Enhancing efficiency in paediatric brain tumour segmentation using a pathologically diverse single-center clinical dataset

Background Brain tumours are the most common solid malignancies in children, encompassing diverse histological, molecular subtypes and imaging features and outcomes. Paediatric brain tumours (PBTs), including high- and low-grade gliomas (HGG, LGG), medulloblastomas (MB), ependymomas, and rarer forms, pose diagnostic and therapeutic challenges. Deep learning (DL)-based segmentation offers promising tools for tumour delineation, yet its performance across heterogeneous PBT subtypes and MRI protocols remains uncertain. Methods A retrospective single-centre cohort of 174 paediatric patients with HGG, LGG, medulloblastomas (MB), ependymomas, and other rarer subtypes was used. MRI sequences included T1, T1 post-contrast (T1-C), T2, and FLAIR. Manual annotations were provided for four tumour subregions: whole tumour (WT), T2-hyperintensity (T2H), enhancing tumour (ET), and cystic component (CC). A 3D nnU-Net model was trained and tested (121/53 split), with segmentation performance assessed using the Dice similarity coefficient (DSC) and compared against intra- and inter-rater variability. Results The model achieved robust performance for WT and T2H (mean DSC: 0.85), comparable to human annotator variability (mean DSC: 0.86). ET segmentation was moderately accurate (mean DSC: 0.75), while CC performance was poor. Segmentation accuracy varied by tumour type, MRI sequence combination, and location. Notably, T1, T1-C, and T2 alone produced results nearly equivalent to the full protocol. Conclusions DL is feasible for PBTs, particularly for T2H and WT. Challenges remain for ET and CC segmentation, highlighting the need for further refinement. These findings support the potential for protocol simplification and automation to enhance volumetric assessment and streamline paediatric neuro-oncology workflows.