Fully convolutional deep neural networks have been asserted to be fast and precise frameworks with great potential in image segmentation. One of the major challenges in utilizing such networks raises when data is unbalanced, which is common in many medical imaging applications such as lesion segmentation where lesion class voxels are often much lower in numbers than non-lesion voxels. A trained network with unbalanced data may make predictions with high precision and low recall, being severely biased towards the non-lesion class which is particularly undesired in medical applications where false negatives are actually more important than false positives. Various methods have been proposed to address this problem including two step training, sample re-weighting, balanced sampling, and similarity loss functions. In this paper we developed a patch-wise 3D densely connected network with an asymmetric loss function, where we used large overlapping image patches for intrinsic and extrinsic data augmentation, a patch selection algorithm, and a patch prediction fusion strategy based on B-spline weighted soft voting to take into account the uncertainty of prediction in patch borders. We applied this method to lesion segmentation based on the MSSEG 2016 and ISBI 2015 challenges, where we achieved average Dice similarity coefficient of 69.9% and 65.74%, respectively. In addition to the proposed loss, we trained our network with focal and generalized Dice loss functions. Significant improvement in $F_1$ and $F_2$ scores and the APR curve was achieved in test using the asymmetric similarity loss layer and our 3D patch prediction fusion. The asymmetric similarity loss based on $F_\beta$ scores generalizes the Dice similarity coefficient and can be effectively used with the patch-wise strategy developed here to train fully convolutional deep neural networks for highly unbalanced image segmentation.

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Biomedical image segmentation is an important task in many medical applications. Segmentation methods based on convolutional neural networks attain state-of-the-art accuracy; however, they typically rely on supervised training with large labeled datasets. Labeling datasets of medical images requires significant expertise and time, and is infeasible at large scales. To tackle the lack of labeled data, researchers use techniques such as hand-engineered preprocessing steps, hand-tuned architectures, and data augmentation. However, these techniques involve costly engineering efforts, and are typically dataset-specific. We present an automated data augmentation method for medical images. We demonstrate our method on the task of segmenting magnetic resonance imaging (MRI) brain scans, focusing on the one-shot segmentation scenario -- a practical challenge in many medical applications. Our method requires only a single segmented scan, and leverages other unlabeled scans in a semi-supervised approach. We learn a model of transforms from the images, and use the model along with the labeled example to synthesize additional labeled training examples for supervised segmentation. Each transform is comprised of a spatial deformation field and an intensity change, enabling the synthesis of complex effects such as variations in anatomy and image acquisition procedures. Augmenting the training of a supervised segmenter with these new examples provides significant improvements over state-of-the-art methods for one-shot biomedical image segmentation. Our code is available at https://github.com/xamyzhao/brainstorm.

Deep neural network models used for medical image segmentation are large because they are trained with high-resolution three-dimensional (3D) images. Graphics processing units (GPUs) are widely used to accelerate the trainings. However, the memory on a GPU is not large enough to train the models. A popular approach to tackling this problem is patch-based method, which divides a large image into small patches and trains the models with these small patches. However, this method would degrade the segmentation quality if a target object spans multiple patches. In this paper, we propose a novel approach for 3D medical image segmentation that utilizes the data-swapping, which swaps out intermediate data from GPU memory to CPU memory to enlarge the effective GPU memory size, for training high-resolution 3D medical images without patching. We carefully tuned parameters in the data-swapping method to obtain the best training performance for 3D U-Net, a widely used deep neural network model for medical image segmentation. We applied our tuning to train 3D U-Net with full-size images of 192 x 192 x 192 voxels in brain tumor dataset. As a result, communication overhead, which is the most important issue, was reduced by 17.1%. Compared with the patch-based method for patches of 128 x 128 x 128 voxels, our training for full-size images achieved improvement on the mean Dice score by 4.48% and 5.32 % for detecting whole tumor sub-region and tumor core sub-region, respectively. The total training time was reduced from 164 hours to 47 hours, resulting in 3.53 times of acceleration.

Deep learning has shown promising results in medical image analysis, however, the lack of very large annotated datasets confines its full potential. Although transfer learning with ImageNet pre-trained classification models can alleviate the problem, constrained image sizes and model complexities can lead to unnecessary increase in computational cost and decrease in performance. As many common morphological features are usually shared by different classification tasks of an organ, it is greatly beneficial if we can extract such features to improve classification with limited samples. Therefore, inspired by the idea of curriculum learning, we propose a strategy for building medical image classifiers using features from segmentation networks. By using a segmentation network pre-trained on similar data as the classification task, the machine can first learn the simpler shape and structural concepts before tackling the actual classification problem which usually involves more complicated concepts. Using our proposed framework on a 3D three-class brain tumor type classification problem, we achieved 82% accuracy on 191 testing samples with 91 training samples. When applying to a 2D nine-class cardiac semantic level classification problem, we achieved 86% accuracy on 263 testing samples with 108 training samples. Comparisons with ImageNet pre-trained classifiers and classifiers trained from scratch are presented.

In this paper, we adopt 3D Convolutional Neural Networks to segment volumetric medical images. Although deep neural networks have been proven to be very effective on many 2D vision tasks, it is still challenging to apply them to 3D tasks due to the limited amount of annotated 3D data and limited computational resources. We propose a novel 3D-based coarse-to-fine framework to effectively and efficiently tackle these challenges. The proposed 3D-based framework outperforms the 2D counterpart to a large margin since it can leverage the rich spatial infor- mation along all three axes. We conduct experiments on two datasets which include healthy and pathological pancreases respectively, and achieve the current state-of-the-art in terms of Dice-S{\o}rensen Coefficient (DSC). On the NIH pancreas segmentation dataset, we outperform the previous best by an average of over 2%, and the worst case is improved by 7% to reach almost 70%, which indicates the reliability of our framework in clinical applications.

Deep neural network architectures have traditionally been designed and explored with human expertise in a long-lasting trial-and-error process. This process requires huge amount of time, expertise, and resources. To address this tedious problem, we propose a novel algorithm to optimally find hyperparameters of a deep network architecture automatically. We specifically focus on designing neural architectures for medical image segmentation task. Our proposed method is based on a policy gradient reinforcement learning for which the reward function is assigned a segmentation evaluation utility (i.e., dice index). We show the efficacy of the proposed method with its low computational cost in comparison with the state-of-the-art medical image segmentation networks. We also present a new architecture design, a densely connected encoder-decoder CNN, as a strong baseline architecture to apply the proposed hyperparameter search algorithm. We apply the proposed algorithm to each layer of the baseline architectures. As an application, we train the proposed system on cine cardiac MR images from Automated Cardiac Diagnosis Challenge (ACDC) MICCAI 2017. Starting from a baseline segmentation architecture, the resulting network architecture obtains the state-of-the-art results in accuracy without performing any trial-and-error based architecture design approaches or close supervision of the hyperparameters changes.

Simultaneous segmentation of multiple organs from different medical imaging modalities is a crucial task as it can be utilized for computer-aided diagnosis, computer-assisted surgery, and therapy planning. Thanks to the recent advances in deep learning, several deep neural networks for medical image segmentation have been introduced successfully for this purpose. In this paper, we focus on learning a deep multi-organ segmentation network that labels voxels. In particular, we examine the critical choice of a loss function in order to handle the notorious imbalance problem that plagues both the input and output of a learning model. The input imbalance refers to the class-imbalance in the input training samples (i.e. small foreground objects embedded in an abundance of background voxels, as well as organs of varying sizes). The output imbalance refers to the imbalance between the false positives and false negatives of the inference model. We introduce a loss function that integrates a weighted cross-entropy with a Dice similarity coefficient to tackle both types of imbalance during training and inference. We evaluated the proposed loss function on three datasets of whole body PET scans with 5 target organs, MRI prostate scans, and ultrasound echocardigraphy images with a single target organ. We show that a simple network architecture with the proposed integrative loss function can outperform state-of-the-art methods and results of the competing methods can be improved when our proposed loss is used.

The Normalized Cut (NCut) objective function, widely used in data clustering and image segmentation, quantifies the cost of graph partitioning in a way that biases clusters or segments that are balanced towards having lower values than unbalanced partitionings. However, this bias is so strong that it avoids any singleton partitions, even when vertices are very weakly connected to the rest of the graph. Motivated by the B\"uhler-Hein family of balanced cut costs, we propose the family of Compassionately Conservative Balanced (CCB) Cut costs, which are indexed by a parameter that can be used to strike a compromise between the desire to avoid too many singleton partitions and the notion that all partitions should be balanced. We show that CCB-Cut minimization can be relaxed into an orthogonally constrained $\ell_{\tau}$-minimization problem that coincides with the problem of computing Piecewise Flat Embeddings (PFE) for one particular index value, and we present an algorithm for solving the relaxed problem by iteratively minimizing a sequence of reweighted Rayleigh quotients (IRRQ). Using images from the BSDS500 database, we show that image segmentation based on CCB-Cut minimization provides better accuracy with respect to ground truth and greater variability in region size than NCut-based image segmentation.

One of the most common tasks in medical imaging is semantic segmentation. Achieving this segmentation automatically has been an active area of research, but the task has been proven very challenging due to the large variation of anatomy across different patients. However, recent advances in deep learning have made it possible to significantly improve the performance of image recognition and semantic segmentation methods in the field of computer vision. Due to the data driven approaches of hierarchical feature learning in deep learning frameworks, these advances can be translated to medical images without much difficulty. Several variations of deep convolutional neural networks have been successfully applied to medical images. Especially fully convolutional architectures have been proven efficient for segmentation of 3D medical images. In this article, we describe how to build a 3D fully convolutional network (FCN) that can process 3D images in order to produce automatic semantic segmentations. The model is trained and evaluated on a clinical computed tomography (CT) dataset and shows state-of-the-art performance in multi-organ segmentation.

This work presents a region-growing image segmentation approach based on superpixel decomposition. From an initial contour-constrained over-segmentation of the input image, the image segmentation is achieved by iteratively merging similar superpixels into regions. This approach raises two key issues: (1) how to compute the similarity between superpixels in order to perform accurate merging and (2) in which order those superpixels must be merged together. In this perspective, we firstly introduce a robust adaptive multi-scale superpixel similarity in which region comparisons are made both at content and common border level. Secondly, we propose a global merging strategy to efficiently guide the region merging process. Such strategy uses an adpative merging criterion to ensure that best region aggregations are given highest priorities. This allows to reach a final segmentation into consistent regions with strong boundary adherence. We perform experiments on the BSDS500 image dataset to highlight to which extent our method compares favorably against other well-known image segmentation algorithms. The obtained results demonstrate the promising potential of the proposed approach.

We propose an Active Learning approach to image segmentation that exploits geometric priors to streamline the annotation process. We demonstrate this for both background-foreground and multi-class segmentation tasks in 2D images and 3D image volumes. Our approach combines geometric smoothness priors in the image space with more traditional uncertainty measures to estimate which pixels or voxels are most in need of annotation. For multi-class settings, we additionally introduce two novel criteria for uncertainty. In the 3D case, we use the resulting uncertainty measure to show the annotator voxels lying on the same planar patch, which makes batch annotation much easier than if they were randomly distributed in the volume. The planar patch is found using a branch-and-bound algorithm that finds a patch with the most informative instances. We evaluate our approach on Electron Microscopy and Magnetic Resonance image volumes, as well as on regular images of horses and faces. We demonstrate a substantial performance increase over state-of-the-art approaches.

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