CellDETR: A Detection-Guided Framework for Scalable Cell Representation Learning from Histopathology Images

Shikang Zhang; Guojun Li; Yicong Mao; Chulin Sha

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arXiv · 2606.29463

CellDETR: A Detection-Guided Framework for Scalable Cell Representation Learning from Histopathology Images

Shikang Zhang·Guojun Li·Yicong Mao·Chulin Sha

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Abstract

Recent advances in pathology foundation models have substantially improved patch and slide level representation learning from whole-slide images (WSIs).However, cell-level representations learning remain underexplored, limiting cell resolved interpretability, biological discovery, and clinical translation. We propose CellDETR, a detection-guided framework built on Deformable DETR for scalable cell representation learning from WSIs. By introducing location feature decoupling and box-constrained attention mechanism, CellDETR enables automated extraction of cell-level embeddings, and outperform existing state-of-the-art methods in supervised cell classification on PanNuke data. In addition, by incorporating contrastive learning design, we build a CellDETR-based pretraining model for scalable cell representation learning from unlabeled WSIs, which improves downstream cell classification performance. Furthermore, we show that after pretraining with Xenium spatial transcriptomics-derived cell annotations, CellDETR achieves accurate cross-dataset cell classification, demonstrating the transferability and biological relevance of the learned cell embeddings. Together, CellDETR provides a scalable route toward general cell-level representation learning framework for interpretable computational patholog

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Shikang Zhang, Guojun Li, Yicong Mao, Chulin Sha. 2026-06-28. CellDETR: A Detection-Guided Framework for Scalable Cell Representation Learning from Histopathology Images. https://arxiv.org/abs/2606.29463

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