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Register a new userTransClaw U-Net: Claw U-Net with Transformers for Medical Image Segmentation
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Added by
Menghan Hu
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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In recent years, computer-aided diagnosis has become an increasingly popular topic. Methods based on convolutional neural networks have achieved good performance in medical image segmentation and classification. Due to the limitations of the convolution operation, the long-term spatial features are often not accurately obtained. Hence, we propose a TransClaw U-Net network structure, which combines the convolution operation with the transformer operation in the encoding part. The convolution part is applied for extracting the shallow spatial features to facilitate the recovery of the image resolution after upsampling. The transformer part is used to encode the patches, and the self-attention mechanism is used to obtain global information between sequences. The decoding part retains the bottom upsampling structure for better detail segmentation performance. The experimental results on Synapse Multi-organ Segmentation Datasets show that the performance of TransClaw U-Net is better than other network structures. The ablation experiments also prove the generalization performance of TransClaw U-Net.
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The U-Net was presented in 2015. With its straight-forward and successful architecture it quickly evolved to a commonly used benchmark in medical image segmentation. The adaptation of the U-Net to novel problems, however, comprises several degrees of freedom regarding the exact architecture, preprocessing, training and inference. These choices are not independent of each other and substantially impact the overall performance. The present paper introduces the nnU-Net (no-new-Net), which refers to a robust and self-adapting framework on the basis of 2D and 3D vanilla U-Nets. We argue the strong case for taking away superfluous bells and whistles of many proposed network designs and instead focus on the remaining aspects that make out the performance and generalizability of a method. We evaluate the nnU-Net in the context of the Medical Segmentation Decathlon challenge, which measures segmentation performance in ten disciplines comprising distinct entities, image modalities, image geometries and dataset sizes, with no manual adjustments between datasets allowed. At the time of manuscript submission, nnU-Net achieves the highest mean dice scores across all classes and seven phase 1 tasks (except class 1 in BrainTumour) in the online leaderboard of the challenge.
Automatic medical image segmentation has made great progress benefit from the development of deep learning. However, most existing methods are based on convolutional neural networks (CNNs), which fail to build long-range dependencies and global context connections due to the limitation of receptive field in convolution operation. Inspired by the success of Transformer in modeling the long-range contextual information, some researchers have expended considerable efforts in designing the robust variants of Transformer-based U-Net. Moreover, the patch division used in vision transformers usually ignores the pixel-level intrinsic structural features inside each patch. To alleviate these problems, we propose a novel deep medical image segmentation framework called Dual Swin Transformer U-Net (DS-TransUNet), which might be the first attempt to concurrently incorporate the advantages of hierarchical Swin Transformer into both encoder and decoder of the standard U-shaped architecture to enhance the semantic segmentation quality of varying medical images. Unlike many prior Transformer-based solutions, the proposed DS-TransUNet first adopts dual-scale encoder subnetworks based on Swin Transformer to extract the coarse and fine-grained feature representations of different semantic scales. As the core component for our DS-TransUNet, a well-designed Transformer Interactive Fusion (TIF) module is proposed to effectively establish global dependencies between features of different scales through the self-attention mechanism. Furthermore, we also introduce the Swin Transformer block into decoder to further explore the long-range contextual information during the up-sampling process. Extensive experiments across four typical tasks for medical image segmentation demonstrate the effectiveness of DS-TransUNet, and show that our approach significantly outperforms the state-of-the-art methods.
With the development of deep encoder-decoder architectures and large-scale annotated medical datasets, great progress has been achieved in the development of automatic medical image segmentation. Due to the stacking of convolution layers and the consecutive sampling operations, existing standard models inevitably encounter the information recession problem of feature representations, which fails to fully model the global contextual feature dependencies. To overcome the above challenges, this paper proposes a novel Transformer based medical image semantic segmentation framework called TransAttUnet, in which the multi-level guided attention and multi-scale skip connection are jointly designed to effectively enhance the functionality and flexibility of traditional U-shaped architecture. Inspired by Transformer, a novel self-aware attention (SAA) module with both Transformer Self Attention (TSA) and Global Spatial Attention (GSA) is incorporated into TransAttUnet to effectively learn the non-local interactions between encoder features. In particular, we also establish additional multi-scale skip connections between decoder blocks to aggregate the different semantic-scale upsampling features. In this way, the representation ability of multi-scale context information is strengthened to generate discriminative features. Benefitting from these complementary components, the proposed TransAttUnet can effectively alleviate the loss of fine details caused by the information recession problem, improving the diagnostic sensitivity and segmentation quality of medical image analysis. Extensive experiments on multiple medical image segmentation datasets of different imaging demonstrate that our method consistently outperforms the state-of-the-art baselines.
Fine-tuning a network which has been trained on a large dataset is an alternative to full training in order to overcome the problem of scarce and expensive data in medical applications. While the shallow layers of the network are usually kept unchanged, deeper layers are modified according to the new dataset. This approach may not work for ultrasound images due to their drastically different appearance. In this study, we investigated the effect of fine-tuning different layers of a U-Net which was trained on segmentation of natural images in breast ultrasound image segmentation. Tuning the contracting part and fixing the expanding part resulted in substantially better results compared to fixing the contracting part and tuning the expanding part. Furthermore, we showed that starting to fine-tune the U-Net from the shallow layers and gradually including more layers will lead to a better performance compared to fine-tuning the network from the deep layers moving back to shallow layers. We did not observe the same results on segmentation of X-ray images, which have different salient features compared to ultrasound, it may therefore be more appropriate to fine-tune the shallow layers rather than deep layers. Shallow layers learn lower level features (including speckle pattern, and probably the noise and artifact properties) which are critical in automatic segmentation in this modality.
Sturge-Weber syndrome (SWS) is a vascular malformation disease, and it may cause blindness if the patients condition is severe. Clinical results show that SWS can be divided into two types based on the characteristics of scleral blood vessels. Therefore, how to accurately segment scleral blood vessels has become a significant problem in computer-aided diagnosis. In this research, we propose to continuously upsample the bottom layers feature maps to preserve image details, and design a novel Claw UNet based on UNet for scleral blood vessel segmentation. Specifically, the residual structure is used to increase the number of network layers in the feature extraction stage to learn deeper features. In the decoding stage, by fusing the features of the encoding, upsampling, and decoding parts, Claw UNet can achieve effective segmentation in the fine-grained regions of scleral blood vessels. To effectively extract small blood vessels, we use the attention mechanism to calculate the attention coefficient of each position in images. Claw UNet outperforms other UNet-based networks on scleral blood vessel image dataset.
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