Anatomically Constrained Neural Networks (ACNN): application to cardiac image enhancement and segmentation

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Title: Anatomically Constrained Neural Networks (ACNN): application to cardiac image enhancement and segmentation
Authors: Oktay, O
Ferrante, E
Kamnitsas, K
Heinrich, M
Bai, W
Caballero, J
Cook, S
De Marvao, A
Dawes, T
O'Regan, D
Kainz, B
Glocker, B
Rueckert, D
Item Type: Journal Article
Abstract: 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 datasets and public benchmarks. Additionally, we demonstrate how the learnt deep models of 3D shapes can be interpreted and used as biomarkers for classification of cardiac pathologies.
Issue Date: 26-Sep-2017
Date of Acceptance: 15-Aug-2017
ISSN: 0278-0062
Publisher: IEEE
Start Page: 384
End Page: 395
Journal / Book Title: IEEE Transactions on Medical Imaging
Volume: 37
Issue: 2
Copyright Statement: © 2017 IEEE. This work is licensed under a Creative Commons Attribution 3.0 License. For more information, see
Sponsor/Funder: British Heart Foundation
Engineering & Physical Science Research Council (EPSRC)
Imperial College Healthcare NHS Trust- BRC Funding
Funder's Grant Number: PG/12/27/29489
Keywords: Science & Technology
Life Sciences & Biomedicine
Computer Science, Interdisciplinary Applications
Engineering, Biomedical
Engineering, Electrical & Electronic
Imaging Science & Photographic Technology
Radiology, Nuclear Medicine & Medical Imaging
Computer Science
Shape prior
convolutional neural network
medical image segmentation
image super-resolution
08 Information And Computing Sciences
09 Engineering
Nuclear Medicine & Medical Imaging
Publication Status: Published
Appears in Collections:Faculty of Engineering
Clinical Sciences
Imaging Sciences
National Heart and Lung Institute
Molecular Sciences
Faculty of Medicine

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