Multi-Stain Fusion of Histopathology Images Using Deep Learning for Pediatric Brain Tumor Classification

The classification of pediatric brain tumors is investigated using deep learning on hematoxylin and eosin (H&E) and antigen Ki-67 (Ki-67) whole slide images (WSIs) from the Children’s Brain Tumor Network (CBTN) dataset. A total of 1,662 unregistered WSIs (1,047 H&E and 615 Ki-67 images) were analyzed, including low-grade glioma/astrocytoma (grades 1, 2) (LGG), high-grade glioma/astrocytoma (grades 3, 4) (HGG), medulloblastoma (MB), ependymoma (EP) and ganglioglioma. The The aim of this study was to effectively classify pediatric brain tumors using H&E and Ki-67 WSIs individually, and to investigate whether early, intermediate, and late fusion could improve the predictive performance. From each WSI, 224× 224 pixel patches were extracted, and the instance (patch)-level features were obtained using the histology foundation model CONCHv1_5. The instances were aggregated using clustering-constrained attention multiple instance learning (CLAM) for patient-level classification. Model interpretability and explainability was assessed through attention heatmaps, cell density and Ki-67 labelling index (LI) maps. In the binary grade classification between LGG and HGG, the intermediate concatenation fusion achieved the best performance with a balanced accuracy of 0.88 ± 0.05, ( p < 0.005) compared to the single-stain models (H&E: 0.84 ± 0.05, Ki-67: 0.86 ± 0.05). For the 5-class tumor type classification, the one-hidden layer late fusion learning model achieved the highest balanced accuracy of 0.83 ± 0.04 ( p < 0.005), outperforming the single-stain models (H&E: 0.77 ± 0.05, Ki-67: 0.74 ± 0.05). Overall, most of the fusion approaches outperformed the single-stain models in both classification tasks ( p < 0.005). The Ki-67 attention maps demonstrated moderate to strong Spearman correlation ( ρ = 0.576 − 0.823) with the cell density and Ki-67 LI maps, suggesting that these features are associated with the model’s predictions, although additional features may contribute. The results show that H&E and Ki-67 images provide complementary information, and most of the multi-stain fusion approaches using deep learning improve pediatric brain tumor diagnosis.