Due to the increasing availability of whole slide scanners facilitating digitization of histopathological tissue, there is a strong demand for the development of computer based image analysis systems. In this work, the focus is on the segmentation of the glomeruli constituting a highly relevant structure in renal histopathology, which has not been investigated before in combination with CNNs. We propose two different CNN cascades for segmentation applications with sparse objects. These approaches are applied to the problem of glomerulus segmentation and compared with conventional fully-convolutional networks. Overall, with the best performing cascade approach, single CNNs are outperformed and a pixel-level Dice similarity coefficient of 0.90 is obtained. Combined with qualitative and further object-level analyses the obtained results are assessed as excellent also compared to recent approaches. In conclusion, we can state that especially one of the proposed cascade networks proved to be a highly powerful tool for segmenting the renal glomeruli providing best segmentation accuracies and also keeping the computing time at a low level.
@cite_5 applied a CNN for distinguishing between glomerulus and non-glomerulus texture based on previously extracted patches (similar to @cite_10 @cite_13 ). Although this application is distinct from a segmentation, it provides evidence for the principal effectiveness of CNNs for distinguishing between glomerulus and non-glomerulus tissue. Neural networks were also applied by @cite_4 with focus on a regression on WSI level. Specifically, the authors focussed on directly predicting the kidney function based on biopsies from patients suffering from chronic kidney disease without previously segmenting the glomeruli.
@cite_13 @cite_5 @cite_10 @cite_4
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Convolutional Neural Networks (CNN) are state-of-the-art models for many image classification tasks. However, to recognize cancer subtypes automatically, training a CNN on gigapixel resolution Whole Slide Tissue Images (WSI) is currently computationally impossible. The differentiation of cancer subtypes is based on cellular-level visual features observed on image patch scale. Therefore, we argue that in this situation, training a patch-level classifier on image patches will perform better than or similar to an image-level classifier. The challenge becomes how to intelligently combine patch-level classification results and model the fact that not all patches will be discriminative. We propose to train a decision fusion model to aggregate patch-level predictions given by patch-level CNNs, which to the best of our knowledge has not been shown before. Furthermore, we formulate a novel Expectation-Maximization (EM) based method that automatically locates discriminative patches robustly by utilizing the spatial relationships of patches. We apply our method to the classification of glioma and non-small-cell lung carcinoma cases into subtypes. The classification accuracy of our method is similar to the inter-observer agreement between pathologists. Although it is impossible to train CNNs on WSIs, we experimentally demonstrate using a comparable non-cancer dataset of smaller images that a patch-based CNN can outperform an image-based CNN. Abstract In this paper, we present a fully automatic brain tumor segmentation method based on Deep Neural Networks (DNNs). The proposed networks are tailored to glioblastomas (both low and high grade) pictured in MR images. By their very nature, these tumors can appear anywhere in the brain and have almost any kind of shape, size, and contrast. These reasons motivate our exploration of a machine learning solution that exploits a flexible, high capacity DNN while being extremely efficient. Here, we give a description of different model choices that we’ve found to be necessary for obtaining competitive performance. We explore in particular different architectures based on Convolutional Neural Networks (CNN), i.e. DNNs specifically adapted to image data. We present a novel CNN architecture which differs from those traditionally used in computer vision. Our CNN exploits both local features as well as more global contextual features simultaneously. Also, different from most traditional uses of CNNs, our networks use a final layer that is a convolutional implementation of a fully connected layer which allows a 40 fold speed up. We also describe a 2-phase training procedure that allows us to tackle difficulties related to the imbalance of tumor labels. Finally, we explore a cascade architecture in which the output of a basic CNN is treated as an additional source of information for a subsequent CNN. Results reported on the 2013 BRATS test data-set reveal that our architecture improves over the currently published state-of-the-art while being over 30 times faster. Convolutional neural networks (CNN) have been widely used for visual recognition tasks including semantic segmentation of images. While the existing methods consider uniformly sampled single-or multi-scale patches from the neighborhood of each voxel, this approach might be sub-optimal as it captures and processes unnecessary details far away from the center of the patch. We instead propose to train CNNs with non-uniformly sampled patches that allow a wider extent for the sampled patches. This results in more captured contextual information, which is in particular of interest for biomedical image analysis, where the anatomical location of imaging features are often crucial. We evaluate and compare this strategy for white matter hyperintensity segmentation on a test set of 46 MRI scans. We show that the proposed method not only outperforms identical CNNs with uniform patches of the same size (0.780 Dice coefficient compared to 0.736), but also gets very close to the performance of an independent human expert (0.796 Dice coefficient). Recently, very deep convolutional neural networks (CNNs) have shown outstanding performance in object recognition and have also been the first choice for dense classification problems such as semantic segmentation. However, repeated subsampling operations like pooling or convolution striding in deep CNNs lead to a significant decrease in the initial image resolution. Here, we present RefineNet, a generic multi-path refinement network that explicitly exploits all the information available along the down-sampling process to enable high-resolution prediction using long-range residual connections. In this way, the deeper layers that capture high-level semantic features can be directly refined using fine-grained features from earlier convolutions. The individual components of RefineNet employ residual connections following the identity mapping mindset, which allows for effective end-to-end training. Further, we introduce chained residual pooling, which captures rich background context in an efficient manner. We carry out comprehensive experiments and set new state-of-the-art results on seven public datasets. In particular, we achieve an intersection-over-union score of 83.4 on the challenging PASCAL VOC 2012 dataset, which is the best reported result to date.