Cited by 63Medical Image Segmentation TechniquesAdvanced Neural Network ApplicationsRetinal Imaging and Analysis

clDice - a Novel Topology-Preserving Loss Function for Tubular Structure Segmentation

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Shit, Suprosanna, Paetzold, Johannes C., Sekuboyina, Anjany, Ezhov, Ivan, Unger, Alexander, Zhylka, Andrey, Pluim, Josien P. W., Bauer, Ulrich +1 more·2021·2021 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)

Abstract

Accurate segmentation of tubular, network-like structures, such as vessels, neurons, or roads, is relevant to many fields of research. For such structures, the topology is their most important characteristic; particularly preserving connectedness: in the case of vascular networks, missing a connected vessel entirely alters the blood-flow dynamics. We introduce a novel similarity measure termed centerlineDice (short clDice), which is calculated on the inter-section of the segmentation masks and their (morphological) skeleta. We theoretically prove that clDice guarantees topology preservation up to homotopy equivalence for binary 2D and 3D segmentation. Extending this, we pro-pose a computationally efficient, differentiable loss function (soft-clDice) for training arbitrary neural segmentation networks. We benchmark the soft-clDice loss on five public datasets, including vessels, roads and neurons (2D and 3D). Training on soft-clDice leads to segmentation with more accurate connectivity information, higher graph similarity, and better volumetric scores.

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  • We compared our nerve segmentation model with other advanced 3D image segmentation networks, training each on the same training dataset until full convergence.

    “We compared our nerve segmentation model with other advanced 3D image segmentation networks50 (Supplementary Table 1): VNet51, Attention U-Net52, nnFormer53, UNETR54, SwinUNETR55, nnU-Net56 and nnUNetRes56. Each network was trained on the same training dataset until full convergence, defined as no decrease in the training loss for ten consecutive epochs.”

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  1. [40][40] Azriel Rosenfeld. Digital topology. The American Mathematical Monthly , 86(8):621-630, 1979. 11 -

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Authors
Shit, S., Paetzold, J. C., Sekuboyina, A., Ezhov, I., Unger, A., Zhylka, A., Pluim, J. P. W., Bauer, U., & Menze, B. H.
Affiliations
  • Technical University of Munich (DE)
  • Eindhoven University of Technology (NL)
Venue
2021 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)
Publisher
IEEE
Published
2021-06
Pages
16555-16564
ISSN
1063-6919 (ISSN-L)
OpenAlex
W3010789210
Cited by
60
References
64
Citations by year
2025: 20 · 2024: 9 · 2023: 15 · 2022: 9 · 2021: 6 · 2020: 1
FWCI
3.19
Type
conference paper
Language
en
Open access
Locations
  • IEEE Computer Society Conference on Computer Vision and Pattern Recognition/Proceedings - IEEE Computer Society Conference on Computer Vision and Pattern Recognition/Proceedings (publishedVersion)
  • arXiv (Cornell University) (submittedVersion)
  • TU/e Research Portal (submittedVersion, other-oa)
  • arXiv (Cornell University)
Topics
  • Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Medical Image Segmentation Techniques
  • Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Advanced Neural Network Applications
  • Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Retinal Imaging and Analysis
Keywords
topology preservation, tubular structure segmentation, skeletonization, homotopy equivalence, differentiable loss function, vessel segmentation, neuron segmentation, road network segmentation, graph similarity, connectedness

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