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Medical image segmentation has been so far achieving promising results with Convolutional Neural Networks (CNNs). However, it is arguable that in traditional CNNs, its pooling layer tends to discard important information such as positions. Moreover, CNNs are sensitive to rotation and ane transformation. Capsule network is a data-ecient network design proposed to overcome such limitations by replacing pooling layers with dynamic routing and convolutional strides, which aims to preserve the part-whole relationships. Capsule network has shown a great performance in image recognition and natural language processing, but applications for medical image segmentation, particularly volumetric image segmentation, has been limited. In this work, we propose 3D-UCaps, a 3D voxel-based Capsule network for medical volumetric image segmentation. We build the concept of capsules into a CNN by designing a network with two pathways: the rst pathway is encoded by 3D Capsule blocks, whereas the second pathway is decoded by 3D CNNs blocks. 3D-UCaps, therefore inherits the merits from both Capsule network to preserve the spatial relationship and CNNs to learn visual representation. We conducted experiments on various datasets to demonstrate the robustness of 3D-UCaps including iSeg-2017, LUNA16, Hippocampus, and Cardiac, where our method outperforms previous Capsule networks and 3D-Unets. 

Medical image analysis using deep learning has recently been prevalent, showing great performance for various downstream tasks including medical image segmentation and its sibling, volumetric image segmentation. Particularly, a typical volumetric segmentation network strongly relies on a voxel grid representation which treats volumetric data as a stack of individual voxel `slices', which allows learning to segment a voxel grid to be as straightforward as extending existing image-based segmentation networks to the 3D domain. However, using a voxel grid representation requires a large memory footprint, expensive test-time and limiting the scalability of the solutions. In this paper, we propose Point-Unet, a novel method that incorporates the eciency of deep learning with 3D point clouds into volumetric segmentation. Our key idea is to rst predict the regions of interest in the volume by learning an attentional probability map, which is then used for sampling the volume into a sparse point cloud that is subsequently segmented using a point-based neural network. We have conducted the experiments on the medical volumetric segmentation task with both a small-scale dataset Pancreas and large-scale datasets BraTS18, BraTS19, and BraTS20 challenges. A comprehensive benchmark on dierent metrics has shown that our context-aware Point-Unet robustly outperforms the SOTA voxel-based networks at both accuracies, memory usage during training, and time consumption during testing. 

Medical image segmentation is one of the most challenging tasks in medical image analysis and has been widely developed for many clinical applications. Most of the existing metrics have been first designed for natural images and then extended to medical images. While object surface plays an important role in medical segmentation and quantitative analysis i.e. analyze brain tumor surface, measure gray matter volume, most of the existing metrics are limited when it comes to analyzing the object surface, especially to tell about surface smoothness or roughness of a given volumetric object or to analyze the topological errors. In this paper, we first analysis both pros and cons of all existing medical image segmentation metrics, specially on volumetric data. We then propose an appropriate roughness index and roughness distance for medical image segmentation analysis and evaluation. Our proposed method addresses two kinds of segmentation errors, i.e. (i) topological errors on boundary/surface and (ii) irregularities on the boundary/surface. The contribution of this work is four-fold: (i) detect irregular spikes/holes on a surface, (ii) propose roughness index to measure surface roughness of a given object, (iii) propose a roughness distance to measure the distance of two boundaries/surfaces by utilizing the proposed roughness index and (iv) suggest an algorithm which helps to remove the irregular spikes/holes to smooth the surface. Our proposed roughness index and roughness distance are built upon the solid surface roughness parameter which has been successfully developed in the civil engineering.