A finite element-based image segmentation strategy enhanced by an anisotropic mesh adaptation procedure is presented. The methodology relies on a split Bregman algorithm for the minimisation of a region-based energy functional and on an anisotropic recovery-based error estimate to drive mesh adaptation. More precisely, a Bayesian energy functional is considered to account for image spatial information, ensuring that the methodology is able to identify inhomogeneous spatial patterns in complex images. In addition, the anisotropic mesh adaptation guarantees a sharp detection of the interface between background and foreground of the image, with a reduced number of degrees of freedom. The resulting split-adapt Bregman algorithm is tested on a set of real images showing the accuracy and robustness of the method, even in the presence of Gaussian, salt and pepper and speckle noise.
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In this paper, we propose a multi-stage image segmentation framework that incorporates a weighted difference of anisotropic and isotropic total variation (AITV). The segmentation framework generally consists of two stages: smoothing and thresholding, thus referred to as SaT. In the first stage, a smoothed image is obtained by an AITV-regularized Mumford-Shah (MS) model, which can be solved efficiently by the alternating direction method of multipliers (ADMM) with a closed-form solution of a proximal operator of the $\ell_1 -\alpha \ell_2$ regularizer. Convergence of the ADMM algorithm is analyzed. In the second stage, we threshold the smoothed image by $k$-means clustering to obtain the final segmentation result. Numerical experiments demonstrate that the proposed segmentation framework is versatile for both grayscale and color images, efficient in producing high-quality segmentation results within a few seconds, and robust to input images that are corrupted with noise, blur, or both. We compare the AITV method with its original convex and nonconvex TV$^p (0<p<1)$ counterparts, showcasing the qualitative and quantitative advantages of our proposed method.
Recently, deep neural networks have gained increasing popularity in the field of time series forecasting. A primary reason for their success is their ability to effectively capture complex temporal dynamics across multiple related time series. The advantages of these deep forecasters only start to emerge in the presence of a sufficient amount of data. This poses a challenge for typical forecasting problems in practice, where there is a limited number of time series or observations per time series, or both. To cope with this data scarcity issue, we propose a novel domain adaptation framework, Domain Adaptation Forecaster (DAF). DAF leverages statistical strengths from a relevant domain with abundant data samples (source) to improve the performance on the domain of interest with limited data (target). In particular, we use an attention-based shared module with a domain discriminator across domains and private modules for individual domains. We induce domain-invariant latent features (queries and keys) and retrain domain-specific features (values) simultaneously to enable joint training of forecasters on source and target domains. A main insight is that our design of aligning keys allows the target domain to leverage source time series even with different characteristics. Extensive experiments on various domains demonstrate that our proposed method outperforms state-of-the-art baselines on synthetic and real-world datasets, and ablation studies verify the effectiveness of our design choices.
Accurate segmentation of the prostate from magnetic resonance (MR) images provides useful information for prostate cancer diagnosis and treatment. However, automated prostate segmentation from 3D MR images still faces several challenges. For instance, a lack of clear edge between the prostate and other anatomical structures makes it challenging to accurately extract the boundaries. The complex background texture and large variation in size, shape and intensity distribution of the prostate itself make segmentation even further complicated. With deep learning, especially convolutional neural networks (CNNs), emerging as commonly used methods for medical image segmentation, the difficulty in obtaining large number of annotated medical images for training CNNs has become much more pronounced that ever before. Since large-scale dataset is one of the critical components for the success of deep learning, lack of sufficient training data makes it difficult to fully train complex CNNs. To tackle the above challenges, in this paper, we propose a boundary-weighted domain adaptive neural network (BOWDA-Net). To make the network more sensitive to the boundaries during segmentation, a boundary-weighted segmentation loss (BWL) is proposed. Furthermore, an advanced boundary-weighted transfer leaning approach is introduced to address the problem of small medical imaging datasets. We evaluate our proposed model on the publicly available MICCAI 2012 Prostate MR Image Segmentation (PROMISE12) challenge dataset. Our experimental results demonstrate that the proposed model is more sensitive to boundary information and outperformed other state-of-the-art methods.
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.
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.
Tumor detection in biomedical imaging is a time-consuming process for medical professionals and is not without errors. Thus in recent decades, researchers have developed algorithmic techniques for image processing using a wide variety of mathematical methods, such as statistical modeling, variational techniques, and machine learning. In this paper, we propose a semi-automatic method for liver segmentation of 2D CT scans into three labels denoting healthy, vessel, or tumor tissue based on graph cuts. First, we create a feature vector for each pixel in a novel way that consists of the 59 intensity values in the time series data and propose a simplified perimeter cost term in the energy functional. We normalize the data and perimeter terms in the functional to expedite the graph cut without having to optimize the scaling parameter $\lambda$. In place of a training process, predetermined tissue means are computed based on sample regions identified by expert radiologists. The proposed method also has the advantage of being relatively simple to implement computationally. It was evaluated against the ground truth on a clinical CT dataset of 10 tumors and yielded segmentations with a mean Dice similarity coefficient (DSC) of .77 and mean volume overlap error (VOE) of 36.7%. The average processing time was 1.25 minutes per slice.
In two-phase image segmentation, convex relaxation has allowed global minimisers to be computed for a variety of data fitting terms. Many efficient approaches exist to compute a solution quickly. However, we consider whether the nature of the data fitting in this formulation allows for reasonable assumptions to be made about the solution that can improve the computational performance further. In particular, we employ a well known dual formulation of this problem and solve the corresponding equations in a restricted domain. We present experimental results that explore the dependence of the solution on this restriction and quantify imrovements in the computational performance. This approach can be extended to analogous methods simply and could provide an efficient alternative for problems of this type.
In this work, we evaluate the use of superpixel pooling layers in deep network architectures for semantic segmentation. Superpixel pooling is a flexible and efficient replacement for other pooling strategies that incorporates spatial prior information. We propose a simple and efficient GPU-implementation of the layer and explore several designs for the integration of the layer into existing network architectures. We provide experimental results on the IBSR and Cityscapes dataset, demonstrating that superpixel pooling can be leveraged to consistently increase network accuracy with minimal computational overhead. Source code is available at //github.com/bermanmaxim/superpixPool
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.
In this paper we introduce a covariance framework for the analysis of EEG and MEG data that takes into account observed temporal stationarity on small time scales and trial-to-trial variations. We formulate a model for the covariance matrix, which is a Kronecker product of three components that correspond to space, time and epochs/trials, and consider maximum likelihood estimation of the unknown parameter values. An iterative algorithm that finds approximations of the maximum likelihood estimates is proposed. We perform a simulation study to assess the performance of the estimator and investigate the influence of different assumptions about the covariance factors on the estimated covariance matrix and on its components. Apart from that, we illustrate our method on real EEG and MEG data sets. The proposed covariance model is applicable in a variety of cases where spontaneous EEG or MEG acts as source of noise and realistic noise covariance estimates are needed for accurate dipole localization, such as in evoked activity studies, or where the properties of spontaneous EEG or MEG are themselves the topic of interest, such as in combined EEG/fMRI experiments in which the correlation between EEG and fMRI signals is investigated.
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