Heatmap Guided Query Transformers for Robust Astrocyte Detection across Immunostains and Resolutions

Abstract: Astrocytes are critical glial cells whose altered morphology and density are hallmarks of many neurological disorders. However, their intricate branching and stain dependent variability make automated detection of histological images a highly challenging task. To address these challenges, we propose a hybrid CNN Transformer detector that combines local feature extraction with global contextual reasoning. A heatmap guided query mechanism generates spatially grounded anchors for small and faint astrocytes, while a lightweight Transformer module improves discrimination in dense clusters. Evaluated on ALDH1L1 and GFAP stained astrocyte datasets, the model consistently outperformed Faster R-CNN, YOLOv11 and DETR, achieving higher sensitivity with fewer false positives, as confirmed by FROC analysis. These results highlight the potential of hybrid CNN Transformer architectures for robust astrocyte detection and provide a foundation for advanced computational pathology tools.