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README.md

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 license: apache-2.0
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+# StainEval: Robustness Evaluation Framework for H&E Staining in Computational Pathology
+
+This repository contains the data, simulation parameters, and results for evaluating robustness of computational pathology (CPath) models to H&E staining variation, as presented in:
+
+**Title:** A protocol for evaluating robustness to H&E staining variation in computational pathology models  
+**Use case:** Microsatellite instability (MSI) prediction in colorectal cancer (CRC)
+
+The framework systematically tests trained models under controlled, reference-based staining variations, enabling interpretable assessment of model performance and robustness.
+
+---
+
+## Repository Structure
+
+### `abmil_simulation_hyperparams/`
+Contains hyperparameter and data split information for the 300 simulated ABMIL models.
+
+- `fixed_simulation_hps_n=300.csv` – Hyperparameters used for the 300 ABMIL training runs.  
+- `fixed_splits_n=300/` – Train/validation splits for each run.  
+  - `train_{idx}.csv` – Patient/slide allocation to training set for run `idx`.  
+  - `val_{idx}.csv` – Patient/slide allocation to validation set for run `idx`.  
+
+---
+
+### `exp_results/`
+Contains prediction, logit, and label results per model for all controlled staining experiments and the original reference dataset.
+
+- **Staining-specific folders** (each contains results for N=306 models):
+  - `concentration=GV_AT2_stain=None/` – High H&E concentration  
+  - `concentration=KRH_GT450_stain=None/` – Low H&E concentration  
+  - `concentration=None_stain=GV_GT450/` – High H&E color similarity  
+  - `concentration=None_stain=HRH_S60/` – Low H&E color similarity  
+
+- **Performance summary CSVs**:
+  - `performance_auc_concentration=GV_AT2_stain=None.csv` – AUC + 95% CI, high concentration  
+  - `performance_auc_concentration=KRH_GT450_stain=None.csv` – AUC + 95% CI, low concentration  
+  - `performance_auc_concentration=None_stain=GV_GT450.csv` – AUC + 95% CI, high color similarity  
+  - `performance_auc_concentration=None_stain=HRH_S60.csv` – AUC + 95% CI, low color similarity  
+  - `performance_auc_reference.csv` – AUC + 95% CI, original dataset  
+
+- **Robustness metric**:
+  - `robustness_auc_minmax_range.csv` – Min-max AUC range across all staining settings with CIs.
+
+- **Reference dataset**:
+  - `reference/` – Predictions, logits, and labels for the original dataset (N=306 models).
+
+---
+
+### `plism-wsi_stain_references/`
+PLISM-derived reference H&E stain vectors and intensity values.
+
+- `img_stats/` – Tile-level image statistics (entropy, Laplacian variance, average hue) for 91 unique stain-device combinations.  
+- `intensities/` – CSV file per stain-device combination with per-image H&E intensities.  
+- `stain_vectors/` – NPZ files with median stain vectors per unique stain-device combination.
+
+---
+
+### `surgen_stain_properties/`
+Staining properties derived from SurGen slides.
+
+- `intensities/` – H&E intensity values per selected tile and median per slide:
+  - `intensity_slide_medians.csv`  
+  - `intensity_stats_tiles.csv`  
+- `stain_vectors/` – NPZ file per slide ID containing median stain vectors of selected tiles.
+
+---
+
+## Usage Notes
+
+1. The `abmil_simulation_hyperparams` folder allows exact replication of the 300 simulated ABMIL models.  
+2. `exp_results` contains the main outputs for evaluating model robustness under controlled H&E variations.  
+3. Reference stain information from PLISM and SurGen can be used to generate new staining perturbations or define operational stain ranges for QC.  
+
+---
+
+## Citation
+
+If you use this dataset or framework, please cite:
+...