Ensemble uncertainty as a criterion for dataset expansion in distinct bone segmentation from upper-body CT images

TL;DR

This paper presents an end-to-end neural network for segmenting 125 bones in upper-body CT scans, and introduces an ensemble-based uncertainty measure to identify scans that efficiently improve training data quality.

Contribution

The study develops a fully automated bone segmentation method and demonstrates that ensemble uncertainty can guide dataset expansion by reducing annotation effort.

Findings

Median dice score of 0.83 on test data.

Ensemble uncertainty correlates with manual correction effort.

Low-uncertainty scans are optimal for dataset augmentation.

Abstract

Purpose: The localisation and segmentation of individual bones is an important preprocessing step in many planning and navigation applications. It is, however, a time-consuming and repetitive task if done manually. This is true not only for clinical practice but also for the acquisition of training data. We therefore not only present an end-to-end learnt algorithm that is capable of segmenting 125 distinct bones in an upper-body CT, but also provide an ensemble-based uncertainty measure that helps to single out scans to enlarge the training dataset with. Methods We create fully automated end-to-end learnt segmentations using a neural network architecture inspired by the 3D-Unet and fully supervised training. The results are improved using ensembles and inference-time augmentation. We examine the relationship of ensemble-uncertainty to an unlabelled scan's prospective usefulness as part of the training dataset. Results: Our methods are evaluated on an in-house dataset of 16 upper-body CT scans with a resolution of \SI{2}{\milli\meter} per dimension. Taking into account all 125 bones in our label set, our most successful ensemble achieves a median dice score coefficient of 0.83. We find a lack of correlation between a scan's ensemble uncertainty and its prospective influence on the accuracies achieved within an enlarged training set. At the same time, we show that the ensemble uncertainty correlates to the number of voxels that need manual correction after an initial automated segmentation, thus minimising the time required to finalise a new ground truth segmentation. Conclusion: In combination, scans with low ensemble uncertainty need less annotator time while yielding similar future DSC improvements. They are thus ideal candidates to enlarge a training set for upper-body distinct bone segmentation from CT scans. }