cs.CVMar 16, 2026
SaveA Comprehensive Benchmark of Histopathology Foundation Models for Kidney Digital Pathology Images
Organizations: Department of Electrical and Computer Engineering, University of Florida, Gainesville, FL, USA · Seed Production Innovation, Crop Science Division, Bayer Company, St. Louis, MO, USA · Division of Medicine – Quantitative Health, University of Florida, Gainesville, FL, USA · Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, FL, USA · Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, USA · Kidney Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA · Indiana University School of Medicine, Indianapolis, IN, USA · Departments of Medicine, Washington University School of Medicine, St. Louis, MO, USA · Universidade de Coimbra, Coimbra, Coimbra District, Portugal · Department of Pathology and Laboratory Medicine, University of California at Davis School of Medicine, Sacramento, CA, USA · Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA · Department of Pathology, University of Michigan, Ann Arbor, MI, USA
Abstract
Histopathology foundation models (HFMs), pretrained on large-scale cancer datasets, have advanced computational pathology. However, their applicability to non-cancerous chronic kidney disease remains underexplored, despite coexistence of renal pathology with malignancies such as renal cell and urothelial carcinoma. We systematically evaluate 11 publicly available HFMs across 11 kidney-specific downstream tasks spanning multiple stains (PAS, H&E, PASM, and IHC), spatial scales (tile and slide-level), task types (classification, regression, and copy detection), and clinical objectives, including detection, diagnosis, and prognosis. Tile-level performance is assessed using repeated stratified group cross-validation, while slide-level tasks are evaluated using repeated nested stratified cross-validation. Statistical significance is examined using Friedman test followed by pairwise Wilcoxon signed-rank testing with Holm-Bonferroni correction and compact letter display visualization. To promote reproducibility, we release an open-source Python package, kidney-hfm-eval, available at https://pypi.org/project/kidney-hfm-eval/ , that reproduces the evaluation pipelines. Results show moderate to strong performance on tasks driven by coarse meso-scale renal morphology, including diagnostic classification and detection of prominent structural alterations. In contrast, performance consistently declines for tasks requiring fine-grained microstructural discrimination, complex biological phenotypes, or slide-level prognostic inference, largely independent of stain type. Overall, current HFMs appear to encode predominantly static meso-scale representations and may have limited capacity to capture subtle renal pathology or prognosis-related signals. Our results highlight the need for kidney-specific, multi-stain, and multimodal foundation models to support clinically reliable decision-making in nephrology.
Figures & tables
| Model Name | Encoder Type | Dataset Size | Pretraining Image Type | SSL Strategy | Image Magnification | Number of Parameters | Feature Dimension |
| H-optimus-0 [ 95 ] | ViT-G | 500k | H&E | DINOv2 [ 83 ] | 20x | 1.10B | 1536* |
| H-optimus-1 [ 8 ] | ViT-G | 1M | H&E | DINOv2 | 20x | 1.10B | 1536* |
| Hibou-B [ 79 ] | ViT-B | 512M | H&E, non-H&E, and cytology | DINOv2 | Not reported | 86M | 768* |
| Hibou-L [ 79 ] | ViT-L | 1.2B | H&E, non-H&E, and cytology | DINOv2 | Not reported | 303M | 1024* |
| Prov-Gigapath [ 115 ] | ViT-G + LongNet [ 28 ] | 171k | H&E and IHC | DINOv2 + MAE [ 37 ] | 20x | 1.10B | 1536*, 768** |
| SP22M [ 13 ] | ViT-S | 423k | H&E | DINO [ 15 ] | 20x | 22M | 384** |
Table 1: Summary of vision histopathology foundation models (HFMs) evaluated in this study. Each model varies in architecture type, pretraining dataset scale (no. of tiles), pretraining image modality (i.e., type of stain), SSL strategy, magnification levels of images and their resolution (i.e., number of pixels), number of HFM parameters, and output feature dimensionality. Note: * indicates tile-level embedding dimension; ** indicates slide-level embedding dimension; indicates number of WSIs; indicates number of tiles.
| Evaluation Task | Level | Task type | Number of Slides | Number of tiles | Data source | Number of classes | Class ratio | Staining Protocol |
| Globally vs. non-globally sclerotic glomerulus classification | Tile | Classification | 215 | 5761 | WUSTL, Vanderbilt University | 2 | 1:4.46 | PAS |
| GBM vs. no GBM spike classification | Tile | Classification | 63 | 695 | NIH/ NIDDK | 2 | 1:1.93 | PASM |
| Reference vs. abnormal tubule classification | Tile | Classification | 12 | 1200 | Indiana University | 2 | 1:1 | H&E |
| Inflammation vs. no inflammation classification | Tile | Classification | 14 | 8245 | UC Davis | 2 | 1.26:1 | H&E |
| Arterial stenosis classification (mild, moderate, severe) | Tile | Classification | 155 | 242 | University of Coimbra, UC Davis | 3 | 5.32:2.08:1 | PAS |
| Cell type proportion estimation | Tile | Regression | 12 | 17,478 | Indiana University | NA | NA | H&E |
Table 2: Summary of datasets being used for evaluating histopathology foundation models. Abbreviations: WUSTL = Washington University in St. Louis, NIH = National Institutes of Health, NIDDK = National Institute of Diabetes and Digestive and Kidney Diseases, UC Davis = University of California Davis, JHU = Johns Hopkins University, NA = Not Applicable, GBM = Glomerular Basement Membrane, eGFR = estimated Glomerular Filtration Rate, MN = Membranous Nephropathy, DN = Diabetic Nephropathy.
Figure 1: Representative histopathology examples of glomerulosclerosis.
Figure 2: Representative histopathology examples of GBM spike detection.
Figure 3: Representative histopathology examples reference and abnormal tubules.
Figure 4: Representative histopathology examples with and without inflammation.
Figure 5: Representative histopathology examples of mild, moderate, and severe arteriolar stenosis.
Figure 6: Sample histology image patch from which the cell type is estimated.
Figure 7: Representative histopathology examples of the augmentations applied to a single microvascular inflammation tissue patch for the copy detection task.
Figure 8: Overview of the tile-level evaluation workflow for benchmarking histopathology foundation models (HFMs). (A) An input histology tile is passed through one of 11 HFM encoders (H-optimus-0, H-optimus-1, Hibou-B, Hibou-L, Prov-Gigapath, SP22M, SP85M, UNI, UNI2-h, Virchow, Virchow2) to obtain a fixed-dimensional feature embedding. (B) The extracted embedding is used to train lightweight machine learning models either linear or NN probing for classification tasks, or ridge regression for continuous prediction tasks. (C) Model performance is evaluated using a repeated group five-fold cross-validation framework, followed by bootstrapping of predictions, and a statistical framework integrating Friedman test, Wilcoxon signed-rank tests, and Compact Letter Display (CLD) [ 35 ] analysis to quantify variance and compute generalized predictive performance across all tile-level tasks.
Figure 9: Overview of the slide-level evaluation framework for benchmarking histopathology foundation models (HFMs). (A) Whole-slide images (WSIs) are tiled and filtered to generate high-quality image patches. (B) Each tile is passed through one of 11 HFM encoders (H-optimus-0, H-optimus-1, Hibou-B, Hibou-L, Prov-Gigapath, SP22M, SP85M, UNI, UNI2-h, Virchow, Virchow2) to obtain fixed-dimensional feature embeddings. (C) Tile embeddings belonging to the same slide are aggregated using an attention-based multiple instance learning (ABMIL) model, which is trained for either regression or classification tasks. (D) ABMIL hyperparameter tuning is conducted using a repeated nested stratified five-fold cross-validation framework, where inner folds are used for hyperparameter tuning and outer folds provide unbiased test estimates. (E) Predictions from all folds are bootstrapped, followed by a statistical framework integrating the Friedman test, Wilcoxon signed-rank tests, and Compact Letter Display (CLD) analysis to quantify variance and compute generalized predictive performance across slide-level tasks.
Table 3: Performance comparison of HFMs for global glomerulosclerosis classification. Tables 3(a) and 3(b) rank the performance of 11 HFMs for global glomerulosclerosis classification using logistic regression and -nearest neighbors classifiers, respectively. Performance is reported as the Matthews Correlation Coefficient (MCC) statistics (minimum to maximum) across 1000 bootstraps obtained from repeated stratified group five-fold cross-validation runs. Statistical ranking using Compact Letter Display (CLD): The ’CLD’ column groups models based on their statistical similarity. Models sharing a letter (e.g., ’a’) are not significantly different from one another ( ). Models with different letters (e.g., ’a’ vs. ’b’) have significantly different performance ( , Wilcoxon signed rank test).
Table 4: Performance comparison of HFMs for glomerular basement membrane spike classification. Tables 4(a) and 4(b) rank the performance of 11 HFMs for glomerular basement membrane spike classification using logistic regression and -nearest neighbors classifiers, respectively. Performance is reported as the Matthews Correlation Coefficient (MCC) statistics (minimum to maximum) across 1000 bootstraps obtained from repeated stratified group five-fold cross-validation runs. Statistical ranking using Compact Letter Display (CLD): The ’CLD’ column groups models based on their statistical similarity. Models sharing a letter (e.g., ’a’) are not significantly different from one another ( ). Models with different letters (e.g., ’a’ vs. ’b’) have significantly different performance ( , Wilcoxon signed rank test).
Table 5: Performance comparison of HFMs for tubular classification. Tables 5(a) and 5(b) rank the performance of 11 HFMs for tubular classification using logistic regression and -nearest neighbors classifiers, respectively. Performance is reported as the Matthews Correlation Coefficient (MCC) statistics (minimum to maximum) across 1000 bootstraps obtained from repeated stratified group five-fold cross-validation runs. Statistical Ranking using Compact Letter Display (CLD): The ’CLD’ column groups models based on their statistical similarity. Models sharing a letter (e.g., ’a’) are not significantly different from one another ( ). Models with different letters (e.g., ’a’ vs. ’b’) have significantly different performance ( , Wilcoxon signed rank test).
Table 6: Performance comparison of HFMs for inflammation classification. Tables 6(a) and 6(b) rank the performance of 11 HFMs for inflammation classification using logistic regression and -nearest neighbors classifiers, respectively. Performance is reported as the Matthews Correlation Coefficient (MCC) statistics (minimum to maximum) across 1000 bootstraps obtained from repeated stratified group five-fold cross-validation runs. Statistical Ranking using Compact Letter Display (CLD): The ’CLD’ column groups models based on their statistical similarity. Models sharing a letter (e.g., ’a’) are not significantly different from one another ( ). Models with different letters (e.g., ’a’ vs. ’b’) have significantly different performance ( , Wilcoxon signed rank test).
Table 7: Performance comparison of HFMs for arterial stenosis classification. Tables 7(a) and 7(b) rank the performance of 11 HFMs for arterial stenosis classification using logistic regression and -nearest neighbors classifiers, respectively. Performance is reported as the Matthews Correlation Coefficient (MCC) statistics (minimum to maximum) across 1000 bootstraps obtained from repeated stratified group five-fold cross-validation runs. Statistical Ranking using Compact Letter Display (CLD): The ’CLD’ column groups models based on their statistical similarity. Models sharing a letter (e.g., ’a’) are not significantly different from one another ( ). Models with different letters (e.g., ’a’ vs. ’b’) have significantly different performance ( , Wilcoxon signed rank test).
| CLD | Model | Min | 1st Quart. | Median | Mean | 3rd Quart. | Max |
| a | UNI2-h | 0.3533 | 0.3612 | 0.3634 | 0.3635 | 0.3657 | 0.3737 |
| b | H-optimus-1 | 0.3286 | 0.3364 | 0.3388 | 0.3387 | 0.3411 | 0.3487 |
| c | H-optimus-0 | 0.3035 | 0.3129 | 0.3150 | 0.3150 | 0.3171 | 0.3245 |
| d | UNI | 0.2910 | 0.3017 | 0.3042 | 0.3041 | 0.3063 | 0.3139 |
| e | Virchow2 | 0.2797 | 0.2886 | 0.2910 | 0.2910 | 0.2934 | 0.3025 |
| f | Virchow | 0.2760 | 0.2836 | 0.2858 | 0.2858 | 0.2881 | 0.2986 |
Table 8: Performance comparison of HFMs for cell type estimation. Table 8 ranks the performance of 11 HFMs for cell type estimation using ridge regression. Performance is reported as the Pearson Correlation Coefficient (PCC) statistics (minimum to maximum) across 1000 bootstraps obtained from repeated group five-fold cross-validation runs. Ranking of model performance for cell type estimation. Statistical Ranking using Compact Letter Display (CLD): The ’CLD’ column groups models based on their statistical similarity. Models sharing a letter (e.g., ’a’) are not significantly different from one another ( ). Models with different letters (e.g., ’a’ vs. ’b’) have significantly different performance ( , Wilcoxon signed rank test).
| Augmentation | H-optimus-0 | H-optimus-1 | Hibou-B | Hibou-L | Prov-Gigapath | SP22M | SP85M | UNI | UNI2-h | Virchow | Virchow2 |
| color | 0.9343 | 0.9359 | 0.8997 | 0.8735 | 0.9538 | 0.8669 | 0.8798 | 0.9480 | 0.9397 | 0.9255 | 0.9555 |
| deform | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 0.9717 | 0.9995 |
| geo | 0.9979 | 0.9954 | 0.9891 | 0.8827 | 1.0000 | 0.9987 | 0.9991 | 0.9987 | 0.9879 | 0.9663 | 0.9575 |
| noise | 0.8124 | 0.6715 | 0.2457 | 0.4324 | 0.8656 | 0.8074 | 0.6307 | 0.8112 | 0.7758 | 0.6216 | 0.6199 |
Table 9: Top-1 classification accuracy for HFMs under four augmentation types (color, deform, geometric, noise), evaluating representation robustness.
| CLD | Model | Min | 1st Quart. | Median | Mean | 3rd Quart. | Max |
| a | H-optimus-0 | 0.7266 | 0.9270 | 1.0000 | 0.9685 | 1.0000 | 1.0000 |
| b | Virchow | 0.6574 | 0.9220 | 1.0000 | 0.9538 | 1.0000 | 1.0000 |
| c | Virchow2 | 0.5883 | 0.9117 | 0.9282 | 0.9381 | 1.0000 | 1.0000 |
| d | SP85M | 0.5416 | 0.9035 | 0.9250 | 0.9269 | 1.0000 | 1.0000 |
| d | UNI2-h | 0.6064 | 0.9035 | 0.9250 | 0.9268 | 1.0000 | 1.0000 |
| d | UNI | 0.6064 | 0.8748 | 0.9250 | 0.9240 | 1.0000 | 1.0000 |
Table 10: Performance comparison of HFMs for healthy reference samples vs. DN classification. Table 10 ranks the performance of 11 HFMs for healthy reference samples vs. DN classification using attention based multiple instance learning (ABMIL) classifier. Performance is reported as the Matthews Correlation Coefficient (MCC) statistics (minimum to maximum) across 1000 bootstraps obtained from repeated nested stratified five-fold cross-validation runs. Statistical ranking using Compact Letter Display (CLD): The ’CLD’ column groups models based on their statistical similarity. Models sharing a letter (e.g., ’a’) are not significantly different from one another ( ). Models with different letters (e.g., ’a’ vs. ’b’) have significantly different performance ( , Wilcoxon signed rank test).
| CLD | Model | Min | 1st Quart. | Median | Mean | 3rd Quart. | Max |
| a | H-optimus-1 | -0.2025 | 0.0000 | 0.0000 | 0.0488 | 0.0000 | 1.0000 |
| a | UNI2-h | -0.2988 | -0.0913 | 0.0000 | 0.0484 | 0.0000 | 1.0000 |
| b | Virchow2 | -0.2988 | -0.0913 | 0.0000 | 0.0148 | 0.0000 | 1.0000 |
| b | Hibou-L | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.0000 |
| b | Hibou-B | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.0000 |
| c | UNI | -0.4767 | -0.1333 | -0.0625 | -0.0099 | 0.0000 | 1.0000 |
Table 11: Performance comparison of HFMs for MN treatment response classification. Table 11 ranks the performance of 11 HFMs for MN treatment response classification using attention based multiple instance learning (ABMIL) classifier. Performance is reported as the Matthews Correlation Coefficient (MCC) statistics (minimum to maximum) across 1000 bootstraps obtained from repeated nested stratified five-fold cross-validation runs. Statistical Ranking using Compact Letter Display (CLD): The ’CLD’ column groups models based on their statistical similarity. Models sharing a letter (e.g., ’a’) are not significantly different from one another ( ). Models with different letters (e.g., ’a’ vs. ’b’) have significantly different performance ( , Wilcoxon signed rank test).
| CLD | Model | Min | 1st Quart. | Median | Mean | 3rd Quart. | Max |
| a | Hibou-B | -0.5449 | -0.0339 | 0.1038 | 0.1039 | 0.2381 | 0.7542 |
| b | Virchow2 | -0.5449 | -0.1340 | 0.0000 | 0.0169 | 0.1581 | 0.6325 |
| b | H-optimus-1 | -0.6172 | -0.1372 | 0.0000 | 0.0012 | 0.1372 | 0.7688 |
| b | Virchow | -0.7006 | -0.1494 | -0.0109 | -0.0060 | 0.1340 | 0.6720 |
| c | Hibou-L | -0.5709 | -0.1682 | -0.0369 | -0.0393 | 0.0895 | 0.5916 |
| d | UNI | -0.6231 | -0.2186 | -0.0714 | -0.0687 | 0.0778 | 0.6706 |
Table 12: Performance comparison of HFMs for eGFR decline classification in post-renal transplantation. Table 12 ranks the performance of 11 HFMs for eGFR decline classification in post-renal transplant cases using an attention-based multiple instance learning (ABMIL) classifier. Performance is reported as the Matthews Correlation Coefficient (MCC) statistics (minimum to maximum) across 1000 bootstraps obtained from repeated nested stratified five-fold cross-validation runs. Statistical ranking using Compact Letter Display (CLD): The ’CLD’ column groups models based on their statistical similarity. Models sharing a letter (e.g., ’a’) are not significantly different from one another ( ). Models with different letters (e.g., ’a’ vs. ’b’) have significantly different performance ( , Wilcoxon signed rank test).
| CLD | Model | Min | 1st Quart. | Median | Mean | 3rd Quart. | Max |
| a | Hibou-L | -0.4802 | -0.1604 | -0.0808 | -0.0925 | -0.0133 | 0.2477 |
| b | Hibou-B | -0.6246 | -0.2143 | -0.1234 | -0.1320 | -0.0372 | 0.2657 |
| c | Virchow2 | -1.0401 | -0.3271 | -0.1756 | -0.1888 | -0.0375 | 0.3247 |
| d | UNI2-h | -0.9761 | -0.3342 | -0.1883 | -0.2131 | -0.0713 | 0.2603 |
| e | SP22M | -1.0089 | -0.3750 | -0.2259 | -0.2453 | -0.0991 | 0.2664 |
| f | SP85M | -0.9875 | -0.4216 | -0.2682 | -0.2827 | -0.1330 | 0.3867 |
Table 13: Performance comparison of HFMs for one-year eGFR prediction in post-renal transplantation. Table 13 ranks the performance of 11 HFMs for eGFR prediction using an attention-based multiple instance learning (ABMIL) regressor. Performance is reported as the statistics (minimum to maximum) across 1000 bootstraps obtained from repeated nested five-fold cross-validation runs. Statistical ranking using Compact Letter Display (CLD): The ’CLD’ column groups models based on their statistical similarity. Models sharing a letter (e.g., ’a’) are not significantly different from one another ( ). Models with different letters (e.g., ’a’ vs. ’b’) have significantly different performance ( , Wilcoxon signed rank test).
Figure 10: Violin plots showing the distribution of Matthews correlation coefficient (MCC) values across HFMs for multiple downstream tasks. Each subplot represents a specific task and probing method: (a)–(b) globally vs. non-globally sclerotic glomeruli classification using logistic regression (LR) and NN, (c)–(d) GBM spike vs. no-GBM spike classification (LR, NN), (e)–(f) normal vs. abnormal tubule classification (LR, NN), (g)–(h) inflammation vs. non-inflammation classification (LR, NN), (i)–(j) arteriolar stenosis multi-class classification (LR, NN), (k) cell type estimation (ridge regression), (l) diabetic nephropathy vs. control classification using MIL. (m) membranous nephropathy treatment-response prediction using multiple-instance learning (MIL), (n) renal transplant eGFR decline classification using MIL, (o) renal transplant eGFR prediction using MIL. Wider violins indicate greater performance variability, and higher median lines indicate more consistent model performance across cross-validation replicates.
Appendix figures & tables3 assets
Supplementary material from the paper’s appendix.
Appendix
Supplementary Figure 1 : Pipeline for generating ground truth labels for tubules using spatial transcriptomics and histology. (A) H&E-stained histology image patch with segmented tubules ( ) and Visium spatial transcriptomics spot locations ( ). (B) Seurat-based cell deconvolution workflow: kidney reference single-cell RNA-seq data (cell-by-gene matrix with cell-type annotations) is integrated with Visium spot-level gene expression (spot-by-gene matrix) to estimate cell-type proportions per spatial spot. (C) Deconvolved Visium spots overlaid on the histology image, each showing estimated proportions of multiple cell types. (D) Assignment of each spatial spot to its nearest tubule segment transferring spot-specific cell-type proportions to the corresponding tubule. (E) Final tubule-level ground truth labels, obtained by taking weighted ( ) combination of where each tubule ( ) is associated with its aggregated cell-type proportion vector ( ) for downstream task.
| Category | Hyperparameter | Value(s) |
| Model / Architecture | Instance embedding dimension ( ) | |
| Attention hidden dimension ( ) | ||
| Dropout | (fixed) | |
| Optimization | Optimizer | AdamW |
| Learning rate ( ) | ||
| Weight decay | (fixed) |
Supplementary Table 1: Hyperparameters used for repeated nested stratified ABMIL training for slide-level evaluation.
Supplementary Figure 2 : Heatmap plots showing the p -values obtained from comparing the Matthews correlation coefficient (MCC) values across HFMs for multiple downstream tasks. Each subplot represents a specific task and probing method: (a)–(b) globally vs. non-globally sclerotic glomeruli classification using logistic regression (LR) and NN, (c)–(d) GBM spike vs. no-GBM spike classification (LR, NN), (e)–(f) normal vs. abnormal tubule classification (LR, NN), (g)–(h) inflammation vs. non-inflammation classification (LR, NN), (i)–(j) arteriolar stenosis multi-class classification (LR, NN), (k) cell type estimation (ridge regression) (i) diabetic nephropathy vs. control classification using MIL. (m) membranous nephropathy treatment-response prediction using multiple-instance learning (MIL), (n) renal transplant eGFR decline classification using MIL, (o) renal transplant eGFR prediction using MIL, and Wider violins indicate greater performance variability, and higher median lines indicate more consistent model performance across cross-validation replicates.