Robust localisation and identification of vertebrae, jointly termed vertebrae labelling, in computed tomography (CT) images is an essential component of automated spine analysis. Current approaches for this task mostly work with 3D scans and are comprised of a sequence of multiple networks. Contrarily, our approach relies only on 2D reformations, enabling us to design an end-to-end trainable, standalone network. Our contribution includes: (1) Inspired by the workflow of human experts, a novel butterfly-shaped network architecture (termed Btrfly net) that efficiently combines information across sufficiently-informative sagittal and coronal reformations. (2) Two adversarial training regimes that encode an anatomical prior of the spine's shape into the Btrfly net, each enforcing the prior in a distinct manner. We evaluate our approach on a public benchmarking dataset of 302 CT scans achieving a performance comparable to state-of-art methods (identification rate of @math 88 ) without any post-processing stages. Addressing its translation to clinical settings, an in-house dataset of 65 CT scans with a higher data variability is introduced, where we discuss refinements that render our approach robust to such scenarios.
@PARASPLIT Recent work in @cite_4 propose encoding (anatomical) segmentation priors into an FCN by learning the shape representation using an auto encoder (AE) alongside the primary segmentation network. The AE once trained projects a new prediction onto the space of the learnt, true segmentations, thus repeating the shape'. Different from this, in @cite_12 , the encoder of a similarly pre-trained AE is used to provide projection-loss (euclidean distance in latent space) to train the primary network.
@cite_4 @cite_12
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Semantic segmentation has been popularly addressed using Fully convolutional networks (FCN) (e.g. U-Net) with impressive results and has been the forerunner in recent segmentation challenges. However, FCN approaches do not necessarily incorporate local geometry such as smoothness and shape, whereas traditional image analysis techniques have benefitted greatly by them in solving segmentation and tracking problems. In this work, we address the problem of incorporating shape priors within the FCN segmentation framework. We demonstrate the utility of such a shape prior in robust handling of scenarios such as loss of contrast and artifacts. Our experiments show ( 5 ) improvement over U-Net for the challenging problem of ultrasound kidney segmentation. 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.