Refining deep learning segmentation in gallium-68-prostate-specific membrane antigen-11 positron emission tomography: evaluation of small lesion filtering and intersection-over-union thresholds

Purpose Evaluate how small lesion filtering and different intersection-over-union (IoU) thresholds influence deep learning segmentation of Ga-68-PSMA-11 PET images in prostate cancer. Methods A 3D U-Net was trained on 115 patient scans with manual contours as ground truth. Performance was assessed at voxel, lesion and patient levels. Lesions less than 8 voxels (195 mm 3 ) or less than 27 voxels (658 mm 3 ) were optionally discarded, and lesion-level metrics were computed across 10–50% IoU thresholds. Results Excluding lesions less than 27 voxels increased voxel-level Dice from 0.7975 to 0.8173 and improved precision. Lesion-level metrics were stable across IoU thresholds of 20–40% after 27-voxel filtering, while sensitivity declined at higher overlap thresholds. Patient-level sensitivity and positive predictive value reached 96.6 and 94.5%, respectively. Conclusion Implementing small lesion filtering criteria improves the reliability of automated segmentation outputs, particularly for quantitative evaluation. For lesion-level metrics, defining true positives within the range of 20–40% IoU thresholds is optimal. Further validation through multicenter studies and larger datasets is essential to ensure the generalizability of these findings.