Cello: A Universal Cell-wise Feature Aggregation framework for Reliable Pathology Images Analysis

Computational pathology has made progress in diagnosis and prognosis prediction from whole slide images (WSIs), yet pipelines still rely on patch-level feature extraction and aggregation, departing from the cell-centric reasoning used by pathologists. This gap limits sensitivity to micro-lesions and subtle changes, and current methods rarely provide a unified solution that supports both local and global tasks with trustworthy evidence. We propose Cello, a universal cell-wise feature aggregation framework for reliable pathology image analysis. Cello integrates cell-level representations into WSI modeling via protein-signal–supervised cell-wise learning, preserving fine-grained cellular cues under gigapixel constraints. For local tasks, Cello introduces a flexible prototype-based contrastive module for scalable, task-adaptive representation learning. For global tasks, Cello adopts a weakly supervised gated aggregation that can widely leverage WSI labels. Finally, a cell–local–global decision-route consistency objective dynamically aggregates cellular evidence and aligns local predictions with global outcomes, improving reliability and faithfulness. Trained with only hundreds to thousands of samples, Cello achieves performance gains of 3.0% 7.6% and outperforms SOTA pathology foundation models pretrained on tens of thousands of samples. Code is available at https://github.com/HengruiLou/Cello.