Convolutional neural networks have been successfully applied to semantic segmentation problems. However, there are many problems that are inherently not pixel-wise classification problems but are nevertheless frequently formulated as semantic segmentation. This ill-posed formulation consequently necessitates hand-crafted scenario-specific and computationally expensive post-processing methods to convert the per pixel probability maps to final desired outputs. Generative adversarial networks (GANs) can be used to make the semantic segmentation network output to be more realistic or better structure-preserving, decreasing the dependency on potentially complex post-processing.
Several methods have proposed to add property-targeted loss terms @cite_0 @cite_18 or to use pair-wise or higher-order term CRFs @cite_21 @cite_23 @cite_20 , to enforce neural networks to preserve certain qualities such as smoothness, topology and neighborhood consistency. In contrast to our work, such approaches are mostly only capable of preserving lower-level consistencies and also impose additional costs at inference time. Hand-engineering extra loss terms that target enforcing certain qualities is often challenging as identifying the target qualities in the first place and then coming up with efficient differentiable loss terms is often not straight-forward.
@cite_18 @cite_21 @cite_0 @cite_23 @cite_20
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Incorporation of prior knowledge about organ shape and location is key to improve performance of image analysis approaches. In particular, priors can be useful in cases where images are corrupted and contain artefacts due to limitations in image acquisition. The highly constrained nature of anatomical objects can be well captured with learning-based techniques. However, in most recent and promising techniques such as CNN-based segmentation it is not obvious how to incorporate such prior knowledge. State-of-the-art methods operate as pixel-wise classifiers where the training objectives do not incorporate the structure and inter-dependencies of the output. To overcome this limitation, we propose a generic training strategy that incorporates anatomical prior knowledge into CNNs through a new regularisation model, which is trained end-to-end. The new framework encourages models to follow the global anatomical properties of the underlying anatomy ( e.g. shape, label structure) via learnt non-linear representations of the shape. We show that the proposed approach can be easily adapted to different analysis tasks ( e.g. image enhancement, segmentation) and improve the prediction accuracy of the state-of-the-art models. The applicability of our approach is shown on multi-modal cardiac data sets and public benchmarks. In addition, we demonstrate how the learnt deep models of 3-D shapes can be interpreted and used as biomarkers for classification of cardiac pathologies. Most state-of-the-art techniques for multi-class image segmentation and labeling use conditional random fields defined over pixels or image regions. While region-level models often feature dense pairwise connectivity, pixel-level models are considerably larger and have only permitted sparse graph structures. In this paper, we consider fully connected CRF models defined on the complete set of pixels in an image. The resulting graphs have billions of edges, making traditional inference algorithms impractical. Our main contribution is a highly efficient approximate inference algorithm for fully connected CRF models in which the pairwise edge potentials are defined by a linear combination of Gaussian kernels. Our experiments demonstrate that dense connectivity at the pixel level substantially improves segmentation and labeling accuracy. The recent success of deep learning techniques in classification and object detection tasks has been leveraged for segmentation tasks. However, a weakness of these deep segmentation models is their limited ability to encode high level shape priors, such as smoothness and preservation of complex interactions between object regions, which can result in implausible segmentations. In this work, by formulating and optimizing a new loss, we introduce the first deep network trained to encode geometric and topological priors of containment and detachment. Our results on the segmentation of histology glands from a dataset of 165 images demonstrate the advantage of our novel loss terms and show how our topology aware architecture outperforms competing methods by up to 10 in both pixel-level accuracy and object-level Dice. 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. Convolutional neural networks with many layers have recently been shown to achieve excellent results on many high-level tasks such as image classification, object detection and more recently also semantic segmentation. Particularly for semantic segmentation, a two-stage procedure is often employed. Hereby, convolutional networks are trained to provide good local pixel-wise features for the second step being traditionally a more global graphical model. In this work we unify this two-stage process into a single joint training algorithm. We demonstrate our method on the semantic image segmentation task and show encouraging results on the challenging PASCAL VOC 2012 dataset.