# Rank-Aware Agglomeration of Foundation Models for Immunohistochemistry Image Cell Counting

arXiv: https://arxiv.org/abs/2511.12588 · HTML: https://mlsanity.com/paper/2511.12588/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 34 of its 67 references that are in the map.
- First posted on arXiv 16 Nov 2025.

## Builds on (most cited first, 30 of 34)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
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- [Distilling the Knowledge in a Neural Network](https://mlsanity.com/paper/1503.02531/) (2015)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [Mask R-CNN](https://mlsanity.com/paper/1703.06870/) (2017)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [iBOT: Image BERT Pre-Training with Online Tokenizer](https://mlsanity.com/paper/2111.07832/) (2021)
- [HoVer-Net: Simultaneous Segmentation and Classification of Nuclei in Multi-Tissue Histology Images](https://mlsanity.com/paper/1812.06499/) (2018)
- [CSRNet: Dilated Convolutional Neural Networks for Understanding the Highly Congested Scenes](https://mlsanity.com/paper/1802.10062/) (2018)
- [AM-RADIO: Agglomerative Vision Foundation Model -- Reduce All Domains Into One](https://mlsanity.com/paper/2312.06709/) (2023)
- [Pathomic Fusion: An Integrated Framework for Fusing Histopathology and Genomic Features for Cancer Diagnosis and Prognosis](https://mlsanity.com/paper/1912.08937/) (2019)
- [Virchow2: Scaling Self-Supervised Mixed Magnification Models in Pathology](https://mlsanity.com/paper/2408.00738/) (2024)
- [Patch-based Convolutional Neural Network for Whole Slide Tissue Image Classification](https://mlsanity.com/paper/1504.07947/) (2015)
- [Distribution Matching for Crowd Counting](https://mlsanity.com/paper/2009.13077/) (2020)
- [CellViT: Vision Transformers for Precise Cell Segmentation and Classification](https://mlsanity.com/paper/2306.15350/) (2023)
- [RADIOv2.5: Improved Baselines for Agglomerative Vision Foundation Models](https://mlsanity.com/paper/2412.07679/) (2024)
- [CLIP-Count: Towards Text-Guided Zero-Shot Object Counting](https://mlsanity.com/paper/2305.07304/) (2023)
- [Methods for Segmentation and Classification of Digital Microscopy Tissue Images](https://mlsanity.com/paper/1810.13230/) (2018)
- [OrdinalCLIP: Learning Rank Prompts for Language-Guided Ordinal Regression](https://mlsanity.com/paper/2206.02338/) (2022)
- [Distilling foundation models for robust and efficient models in digital pathology](https://mlsanity.com/paper/2501.16239/) (2025)
- [DUNE: Distilling a Universal Encoder from Heterogeneous 2D and 3D Teachers](https://mlsanity.com/paper/2503.14405/) (2025)
- [Towards A Generalizable Pathology Foundation Model via Unified Knowledge Distillation](https://mlsanity.com/paper/2407.18449/) (2024)
- [NuInsSeg: A Fully Annotated Dataset for Nuclei Instance Segmentation in H&E-Stained Histological Images](https://mlsanity.com/paper/2308.01760/) (2023)
- [UNIC: Universal Classification Models via Multi-teacher Distillation](https://mlsanity.com/paper/2408.05088/) (2024)
- [Highlight Every Step: Knowledge Distillation via Collaborative Teaching](https://mlsanity.com/paper/1907.09643/) (2019)
- [An Aggregation of Aggregation Methods in Computational Pathology](https://mlsanity.com/paper/2211.01256/) (2022)
- [NWPU-MOC: A Benchmark for Fine-grained Multi-category Object Counting in Aerial Images](https://mlsanity.com/paper/2401.10530/) (2024)
- [Deeply-Supervised Density Regression for Automatic Cell Counting in Microscopy Images](https://mlsanity.com/paper/2011.03683/) (2020)

## Abstract (arXiv)

Accurate cell counting in immunohistochemistry (IHC) images is critical for quantifying protein expression and aiding cancer diagnosis. However, the task remains challenging due to the chromogen overlap, variable biomarker staining, and diverse cellular morphologies. Regression-based counting methods offer advantages over detection-based ones in handling overlapped cells, yet rarely support end-to-end multi-class counting. Moreover, the potential of foundation models remains largely underexplored in this paradigm. To address these limitations, we propose a rank-aware agglomeration framework that selectively distills knowledge from multiple strong foundation models, leveraging their complementary representations to handle IHC heterogeneity and obtain a compact yet effective student model, CountIHC. Unlike prior task-agnostic agglomeration strategies that either treat all teachers equally or rely on feature similarity, we design a Rank-Aware Teacher Selecting (RATS) strategy that models global-to-local patch rankings to assess each teacher's inherent counting capacity and enable sample-wise teacher selection. For multi-class cell counting, we introduce a fine-tuning stage that reformulates the task as vision-language alignment. Discrete semantic anchors derived from structured text prompts encode both category and quantity information, guiding the regression of class-specific density maps and improving counting for overlapping cells. Extensive experiments demonstrate that CountIHC surpasses state-of-the-art methods across 12 IHC biomarkers and 5 tissue types, while exhibiting high agreement with pathologists' assessments. Its effectiveness on H&E-stained data further confirms the scalability of the proposed method.