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Topology-Preserving Augmentation for CNN-Based Segmentation of Congenital Heart Defects from 3D Paediatric CMR

  • Nick ByrneEmail author
  • James R. Clough
  • Isra Valverde
  • Giovanni Montana
  • Andrew P. King
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11798)

Abstract

Patient-specific 3D printing of congenital heart anatomy demands an accurate segmentation of the thin tissue interfaces which characterise these diagnoses. Even when a label set has a high spatial overlap with the ground truth, inaccurate delineation of these interfaces can result in topological errors. These compromise the clinical utility of such models due to the anomalous appearance of defects. CNNs have achieved state-of-the-art performance in segmentation tasks. Whilst data augmentation has often played an important role, we show that conventional image resampling schemes used therein can introduce topological changes in the ground truth labelling of augmented samples. We present a novel pipeline to correct for these changes, using a fast-marching algorithm to enforce the topology of the ground truth labels within their augmented representations. In so doing, we invoke the idea of cardiac contiguous topology to describe an arbitrary combination of congenital heart defects and develop an associated, clinically meaningful metric to measure the topological correctness of segmentations. In a series of five-fold cross-validations, we demonstrate the performance gain produced by this pipeline and the relevance of topological considerations to the segmentation of congenital heart defects. We speculate as to the applicability of this approach to any segmentation task involving morphologically complex targets.

Keywords

Image segmentation Data augmentation Topology 

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Nick Byrne
    • 1
    • 2
    Email author
  • James R. Clough
    • 2
  • Isra Valverde
    • 2
    • 3
  • Giovanni Montana
    • 4
  • Andrew P. King
    • 2
  1. 1.Medical PhysicsGuy’s and St. Thomas’ NHS Foundation TrustLondonUK
  2. 2.School of Biomedical Engineering & Imaging SciencesKing’s College LondonLondonUK
  3. 3.Paediatric CardiologyGuy’s and St. Thomas’ NHS Foundation TrustLondonUK
  4. 4.Warwick Manufacturing GroupUniversity of WarwickCoventryUK

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