SegQC: a segmentation network-based framework for multi-metric segmentation quality control and segmentation error detection in volumetric medical images

Quality control of structures segmentation in volumetric medical images is important for identifying segmentation errors in clinical practice and for facilitating model development. This paper introduces SegQC, a novel framework for segmentation quality estimation and segmentation error detection. SegQC computes an estimate measure of the quality of a segmentation in volumetric scans and in their individual slices and identifies possible segmentation error regions within a slice. The key components include: 1. SegQC-Net, a deep network that inputs a scan and its segmentation mask and outputs segmentation error probabilities for each voxel in the scan; 2. three new segmentation quality metrics, two overlap metrics and a structure size metric, computed from the segmentation error probabilities; 3. a new method for detecting possible segmentation errors in scan slices computed from the segmentation error probabilities. We introduce a new evaluation scheme to measure segmentation error discrepancies based on an expert radiologist corrections of automatically produced segmentations that yields smaller observer variability and is closer to actual segmentation errors. We demonstrate SegQC on three fetal structures in 198 fetal MRI scans: fetal brain, fetal body and the placenta. To assess the benefits of SegQC, we compare it to the unsupervised Test Time Augmentation (TTA)-based quality estimation. Our studies indicate that SegQC outperforms TTA-based quality estimation in terms of Pearson correlation and MAE for fetal body and fetal brain structures segmentation. Our segmentation error detection method achieved recall and precision rates of 0.77 and 0.48 for fetal body, and 0.74 and 0.55 for fetal brain segmentation error detection respectively. SegQC enhances segmentation metrics estimation for whole scans and individual slices, as well as provides error regions detection.

Test-time augmentation-based active learning and self-training for label-efficient segmentation

Deep learning techniques depend on large datasets whose annotation is time-consuming. To reduce annotation burden, the self-training (ST) and active-learning (AL) methods have been developed as well as methods that combine them in an iterative fashion. However, it remains unclear when each method is the most useful, and when it is advantageous to combine them. In this paper, we propose a new method that combines ST with AL using Test-Time Augmentations (TTA). First, TTA is performed on an initial teacher network. Then, cases for annotation are selected based on the lowest estimated Dice score. Cases with high estimated scores are used as soft pseudo-labels for ST. The selected annotated cases are trained with existing annotated cases and ST cases with border slices annotations. We demonstrate the method on MRI fetal body and placenta segmentation tasks with different data variability characteristics. Our results indicate that ST is highly effective for both tasks, boosting performance for in-distribution (ID) and out-of-distribution (OOD) data. However, while self-training improved the performance of single-sequence fetal body segmentation when combined with AL, it slightly deteriorated performance of multi-sequence placenta segmentation on ID data. AL was helpful for the high variability placenta data, but did not improve upon random selection for the single-sequence body data. For fetal body segmentation sequence transfer, combining AL with ST following ST iteration yielded a Dice of 0.961 with only 6 original scans and 2 new sequence scans. Results using only 15 high-variability placenta cases were similar to those using 50 cases. Code is available at: https://github.com/Bella31/TTA-quality-estimation-ST-AL