Collagen fiber orientations in bones, visible with Second Harmonic Generation (SHG) microscopy, represent the inner structure and its alteration due to influences like cancer. While analyses of these orientations are valuable for medical research, it is not feasible to analyze the needed large amounts of local orientations manually. Since we have uncertain borders for these local orientations only rough regions can be segmented instead of a pixel-wise segmentation. We analyze the effect of these uncertain borders on human performance by a user study. Furthermore, we compare a variety of 2D and 3D methods such as classical approaches like Fourier analysis with state-of-the-art deep neural networks for the classification of local fiber orientations. We present a general way to use pretrained 2D weights in 3D neural networks, such as Inception-ResNet-3D a 3D extension of Inception-ResNet-v2. In a 10 fold cross-validation our two stage segmentation based on Inception-ResNet-3D and transferred 2D ImageNet weights achieves a human comparable accuracy.
However, the current state-of-the-art approaches for image classification and semantic segmentation have two major drawbacks in the context of uncertain local fiber orientation classification. We have 3D data and a high uncertainty for the borders. Most research focuses on 2D data while @cite_12 showed that it is beneficial to use the 3D information for organ segmentation. Networks like PointNet @cite_8 can classify 3D point clouds yet they do not consider dense 3D input as we have. The network 3D-U-Net @cite_16 represents an expansion of U-Net to 3D data. It is typically used to segment 3D objects like organs @cite_16 . This fixes the first drawback while the second one remains. Objects with uncertain borders like our fiber orientations are not well represented.
@cite_16 @cite_12 @cite_8
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Unlike on images, semantic learning on 3D point clouds using a deep network is challenging due to the naturally unordered data structure. Among existing works, PointNet has achieved promising results by directly learning on point sets. However, it does not take full advantage of a point's local neighborhood that contains fine-grained structural information which turns out to be helpful towards better semantic learning. In this regard, we present two new operations to improve PointNet with a more efficient exploitation of local structures. The first one focuses on local 3D geometric structures. In analogy to a convolution kernel for images, we define a point-set kernel as a set of learnable 3D points that jointly respond to a set of neighboring data points according to their geometric affinities measured by kernel correlation, adapted from a similar technique for point cloud registration. The second one exploits local high-dimensional feature structures by recursive feature aggregation on a nearest-neighbor-graph computed from 3D positions. Experiments show that our network can efficiently capture local information and robustly achieve better performances on major datasets. Our code is available at this http URL Unlike on images, semantic learning on 3D point clouds using a deep network is challenging due to the naturally unordered data structure. Among existing works, PointNet has achieved promising results by directly learning on point sets. However, it does not take full advantage of a point's local neighborhood that contains fine-grained structural information which turns out to be helpful towards better semantic learning. In this regard, we present two new operations to improve PointNet with a more efficient exploitation of local structures. The first one focuses on local 3D geometric structures. In analogy to a convolution kernel for images, we define a point-set kernel as a set of learnable 3D points that jointly respond to a set of neighboring data points according to their geometric affinities measured by kernel correlation, adapted from a similar technique for point cloud registration. The second one exploits local high-dimensional feature structures by recursive feature aggregation on a nearest-neighbor-graph computed from 3D positions. Experiments show that our network can efficiently capture local information and robustly achieve better performances on major datasets. Our code is available at http: www.merl.com research license#KCNet Semantic parsing of large-scale 3D point clouds is an important research topic in computer vision and remote sensing fields. Most existing approaches utilize hand-crafted features for each modality independently and combine them in a heuristic manner. They often fail to consider the consistency and complementary information among features adequately, which makes them difficult to capture high-level semantic structures. The features learned by most of the current deep learning methods can obtain high-quality image classification results. However, these methods are hard to be applied to recognize 3D point clouds due to unorganized distribution and various point density of data. In this paper, we propose a 3DCNN-DQN-RNN method which fuses the 3D convolutional neural network (CNN), Deep Q-Network (DQN) and Residual recurrent neural network (RNN)for an efficient semantic parsing of large-scale 3D point clouds. In our method, an eye window under control of the 3D CNN and DQN can localize and segment the points of the object's class efficiently. The 3D CNN and Residual RNN further extract robust and discriminative features of the points in the eye window, and thus greatly enhance the parsing accuracy of large-scale point clouds. Our method provides an automatic process that maps the raw data to the classification results. It also integrates object localization, segmentation and classification into one framework. Experimental results demonstrate that the proposed method outperforms the state-of-the-art point cloud classification methods. This paper proposes RIU-Net (for Range-Image U-Net), the adaptation of a popular semantic segmentation network for the semantic segmentation of a 3D LiDAR point cloud. The point cloud is turned into a 2D range-image by exploiting the topology of the sensor. This image is then used as input to a U-net. This architecture has already proved its efficiency for the task of semantic segmentation of medical images. We demonstrate how it can also be used for the accurate semantic segmentation of a 3D LiDAR point cloud and how it represents a valid bridge between image processing and 3D point cloud processing. Our model is trained on range-images built from KITTI 3D object detection dataset. Experiments show that RIU-Net, despite being very simple, offers results that are comparable to the state-of-the-art of range-image based methods. Finally, we demonstrate that this architecture is able to operate at 90fps on a single GPU, which enables deployment for real-time segmentation.