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  1. Temporal correlation in dynamic magnetic resonance imaging (MRI), such as cardiac MRI, is in- formative and important to understand motion mechanisms of body regions. Modeling such in- formation into the MRI reconstruction process produces temporally coherent image sequence and reduces imaging artifacts and blurring. However, existing deep learning based approaches neglect motion information during the reconstruction procedure, while traditional motion-guided methods are hindered by heuristic parameter tuning and long inference time. We propose a novel dynamic MRI reconstruction approach called MODRN that unitizes deep neural networks with motion in- formation to improve reconstruction quality. The central idea is to decomposemore »the motion-guided optimization problem of dynamic MRI reconstruction into three components: dynamic reconstruc- tion, motion estimation and motion compensation. Extensive experiments have demonstrated the effectiveness of our proposed approach compared to other state-of-the-art approaches.« less
  2. Existing neural cell tracking methods generally use the morphology cell features for data association. However, these features are limited to the quality of cell segmentation and are prone to errors for mitosis determination. To over- come these issues, in this work we propose an online multi- object tracking method that leverages both cell appearance and motion features for data association. In particular, we propose a supervised blob-seed network (BSNet) to predict the cell appearance features and an unsupervised optical flow network (UnFlowNet) for capturing the cell motions. The data association is then solved using the Hungarian al- gorithm. Experimental evaluationmore »shows that our approach achieves better performance than existing neural cell track- ing methods.« less
  3. Nuclei segmentation is a fundamental task in histopathological image analysis. Typically, such segmentation tasks require significant effort to manually generate pixel-wise annotations for fully supervised training. To alleviate the manual effort, in this paper we propose a novel approach using points only annotation. Two types of coarse labels with complementary information are derived from the points annotation, and are then utilized to train a deep neural network. The fully- connected conditional random field loss is utilized to further refine the model without introducing extra computational complexity during inference. Experimental results on two nuclei segmentation datasets reveal that the proposed methodmore »is able to achieve competitive performance compared to the fully supervised counterpart and the state-of-the-art methods while requiring significantly less annotation effort. Our code is publicly available.« less
  4. We consider an MRI reconstruction problem with input of k-space data at a very low undersampled rate. This can prac- tically benefit patient due to reduced time of MRI scan, but it is also challenging since quality of reconstruction may be compromised. Currently, deep learning based methods dom- inate MRI reconstruction over traditional approaches such as Compressed Sensing, but they rarely show satisfactory performance in the case of low undersampled k-space data. One explanation is that these methods treat channel-wise fea- tures equally, which results in degraded representation ability of the neural network. To solve this problem, we propose amore »new model called MRI Cascaded Channel-wise Attention Network (MICCAN), highlighted by three components: (i) a variant of U-net with Channel-wise Attention (UCA) mod- ule, (ii) a long skip connection and (iii) a combined loss. Our model is able to attend to salient information by filtering irrelevant features and also concentrate on high-frequency in- formation by enforcing low-frequency information bypassed to the final output. We conduct both quantitative evaluation and qualitative analysis of our method on a cardiac dataset. The experiment shows that our method achieves very promis- ing results in terms of three common metrics on the MRI reconstruction with low undersampled k-space data. Code is public available« less
  5. Neural cell instance segmentation serves as a valuable tool for the study of neural cell behaviors. In general, the instance segmentation methods compute the region of interest (ROI) through a detection module, where the segmentation is sub- sequently performed. To precisely segment the neural cells, especially their tiny and slender structures, existing work em- ploys a u-net structure to preserve the low-level details and encode the high-level semantics. However, such method is insufficient for differentiating the adjacent cells when large parts of them are included in the same cropped ROI. To solve this problem, we propose a context-refined neural cellmore »instance segmentation model that learns to suppress the back- ground information. In particular, we employ a light-weight context refinement module to recalibrate the deep features and focus the model exclusively on the target cell within each cropped ROI. The proposed model is efficient and accurate, and experimental results demonstrate its superiority com- pared to the state-of-the-arts.« less
  6. Nuclei segmentation and classification are two important tasks in the histopathology image analysis, because the mor- phological features of nuclei and spatial distributions of dif- ferent types of nuclei are highly related to cancer diagnosis and prognosis. Existing methods handle the two problems independently, which are not able to obtain the features and spatial heterogeneity of different types of nuclei at the same time. In this paper, we propose a novel deep learning based method which solves both tasks in a unified framework. It can segment individual nuclei and classify them into tumor, lymphocyte and stroma nuclei. Perceptual loss ismore »utilized to enhance the segmentation of details. We also take advantages of transfer learning to promote the training of deep neural net- works on a relatively small lung cancer dataset. Experimental results prove the effectiveness of the proposed method. The code is publicly available« less
  7. Instance segmentation of neural cells plays an important role in brain study. However, this task is challenging due to the special shapes and behaviors of neural cells. Existing methods are not precise enough to capture their tiny structures, e.g., filopodia and lamellipodia, which are critical to the understanding of cell interaction and behavior. To this end, we propose a novel deep multi-task learning model to jointly detect and segment neural cells instance-wise. Our method is built upon SSD, with ResNet101 as the backbone to achieve both high detection accuracy and fast speed. Furthermore, unlike existing works which tend to producemore »wavy and inaccurate boundaries, we embed a deconvolution module into SSD to better capture details. Experiments on a dataset of neural cell microscopic images show that our method is able to achieve better per- formance in terms of accuracy and efficiency, comparing favorably with current state-of-the-art methods.« less
  8. Accurate cell instance segmentation plays an important role in the study of neural cell interactions, which are critical for understanding the development of brain. These interactions are performed through the filopodia and lamellipodia of neural cells, which are extremely tiny structures and as a result render most existing instance segmentation methods powerless to precisely capture them. To solve this issue, in this paper we present a novel hierarchical neural network comprising object detection and segmentation modules. Compared to previous work, our model is able to efficiently share and make full use of the information at different levels between the twomore »modules. Our method is simple yet powerful, and experimental results show that it captures the contours of neural cells, especially the filopodia and lamellipodia, with high accuracy, and outperforms recent state of the art by a large margin.« less