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Register a new userCIA-Net: Robust Nuclei Instance Segmentation with Contour-aware Information Aggregation
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Added by
Yanning Zhou
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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Accurate segmenting nuclei instances is a crucial step in computer-aided image analysis to extract rich features for cellular estimation and following diagnosis as well as treatment. While it still remains challenging because the wide existence of nuclei clusters, along with the large morphological variances among different organs make nuclei instance segmentation susceptible to over-/under-segmentation. Additionally, the inevitably subjective annotating and mislabeling prevent the network learning from reliable samples and eventually reduce the generalization capability for robustly segmenting unseen organ nuclei. To address these issues, we propose a novel deep neural network, namely Contour-aware Informative Aggregation Network (CIA-Net) with multi-level information aggregation module between two task-specific decoders. Rather than independent decoders, it leverages the merit of spatial and texture dependencies between nuclei and contour by bi-directionally aggregating task-specific features. Furthermore, we proposed a novel smooth truncated loss that modulates losses to reduce the perturbation from outliers. Consequently, the network can focus on learning from reliable and informative samples, which inherently improves the generalization capability. Experiments on the 2018 MICCAI challenge of Multi-Organ-Nuclei-Segmentation validated the effectiveness of our proposed method, surpassing all the other 35 competitive teams by a significant margin.
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Instance segmentation on point clouds is a fundamental task in 3D scene perception. In this work, we propose a concise clustering-based framework named HAIS, which makes full use of spatial relation of points and point sets. Considering clustering-based methods may result in over-segmentation or under-segmentation, we introduce the hierarchical aggregation to progressively generate instance proposals, i.e., point aggregation for preliminarily clustering points to sets and set aggregation for generating complete instances from sets. Once the complete 3D instances are obtained, a sub-network of intra-instance prediction is adopted for noisy points filtering and mask quality scoring. HAIS is fast (only 410ms per frame) and does not require non-maximum suppression. It ranks 1st on the ScanNet v2 benchmark, achieving the highest 69.9% AP50 and surpassing previous state-of-the-art (SOTA) methods by a large margin. Besides, the SOTA results on the S3DIS dataset validate the good generalization ability. Code will be available at https://github.com/hustvl/HAIS.
Most of the modern instance segmentation approaches fall into two categories: region-based approaches in which object bounding boxes are detected first and later used in cropping and segmenting instances; and keypoint-based approaches in which individual instances are represented by a set of keypoints followed by a dense pixel clustering around those keypoints. Despite the maturity of these two paradigms, we would like to report an alternative affinity-based paradigm where instances are segmented based on densely predicted affinities and graph partitioning algorithms. Such affinity-based approaches indicate that high-level graph features other than regions or keypoints can be directly applied in the instance segmentation task. In this work, we propose Deep Affinity Net, an effective affinity-based approach accompanied with a new graph partitioning algorithm Cascade-GAEC. Without bells and whistles, our end-to-end model results in 32.4% AP on Cityscapes val and 27.5% AP on test. It achieves the best single-shot result as well as the fastest running time among all affinity-based models. It also outperforms the region-based method Mask R-CNN.
Direct contour regression for instance segmentation is a challenging task. Previous works usually achieve it by learning to progressively refine the contour prediction or adopting a shape representation with limited expressiveness. In this work, we argue that the difficulty in regressing the contour points in one pass is mainly due to the ambiguity when discretizing a smooth contour into a polygon. To address the ambiguity, we propose a novel differentiable rendering-based approach named textbf{ContourRender}. During training, it first predicts a contour generated by an invertible shape signature, and then optimizes the contour with the more stable silhouette by converting it to a contour mesh and rendering the mesh to a 2D map. This method significantly improves the quality of contour without iterations or cascaded refinements. Moreover, as optimization is not needed during inference, the inference speed will not be influenced. Experiments show the proposed ContourRender outperforms all the contour-based instance segmentation approaches on COCO, while stays competitive with the iteration-based state-of-the-art on Cityscapes. In addition, we specifically select a subset from COCO val2017 named COCO ContourHard-val to further demonstrate the contour quality improvements. Codes, models, and dataset split will be released.
Multi-instance video object segmentation is to segment specific instances throughout a video sequence in pixel level, given only an annotated first frame. In this paper, we implement an effective fully convolutional networks with U-Net similar structure built on top of OSVOS fine-tuned layer. We use instance isolation to transform this multi-instance segmentation problem into binary labeling problem, and use weighted cross entropy loss and dice coefficient loss as our loss function. Our best model achieves F mean of 0.467 and J mean of 0.424 on DAVIS dataset, which is a comparable performance with the State-of-the-Art approach. But case analysis shows this model can achieve a smoother contour and better instance coverage, meaning it better for recall focused segmentation scenario. We also did experiments on other convolutional neural networks, including Seg-Net, Mask R-CNN, and provide insightful comparison and discussion.
Deep learning-based methods are gaining traction in digital pathology, with an increasing number of publications and challenges that aim at easing the work of systematically and exhaustively analyzing tissue slides. These methods often achieve very high accuracies, at the cost of requiring large annotated datasets to train. This requirement is especially difficult to fulfill in the medical field, where expert knowledge is essential. In this paper we focus on nuclei segmentation, which generally requires experienced pathologists to annotate the nuclear areas in gigapixel histological images. We propose an algorithm for instance segmentation that uses pseudo-label segmentations generated automatically from point annotations, as a method to reduce the burden for pathologists. With the generated segmentation masks, the proposed method trains a modified version of HoVer-Net model to achieve instance segmentation. Experimental results show that the proposed method is robust to inaccuracies in point annotations and comparison with Hover-Net trained with fully annotated instance masks shows that a degradation in segmentation performance does not always imply a degradation in higher order tasks such as tissue classification.
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