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Register a new userCombining Fully Convolutional and Recurrent Neural Networks for 3D Biomedical Image Segmentation
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Added by
Jianxu Chen
Publication date
2016
fields
Informatics Engineering
and research's language is
English
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Segmentation of 3D images is a fundamental problem in biomedical image analysis. Deep learning (DL) approaches have achieved state-of-the-art segmentation perfor- mance. To exploit the 3D contexts using neural networks, known DL segmentation methods, including 3D convolution, 2D convolution on planes orthogonal to 2D image slices, and LSTM in multiple directions, all suffer incompatibility with the highly anisotropic dimensions in common 3D biomedical images. In this paper, we propose a new DL framework for 3D image segmentation, based on a com- bination of a fully convolutional network (FCN) and a recurrent neural network (RNN), which are responsible for exploiting the intra-slice and inter-slice contexts, respectively. To our best knowledge, this is the first DL framework for 3D image segmentation that explicitly leverages 3D image anisotropism. Evaluating using a dataset from the ISBI Neuronal Structure Segmentation Challenge and in-house image stacks for 3D fungus segmentation, our approach achieves promising results comparing to the known DL-based 3D segmentation approaches.
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With pervasive applications of medical imaging in health-care, biomedical image segmentation plays a central role in quantitative analysis, clinical diagno- sis, and medical intervention. Since manual anno- tation su ers limited reproducibility, arduous e orts, and excessive time, automatic segmentation is desired to process increasingly larger scale histopathological data. Recently, deep neural networks (DNNs), par- ticularly fully convolutional networks (FCNs), have been widely applied to biomedical image segmenta- tion, attaining much improved performance. At the same time, quantization of DNNs has become an ac- tive research topic, which aims to represent weights with less memory (precision) to considerably reduce memory and computation requirements of DNNs while maintaining acceptable accuracy. In this paper, we apply quantization techniques to FCNs for accurate biomedical image segmentation. Unlike existing litera- ture on quantization which primarily targets memory and computation complexity reduction, we apply quan- tization as a method to reduce over tting in FCNs for better accuracy. Speci cally, we focus on a state-of- the-art segmentation framework, suggestive annotation [22], which judiciously extracts representative annota- tion samples from the original training dataset, obtain- ing an e ective small-sized balanced training dataset. We develop two new quantization processes for this framework: (1) suggestive annotation with quantiza- tion for highly representative training samples, and (2) network training with quantization for high accuracy. Extensive experiments on the MICCAI Gland dataset show that both quantization processes can improve the segmentation performance, and our proposed method exceeds the current state-of-the-art performance by up to 1%. In addition, our method has a reduction of up to 6.4x on memory usage.
We desgin a novel fully convolutional network architecture for shapes, denoted by Shape Fully Convolutional Networks (SFCN). 3D shapes are represented as graph structures in the SFCN architecture, based on novel graph convolution and pooling operations, which are similar to convolution and pooling operations used on images. Meanwhile, to build our SFCN architecture in the original image segmentation fully convolutional network (FCN) architecture, we also design and implement a generating operation} with bridging function. This ensures that the convolution and pooling operation we have designed can be successfully applied in the original FCN architecture. In this paper, we also present a new shape segmentation approach based on SFCN. Furthermore, we allow more general and challenging input, such as mixed datasets of different categories of shapes} which can prove the ability of our generalisation. In our approach, SFCNs are trained triangles-to-triangles by using three low-level geometric features as input. Finally, the feature voting-based multi-label graph cuts is adopted to optimise the segmentation results obtained by SFCN prediction. The experiment results show that our method can effectively learn and predict mixed shape datasets of either similar or different characteristics, and achieve excellent segmentation results.
Accelerating the data acquisition of dynamic magnetic resonance imaging (MRI) leads to a challenging ill-posed inverse problem, which has received great interest from both the signal processing and machine learning community over the last decades. The key ingredient to the problem is how to exploit the temporal correlation of the MR sequence to resolve the aliasing artefact. Traditionally, such observation led to a formulation of a non-convex optimisation problem, which were solved using iterative algorithms. Recently, however, deep learning based-approaches have gained significant popularity due to its ability to solve general inversion problems. In this work, we propose a unique, novel convolutional recurrent neural network (CRNN) architecture which reconstructs high quality cardiac MR images from highly undersampled k-space data by jointly exploiting the dependencies of the temporal sequences as well as the iterative nature of the traditional optimisation algorithms. In particular, the proposed architecture embeds the structure of the traditional iterative algorithms, efficiently modelling the recurrence of the iterative reconstruction stages by using recurrent hidden connections over such iterations. In addition, spatiotemporal dependencies are simultaneously learnt by exploiting bidirectional recurrent hidden connections across time sequences. The proposed algorithm is able to learn both the temporal dependency and the iterative reconstruction process effectively with only a very small number of parameters, while outperforming current MR reconstruction methods in terms of computational complexity, reconstruction accuracy and speed.
Undersampling the k-space data is widely adopted for acceleration of Magnetic Resonance Imaging (MRI). Current deep learning based approaches for supervised learning of MRI image reconstruction employ real-valued operations and representations by treating complex valued k-space/spatial-space as real values. In this paper, we propose complex dense fully convolutional neural network ($mathbb{C}$DFNet) for learning to de-alias the reconstruction artifacts within undersampled MRI images. We fashioned a densely-connected fully convolutional block tailored for complex-valued inputs by introducing dedicated layers such as complex convolution, batch normalization, non-linearities etc. $mathbb{C}$DFNet leverages the inherently complex-valued nature of input k-space and learns richer representations. We demonstrate improved perceptual quality and recovery of anatomical structures through $mathbb{C}$DFNet in contrast to its real-valued counterparts.
Semantic segmentation is pixel-wise classification which retains critical spatial information. The feature map reuse has been commonly adopted in CNN based approaches to take advantage of feature maps in the early layers for the later spatial reconstruction. Along this direction, we go a step further by proposing a fully dense neural network with an encoder-decoder structure that we abbreviate as FDNet. For each stage in the decoder module, feature maps of all the previous blocks are adaptively aggregated to feed-forward as input. On the one hand, it reconstructs the spatial boundaries accurately. On the other hand, it learns more efficiently with the more efficient gradient backpropagation. In addition, we propose the boundary-aware loss function to focus more attention on the pixels near the boundary, which boosts the hard examples labeling. We have demonstrated the best performance of the FDNet on the two benchmark datasets: PASCAL VOC 2012, NYUDv2 over previous works when not considering training on other datasets.
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