skip to main content

Title: CONTEXT-REFINED NEURAL CELL INSTANCE SEGMENTATION
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 cell 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.
Authors:
; ; ; ; ;
Award ID(s):
1747778
Publication Date:
NSF-PAR ID:
10105305
Journal Name:
2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019)
Sponsoring Org:
National Science Foundation
More Like this
  1. 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
  2. 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
  3. Entity types and textual context are essential properties for sentence-level relation extraction (RE). Existing work only encodes these properties within individual instances, which limits the performance of RE given the insufficient features in a single sentence. In contrast, we model these properties from the whole dataset and use the dataset-level information to enrich the semantics of every instance. We propose the GraphCache (Graph Neural Network as Caching) module, that propagates the features across sentences to learn better representations for RE. GraphCache aggregates the features from sentences in the whole dataset to learn global representations of properties, and use them tomore »augment the local features within individual sentences. The global property features act as dataset-level prior knowledge for RE, and a complement to the sentence-level features. Inspired by the classical caching technique in computer systems, we develop GraphCache to update the property representations in an online manner. Overall, GraphCache yields significant effectiveness gains on RE and enables efficient message passing across all sentences in the dataset.« less
  4. Vedaldi, A. (Ed.)
    In state-of-the-art deep neural networks, both feature normalization and feature attention have become ubiquitous. They are usually studied as separate modules, however. In this paper, we propose a light-weight integration between the two schema and present Attentive Normalization (AN). Instead of learning a single affine transformation, AN learns a mixture of affine transformations and utilizes their weighted-sum as the final affine transformation applied to re-calibrate features in an instance-specific way. The weights are learned by leveraging channel-wise feature attention. In experiments, we test the proposed AN using four representative neural architectures. In the ImageNet-1000 classification benchmark and the MS-COCO 2017more »object detection and instance segmentation benchmark. AN obtains consistent performance improvement for different neural architectures in both benchmarks with absolute increase of top-1 accuracy in ImageNet-1000 between 0.5\% and 2.7\%, and absolute increase up to 1.8\% and 2.2\% for bounding box and mask AP in MS-COCO respectively. We observe that the proposed AN provides a strong alternative to the widely used Squeeze-and-Excitation (SE) module. The source codes are publicly available at \href{https://github.com/iVMCL/AOGNet-v2}{the ImageNet Classification Repo} and \href{https://github.com/iVMCL/AttentiveNorm\_Detection}{the MS-COCO Detection and Segmentation Repo}.« less
  5. Most existing methods handle cell instance segmentation problems directly without relying on additional detection boxes. These methods generally fails to separate touching cells due to the lack of global understanding of the objects. In contrast, box-based instance segmentation solves this problem by combining object detection with segmentation. However, existing methods typically utilize anchor box-based detectors, which would lead to inferior instance segmentation performance due to the class imbalance issue. In this paper, we propose a new box-based cell instance segmentation method. In particular, we first detect the five pre-defined points of a cell via keypoints detection. Then we group thesemore »points according to a keypoint graph and subsequently extract the bounding box for each cell. Finally, cell segmentation is performed on feature maps within the bounding boxes. We validate our method on two cell datasets with distinct object shapes, and empirically demonstrate the superiority of our method compared to other instance segmentation techniques.« less