Whole slide image (WSI) normalization remains a vital preprocessing step in computational pathology. Increasingly driven by deep learning, these models learn to approximate data distributions from training examples. This often results in outputs that gravitate toward the average, potentially masking diagnostically important features. More critically, they can introduce hallucinated content, artifacts that appear realistic but are not present in the original tissue, posing a serious threat to downstream analysis. These hallucinations are nearly impossible to detect visually, and current evaluation practices often overlook them. In this work, we demonstrate that the risk of hallucinations is real and underappreciated. While many methods perform adequately on public datasets, we observe a concerning frequency of hallucinations when these same models are retrained and evaluated on real-world clinical data. To address this, we propose a novel image comparison measure designed to automatically detect hallucinations in normalized outputs. Using this measure, we systematically evaluate several well-cited normalization methods retrained on real-world data, revealing significant inconsistencies and failures that are not captured by conventional metrics. Our findings underscore the need for more robust, interpretable normalization techniques and stricter validation protocols in clinical deployment.

Atypical mitotic figures (AMFs) are clinically relevant indicators of abnormal cell division, yet their reliable detection remains challenging due to morphological ambiguity and scanner variability. In this work, we investigated three variants of adapting the pathology foundation model UNI2 for the MIDOG2025 Track 2 challenge: (1) LoRA + UNI2, (2) VPT + UNI2 + Vahadane Normalizer, and (3) VPT + UNI2 + GRL + Stain TTA. We observed that the integration of Visual Prompt Tuning (VPT) with stain normalization techniques contributed to improved generalization. The best robustness was achieved by further incorporating test-time augmentation (TTA) with Vahadane and Macenko stain normalization. Our final submission achieved a balanced accuracy of 0.8837 and an ROC-AUC of 0.9513 on the preliminary leaderboard, ranking within the top 10 teams. These results suggest that prompt-based adaptation combined with stain-normalization TTA offers a promising strategy for atypical mitosis classification under diverse imaging conditions.

The color appearance of a pathological image is highly related to the imaging protocols, the proportion of different dyes, and the scanning devices. Computer-aided diagnostic systems may deteriorate when facing these color-variant pathological images. In this work, we propose a stain normalization method called StainPIDR. We try to eliminate this color discrepancy by decoupling the image into structure features and vector-quantized color features, restaining the structure features with the target color features, and decoding the stained structure features to normalized pathological images. We assume that color features decoupled by different images with the same color should be exactly the same. Under this assumption, we train a fixed color vector codebook to which the decoupled color features will map. In the restaining part, we utilize the cross-attention mechanism to efficiently stain the structure features. As the target color (decoupled from a selected template image) will also affect the performance of stain normalization, we further design a template image selection algorithm to select a template from a given dataset. In our extensive experiments, we validate the effectiveness of StainPIDR and the template image selection algorithm. All the results show that our method can perform well in the stain normalization task. The code of StainPIDR will be publicly available later.

Recent advancements in digital pathology have led to the development of numerous foundational models that utilize self-supervised learning on patches extracted from gigapixel whole slide images (WSIs). While this approach leverages vast amounts of unlabeled data, we have discovered a significant issue: features extracted from these self-supervised models tend to cluster by individual WSIs, a phenomenon we term WSI-specific feature collapse. This problem can potentially limit the model's generalization ability and performance on various downstream tasks. To address this issue, we introduce EXAONEPath, a novel foundational model trained on patches that have undergone stain normalization. Stain normalization helps reduce color variability arising from different laboratories and scanners, enabling the model to learn more consistent features. EXAONEPath is trained using 285,153,903 patches extracted from a total of 34,795 WSIs. Our experiments demonstrate that EXAONEPath significantly mitigates the feature collapse problem, indicating that the model has learned more generalized features rather than overfitting to individual WSI characteristics. We compared EXAONEPath with state-of-the-art models across six downstream task datasets, and our results show that EXAONEPath achieves superior performance relative to the number of WSIs used and the model's parameter count. This suggests that the application of stain normalization has substantially improved the model's efficiency and generalization capabilities.

Deploying deep learning-based imaging tools across various clinical sites poses significant challenges due to inherent domain shifts and regulatory hurdles associated with site-specific fine-tuning. For histopathology, stain normalization techniques can mitigate discrepancies, but they often fall short of eliminating inter-site variations. Therefore, we present Data Alchemy, an explainable stain normalization method combined with test time data calibration via a template learning framework to overcome barriers in cross-site analysis. Data Alchemy handles shifts inherent to multi-site data and minimizes them without needing to change the weights of the normalization or classifier networks. Our approach extends to unseen sites in various clinical settings where data domain discrepancies are unknown. Extensive experiments highlight the efficacy of our framework in tumor classification in hematoxylin and eosin-stained patches. Our explainable normalization method boosts classification tasks' area under the precision-recall curve (AUPR) by 0.165, 0.545 to 0.710. Additionally, Data Alchemy further reduces the multisite classification domain gap, by improving the 0.710 AUPR an additional 0.142, elevating classification performance further to 0.852, from 0.545. Our Data Alchemy framework can popularize precision medicine with minimal operational overhead by allowing for the seamless integration of pre-trained deep learning-based clinical tools across multiple sites.

Stain normalization algorithms aim to transform the color and intensity characteristics of a source multi-gigapixel histology image to match those of a target image, mitigating inconsistencies in the appearance of stains used to highlight cellular components in the images. We propose a new approach, StainFuser, which treats this problem as a style transfer task using a novel Conditional Latent Diffusion architecture, eliminating the need for handcrafted color components. With this method, we curate SPI-2M the largest stain normalization dataset to date of over 2 million histology images with neural style transfer for high-quality transformations. Trained on this data, StainFuser outperforms current state-of-the-art deep learning and handcrafted methods in terms of the quality of normalized images and in terms of downstream model performance on the CoNIC dataset.

Traditional staining normalization approaches, e.g. Macenko, typically rely on the choice of a single representative reference image, which may not adequately account for the diverse staining patterns of datasets collected in practical scenarios. In this study, we introduce a novel approach that leverages multiple reference images to enhance robustness against stain variation. Our method is parameter-free and can be adopted in existing computational pathology pipelines with no significant changes. We evaluate the effectiveness of our method through experiments using a deep-learning pipeline for automatic nuclei segmentation on colorectal images. Our results show that by leveraging multiple reference images, better results can be achieved when generalizing to external data, where the staining can widely differ from the training set.

Mitotic figure count is an important marker of tumor proliferation and has been shown to be associated with patients' prognosis. Deep learning based mitotic figure detection methods have been utilized to automatically locate the cell in mitosis using hematoxylin \& eosin (H\&E) stained images. However, the model performance deteriorates due to the large variation of color tone and intensity in H\&E images. In this work, we proposed a two stage mitotic figure detection framework by fusing a detector and a deep ensemble classification model. To alleviate the impact of color variation in H\&E images, we utilize both stain normalization and data augmentation, aiding model to learn color irrelevant features. The proposed model obtains an F1 score of 0.7550 on the preliminary testing set released by the MIDOG challenge.

Reducing outcome variance is an essential task in deep learning based medical image analysis. Bootstrap aggregating, also known as bagging, is a canonical ensemble algorithm for aggregating weak learners to become a strong learner. Random forest is one of the most powerful machine learning algorithms before deep learning era, whose superior performance is driven by fitting bagged decision trees (weak learners). Inspired by the random forest technique, we propose a simple bagging ensemble deep segmentation (BEDs) method to train multiple U-Nets with partial training data to segment dense nuclei on pathological images. The contributions of this study are three-fold: (1) developing a self-ensemble learning framework for nucleus segmentation; (2) aggregating testing stage augmentation with self-ensemble learning; and (3) elucidating the idea that self-ensemble and testing stage stain augmentation are complementary strategies for a superior segmentation performance. Implementation Detail: https://github.com/xingli1102/BEDs.

Malaria is a female anopheles mosquito-bite inflicted life-threatening disease which is considered endemic in many parts of the world. This article focuses on improving malaria detection from patches segmented from microscopic images of red blood cell smears by introducing a deep convolutional neural network. Compared to the traditional methods that use tedious hand engineering feature extraction, the proposed method uses deep learning in an end-to-end arrangement that performs both feature extraction and classification directly from the raw segmented patches of the red blood smears. The dataset used in this study was taken from National Institute of Health named NIH Malaria Dataset. The evaluation metric accuracy and loss along with 5-fold cross validation was used to compare and select the best performing architecture. To maximize the performance, existing standard pre-processing techniques from the literature has also been experimented. In addition, several other complex architectures have been implemented and tested to pick the best performing model. A holdout test has also been conducted to verify how well the proposed model generalizes on unseen data. Our best model achieves an accuracy of almost 97.77%.