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Background. Functional assessment of right ventricles (RV) using gated myocardial perfusion single-photon emission computed tomography (MPS) heavily relies on the precise extraction of right ventricular contours. In this paper, we present a new deep learning model integrating both the spatial and temporal features in SPECT images to perform the segmentation of RV epicardium and endocardium. Methods. By integrating the spatial features from each cardiac frame of gated MPS and the temporal features from the sequential cardiac frames of the gated MPS, we develop a Spatial-Temporal V-Net (S-T-V-Net) for automatic extraction of RV endocardial and epicardial contours. In the S-T-V-Net, a V-Net is employed to hierarchically extract spatial features, and convolutional long-term short-term memory (ConvLSTM) units are added to the skip-connection pathway to extract the temporal features. The input of the S-T-V-Net is an ECG-gated sequence of the SPECT images and the output is the probability map of the endocardial or epicardial masks. A Dice similarity coefficient (DSC) loss which penalizes the discrepancy between the model prediction and the ground truth is adopted to optimize the segmentation model. Results. Our segmentation model was trained and validated on a retrospective dataset with 34 subjects, and the cardiac cycle of each subject was divided into 8 gates. The proposed ST-V-Net achieved a DSC of 0.7924 and 0.8227 for the RV endocardium and epicardium, respectively. The mean absolute error, the mean squared error, and the Pearson correlation coefficient of the RV ejection fraction between the ground truth and the model prediction are 0.0907, 0.0130 and 0.8411. Conclusion. The results demonstrate that the proposed ST-V-Net is an effective model for RV segmentation. It has great promise for clinical use in RV functional assessment.

Video instance segmentation (VIS) is the task that requires simultaneously classifying, segmenting and tracking object instances of interest in video. Recent methods typically develop sophisticated pipelines to tackle this task. Here, we propose a new video instance segmentation framework built upon Transformers, termed VisTR, which views the VIS task as a direct end-to-end parallel sequence decoding/prediction problem. Given a video clip consisting of multiple image frames as input, VisTR outputs the sequence of masks for each instance in the video in order directly. At the core is a new, effective instance sequence matching and segmentation strategy, which supervises and segments instances at the sequence level as a whole. VisTR frames the instance segmentation and tracking in the same perspective of similarity learning, thus considerably simplifying the overall pipeline and is significantly different from existing approaches. Without bells and whistles, VisTR achieves the highest speed among all existing VIS models, and achieves the best result among methods using single model on the YouTube-VIS dataset. For the first time, we demonstrate a much simpler and faster video instance segmentation framework built upon Transformers, achieving competitive accuracy. We hope that VisTR can motivate future research for more video understanding tasks.

We present our submission to the semantic segmentation contest of the Robust Vision Challenge held at ECCV 2020. The contest requires submitting the same model to seven benchmarks from three different domains. Our approach is based on the SwiftNet architecture with pyramidal fusion. We address inconsistent taxonomies with a single-level 193-dimensional softmax output. We strive to train with large batches in order to stabilize optimization of a hard recognition problem, and to favour smooth evolution of batchnorm statistics. We achieve this by implementing a custom backward step through log-sum-prob loss, and by using small crops before freezing the population statistics. Our model ranks first on the RVC semantic segmentation challenge as well as on the WildDash 2 leaderboard. This suggests that pyramidal fusion is competitive not only for efficient inference with lightweight backbones, but also in large-scale setups for multi-domain application.

In this paper, we address the problem of semantic segmentation and focus on the context aggregation strategy for robust segmentation. Our motivation is that the label of a pixel is the category of the object that the pixel belongs to. We present a simple yet effective approach, object-contextual representations, characterizing a pixel by exploiting the representation of the corresponding object class. First, we construct object regions based on a feature map supervised by the ground-truth segmentation, and then compute the object region representations. Second, we compute the representation similarity between each pixel and each object region, and augment the representation of each pixel with an object contextual representation, which is a weighted aggregation of all the object region representations according to their similarities with the pixel. We empirically demonstrate that the proposed approach achieves competitive performance on six challenging semantic segmentation benchmarks: Cityscapes, ADE20K, LIP, PASCAL VOC 2012, PASCAL-Context and COCO-Stuff. Notably, we achieved the \nth{2} place on the Cityscapes leader-board with a single model.

Despite the state-of-the-art performance for medical image segmentation, deep convolutional neural networks (CNNs) have rarely provided uncertainty estimations regarding their segmentation outputs, e.g., model (epistemic) and image-based (aleatoric) uncertainties. In this work, we analyze these different types of uncertainties for CNN-based 2D and 3D medical image segmentation tasks. We additionally propose a test-time augmentation-based aleatoric uncertainty to analyze the effect of different transformations of the input image on the segmentation output. Test-time augmentation has been previously used to improve segmentation accuracy, yet not been formulated in a consistent mathematical framework. Hence, we also propose a theoretical formulation of test-time augmentation, where a distribution of the prediction is estimated by Monte Carlo simulation with prior distributions of parameters in an image acquisition model that involves image transformations and noise. We compare and combine our proposed aleatoric uncertainty with model uncertainty. Experiments with segmentation of fetal brains and brain tumors from 2D and 3D Magnetic Resonance Images (MRI) showed that 1) the test-time augmentation-based aleatoric uncertainty provides a better uncertainty estimation than calculating the test-time dropout-based model uncertainty alone and helps to reduce overconfident incorrect predictions, and 2) our test-time augmentation outperforms a single-prediction baseline and dropout-based multiple predictions.

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.

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.

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.

In this paper we propose an effective non-rigid object tracking method based on spatial-temporal consistent saliency detection. In contrast to most existing trackers that use a bounding box to specify the tracked target, the proposed method can extract the accurate regions of the target as tracking output, which achieves better description of the non-rigid objects while reduces background pollution to the target model. Furthermore, our model has several unique features. First, a tailored deep fully convolutional neural network (TFCN) is developed to model the local saliency prior for a given image region, which not only provides the pixel-wise outputs but also integrates the semantic information. Second, a multi-scale multi-region mechanism is proposed to generate local region saliency maps that effectively consider visual perceptions with different spatial layouts and scale variations. Subsequently, these saliency maps are fused via a weighted entropy method, resulting in a final discriminative saliency map. Finally, we present a non-rigid object tracking algorithm based on the proposed saliency detection method by utilizing a spatial-temporal consistent saliency map (STCSM) model to conduct target-background classification and using a simple fine-tuning scheme for online updating. Numerous experimental results demonstrate that the proposed algorithm achieves competitive performance in comparison with state-of-the-art methods for both saliency detection and visual tracking, especially outperforming other related trackers on the non-rigid object tracking datasets.

Image segmentation is considered to be one of the critical tasks in hyperspectral remote sensing image processing. Recently, convolutional neural network (CNN) has established itself as a powerful model in segmentation and classification by demonstrating excellent performances. The use of a graphical model such as a conditional random field (CRF) contributes further in capturing contextual information and thus improving the segmentation performance. In this paper, we propose a method to segment hyperspectral images by considering both spectral and spatial information via a combined framework consisting of CNN and CRF. We use multiple spectral cubes to learn deep features using CNN, and then formulate deep CRF with CNN-based unary and pairwise potential functions to effectively extract the semantic correlations between patches consisting of three-dimensional data cubes. Effective piecewise training is applied in order to avoid the computationally expensive iterative CRF inference. Furthermore, we introduce a deep deconvolution network that improves the segmentation masks. We also introduce a new dataset and experimented our proposed method on it along with several widely adopted benchmark datasets to evaluate the effectiveness of our method. By comparing our results with those from several state-of-the-art models, we show the promising potential of our method.