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

arXiv: https://arxiv.org/abs/2606.29463 · HTML: https://mlsanity.com/paper/2606.29463/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 16 of its 25 references that are in the map.
- First posted on arXiv 28 Jun 2026.

## Builds on (most cited first, 16 of 16)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [End-to-End Object Detection with Transformers](https://mlsanity.com/paper/2005.12872/) (2020)
- [Mask R-CNN](https://mlsanity.com/paper/1703.06870/) (2017)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [Deformable DETR: Deformable Transformers for End-to-End Object Detection](https://mlsanity.com/paper/2010.04159/) (2020)
- [DAB-DETR: Dynamic Anchor Boxes are Better Queries for DETR](https://mlsanity.com/paper/2201.12329/) (2022)
- [HoVer-Net: Simultaneous Segmentation and Classification of Nuclei in Multi-Tissue Histology Images](https://mlsanity.com/paper/1812.06499/) (2018)
- [PanNuke Dataset Extension, Insights and Baselines](https://mlsanity.com/paper/2003.10778/) (2020)
- [CellViT: Vision Transformers for Precise Cell Segmentation and Classification](https://mlsanity.com/paper/2306.15350/) (2023)
- [A Clinical Benchmark of Public Self-Supervised Pathology Foundation Models](https://mlsanity.com/paper/2407.06508/) (2024)
- [Micro-Net: A unified model for segmentation of various objects in microscopy images](https://mlsanity.com/paper/1804.08145/) (2018)
- [Benchmarking foundation models as feature extractors for weakly-supervised computational pathology](https://mlsanity.com/paper/2408.15823/) (2024)
- [CellViT++: Energy-Efficient and Adaptive Cell Segmentation and Classification Using Foundation Models](https://mlsanity.com/paper/2501.05269/) (2025)
- [Decoupled DETR: Spatially Disentangling Localization and Classification for Improved End-to-End Object Detection](https://mlsanity.com/paper/2310.15955/) (2023)

## Abstract (arXiv)

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