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A persistent homology-based topological loss for CNN-based multi-class segmentation of CMR
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Byrne, Nick, Clough, James R., Valverde, Israel, Montana, Giovanni and King, Andrew P. (2023) A persistent homology-based topological loss for CNN-based multi-class segmentation of CMR. IEEE Transactions on Medical Imaging, 42 (1). pp. 3-14. doi:10.1109/tmi.2022.3203309 ISSN 0278-0062.
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Official URL: https://doi.org/10.1109/tmi.2022.3203309
Abstract
Multi-class segmentation of cardiac magnetic resonance (CMR) images seeks a separation of data into anatomical components with known structure and configuration. The most popular CNN-based methods are optimised using pixel wise loss functions, ignorant of the spatially extended features that characterise anatomy. Therefore, whilst sharing a high spatial overlap with the ground truth, inferred CNN-based segmentations can lack coherence, including spurious connected components, holes and voids. Such results are implausible, violating anticipated anatomical topology. In response, (single-class) persistent homology-based loss functions have been proposed to capture global anatomical features. Our work extends these approaches to the task of multi-class segmentation. Building an enriched topological description of all class labels and class label pairs, our loss functions make predictable and statistically significant improvements in segmentation topology using a CNN-based post-processing framework. We also present (and make available) a highly efficient implementation based on cubical complexes and parallel execution, enabling practical application within high resolution 3D data for the first time. We demonstrate our approach on 2D short axis and 3D whole heart CMR segmentation, advancing a detailed and faithful analysis of performance on two publicly available datasets.
| Item Type: | Journal Article | ||||||||
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| Divisions: | Faculty of Science, Engineering and Medicine > Engineering > WMG (Formerly the Warwick Manufacturing Group) | ||||||||
| SWORD Depositor: | Library Publications Router | ||||||||
| Journal or Publication Title: | IEEE Transactions on Medical Imaging | ||||||||
| Publisher: | IEEE | ||||||||
| ISSN: | 0278-0062 | ||||||||
| Official Date: | January 2023 | ||||||||
| Dates: |
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| Volume: | 42 | ||||||||
| Number: | 1 | ||||||||
| Page Range: | pp. 3-14 | ||||||||
| DOI: | 10.1109/tmi.2022.3203309 | ||||||||
| Status: | Peer Reviewed | ||||||||
| Publication Status: | Published | ||||||||
| Access rights to Published version: | Restricted or Subscription Access |
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