Organizations: Faculty of Science and Engineering, University of Liverpool, Liverpool, L69 3GJ, U.K. · Department of Eye and Vision Sciences, University of Liverpool, Liverpool, L7 8TX, U.K. · School of AI and Advanced Computing, Xi’an Jiaotong-Liverpool University, Suzhou, 215400, China · College of Mathematical Medicine, Zhejiang Normal University, Jinhua, 321004, China · School of Mathematical Sciences, Zhejiang University, Hangzhou, 310027, China · School of Systems Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
Abstract
Accurate cell detection and classification are crucial for pathological analysis, directly affecting diagnostic accuracy and treatment planning. To capture complex cellular interactions beyond visual appearance within the tumor microenvironment, several approaches have employed graph neural networks to model spatial and relational patterns among cell nuclei, yielding promising results. However, these methods typically adopt a two-stage paradigm of visual extraction followed by relational modeling, which necessitates separate tuning for each stage, thereby increasing pipeline complexity and hindering end-to-end joint optimization. In this paper, we propose an end-to-end framework for cell detection and classification that jointly models patch-level visual representations and instance-level interactions, which incorporates a dynamic graph construction module and an instance-aware graph network. Specifically, the graph construction module dynamically builds the graph structure using learnable queries derived from patch-level features as cell instance representations, with adjacency defined by integrating feature similarity and spatial distances. The instance-aware graph network performs adaptive instance filtering and feature reorganization, aggregating them over the cell graph into a topological latent state for a selective state-space transition driven by visual cues, fusing appearance and relational evidence. When evaluated on multiple datasets with different staining protocols for cell and nucleus detection, our method significantly outperforms existing approaches in both detection and classification performance. The code will be released at https://github.com/RuochenLiu23/IGM.
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
Cell detection in histopathology images strongly depends on surrounding tissue context, where visually similar cells may belong to different classes under different microenvironments. Recent tissue-aware methods incorporate contextual priors, but often rely on static fusion strategies that may propagate noisy information. In this work, we propose DualGate-Net, a prior-aware dual-encoder framework that combines a ConvNeXtV2-based local encoder and a SegFormer-based global encoder through a learnable prior-gated fusion mechanism. The proposed module adaptively regulates the influence of tissue priors across spatial locations, while an auxiliary foreground reconstruction branch preserves high-frequency cellular structures during training. In addition, auxiliary cellness-guided cues are incorporated to further improve localization robustness. Experiments on the OCELOT benchmark demonstrate consistent improvements, achieving macro F1-scores of 0.7722 on the validation set and 0.7345 on the test set, highlighting the effectiveness of adaptive prior integration for robust histopathology cell detection.
Reconstructing lineages from live-imaging microscopy requires linking cell detections across time, including through cell divisions. A common approach is to construct a candidate graph and associate cell segmentations (nodes) across frames. However, these and other existing methods overlook two structural obstacles in candidate tracking graphs: (i) cell divisions entangle distinct lineage paths in the node embedding space, and (ii) edges sharing a node have near-random label agreement, so the candidate-graph topology carries no useful information for graph neural networks to aggregate. We propose the \textbf{Higher-Order Cell Tracking Transformer} (HOCT), an edge-centric architecture in which candidate cell links attend to one another under a 3D geometric prior, resolving both issues. Evaluated on the Cell Tracking Challenge and a bacteria division benchmark, HOCT achieves state-of-the-art results without deep pre-trained image encoders. Moreover, the proposed approach is easier to fine-tune, quickly reducing tracking errors by 59% with 400 annotations in a human-in-the-loop setting, outperforming LoRA fine-tuning of competing transformer baselines (6.75% improvement).