets [40] but still having lower complexity. An ensemble of these residual nets achieves 3.57% error on the ImageNet test set. This result won the 1st place on the ILSVRC 2015 classification task. We also present analysis on CIFAR-10 with 100 and 1000 layers. The depth of representations is of central importance for many visual recognition tasks. Solely due to our extremely deep representations, we obtain a 28% relative improvement on the COCO object detection dataset. Deep residual nets are foundations of our submissions to ILSVRC & COCO 2015 competitions1, where we also won the 1st places on the tasks of ImageNet detection, ImageNet localization, COCO detection, and COCO segmentation.

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TL;DR: This work investigates the effect of the convolutional network depth on its accuracy in the large-scale image recognition setting using an architecture with very small convolution filters, which shows that a significant improvement on the prior-art configurations can be achieved by pushing the depth to 16-19 weight layers.
Abstract: In this work we investigate the effect of the convolutional network depth on its accuracy in the large-scale image recognition setting. Our main contribution is a thorough evaluation of networks of increasing depth using an architecture with very small (3x3) convolution filters, which shows that a significant improvement on the prior-art configurations can be achieved by pushing the depth to 16-19 weight layers. These findings were the basis of our ImageNet Challenge 2014 submission, where our team secured the first and the second places in the localisation and classification tracks respectively. We also show that our representations generalise well to other datasets, where they achieve state-of-the-art results. We have made our two best-performing ConvNet models publicly available to facilitate further research on the use of deep visual representations in computer vision.

55,235 citations


"3D deeply supervised network for au..." refers methods in this paper

  • ...3D end-to-end learning for volumetric segmentation In a classic CNN such as the AlexNet ( Krizhevsky et al., 2012 ) nd the VGGNet ( Simonyan and Zisserman, 2014 ), the last several ayers are typically fully-connected ones, which restrict the net- ork to take fixed-sized input image and generate…...

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Proceedings Article
01 Jan 2015
TL;DR: In this paper, the authors investigated the effect of the convolutional network depth on its accuracy in the large-scale image recognition setting and showed that a significant improvement on the prior-art configurations can be achieved by pushing the depth to 16-19 layers.
Abstract: In this work we investigate the effect of the convolutional network depth on its accuracy in the large-scale image recognition setting. Our main contribution is a thorough evaluation of networks of increasing depth using an architecture with very small (3x3) convolution filters, which shows that a significant improvement on the prior-art configurations can be achieved by pushing the depth to 16-19 weight layers. These findings were the basis of our ImageNet Challenge 2014 submission, where our team secured the first and the second places in the localisation and classification tracks respectively. We also show that our representations generalise well to other datasets, where they achieve state-of-the-art results. We have made our two best-performing ConvNet models publicly available to facilitate further research on the use of deep visual representations in computer vision.

49,914 citations

Book ChapterDOI
05 Oct 2015
TL;DR: Neber et al. as discussed by the authors proposed a network and training strategy that relies on the strong use of data augmentation to use the available annotated samples more efficiently, which can be trained end-to-end from very few images and outperforms the prior best method (a sliding-window convolutional network) on the ISBI challenge for segmentation of neuronal structures in electron microscopic stacks.
Abstract: There is large consent that successful training of deep networks requires many thousand annotated training samples. In this paper, we present a network and training strategy that relies on the strong use of data augmentation to use the available annotated samples more efficiently. The architecture consists of a contracting path to capture context and a symmetric expanding path that enables precise localization. We show that such a network can be trained end-to-end from very few images and outperforms the prior best method (a sliding-window convolutional network) on the ISBI challenge for segmentation of neuronal structures in electron microscopic stacks. Using the same network trained on transmitted light microscopy images (phase contrast and DIC) we won the ISBI cell tracking challenge 2015 in these categories by a large margin. Moreover, the network is fast. Segmentation of a 512x512 image takes less than a second on a recent GPU. The full implementation (based on Caffe) and the trained networks are available at http://lmb.informatik.uni-freiburg.de/people/ronneber/u-net .

49,590 citations