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.
Semantic segmentation gives a classification for every pixel in an image and is an extension of a classification problem. @cite_24 first proposed to use fully convolutional networks to solve semantic segmentation. U-Net @cite_25 is a network for semantic segmentation which was designed for medical images. Often semantic segmentation networks consist of a down- and a upsampling part @cite_24 @cite_25 .
@cite_24 @cite_25
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Semantic segmentation requires a detailed labeling of image pixels by object category. Information derived from local image patches is necessary to describe the detailed shape of individual objects. However, this information is ambiguous and can result in noisy labels. Global inference of image content can instead capture the general semantic concepts present. We advocate that high-recall holistic inference of image concepts provides valuable information for detailed pixel labeling. We build a two-stream neural network architecture that facilitates information flow from holistic information to local pixels, while keeping common image features shared among the low-level layers of both the holistic analysis and segmentation branches. We empirically evaluate our network on four standard semantic segmentation datasets. Our network obtains state-of-the-art performance on PASCAL-Context and NYUDv2, and ablation studies verify its effectiveness on ADE20K and SIFT-Flow. Recent work has made significant progress in improving spatial resolution for pixelwise labeling with Fully Convolutional Network (FCN) framework by employing Dilated Atrous convolution, utilizing multi-scale features and refining boundaries. In this paper, we explore the impact of global contextual information in semantic segmentation by introducing the Context Encoding Module, which captures the semantic context of scenes and selectively highlights class-dependent featuremaps. The proposed Context Encoding Module significantly improves semantic segmentation results with only marginal extra computation cost over FCN. Our approach has achieved new state-of-the-art results 51.7 mIoU on PASCAL-Context, 85.9 mIoU on PASCAL VOC 2012. Our single model achieves a final score of 0.5567 on ADE20K test set, which surpass the winning entry of COCO-Place Challenge in 2017. In addition, we also explore how the Context Encoding Module can improve the feature representation of relatively shallow networks for the image classification on CIFAR-10 dataset. Our 14 layer network has achieved an error rate of 3.45 , which is comparable with state-of-the-art approaches with over 10 times more layers. The source code for the complete system are publicly available. Recent work has made significant progress in improving spatial resolution for pixelwise labeling with Fully Convolutional Network (FCN) framework by employing Dilated Atrous convolution, utilizing multi-scale features and refining boundaries. In this paper, we explore the impact of global contextual information in semantic segmentation by introducing the Context Encoding Module, which captures the semantic context of scenes and selectively highlights class-dependent featuremaps. The proposed Context Encoding Module significantly improves semantic segmentation results with only marginal extra computation cost over FCN. Our approach has achieved new state-of-the-art results 51.7 mIoU on PASCAL-Context, 85.9 mIoU on PASCAL VOC 2012. Our single model achieves a final score of 0.5567 on ADE20K test set, which surpasses the winning entry of COCO-Place Challenge 2017. In addition, we also explore how the Context Encoding Module can improve the feature representation of relatively shallow networks for the image classification on CIFAR-10 dataset. Our 14 layer network has achieved an error rate of 3.45 , which is comparable with state-of-the-art approaches with over 10A— more layers. The source code for the complete system are publicly available1. Pixel-level labelling tasks, such as semantic segmentation, play a central role in image understanding. Recent approaches have attempted to harness the capabilities of deep learning techniques for image recognition to tackle pixel-level labelling tasks. One central issue in this methodology is the limited capacity of deep learning techniques to delineate visual objects. To solve this problem, we introduce a new form of convolutional neural network that combines the strengths of Convolutional Neural Networks (CNNs) and Conditional Random Fields (CRFs)-based probabilistic graphical modelling. To this end, we formulate Conditional Random Fields with Gaussian pairwise potentials and mean-field approximate inference as Recurrent Neural Networks. This network, called CRF-RNN, is then plugged in as a part of a CNN to obtain a deep network that has desirable properties of both CNNs and CRFs. Importantly, our system fully integrates CRF modelling with CNNs, making it possible to train the whole deep network end-to-end with the usual back-propagation algorithm, avoiding offline post-processing methods for object delineation. We apply the proposed method to the problem of semantic image segmentation, obtaining top results on the challenging Pascal VOC 2012 segmentation benchmark.