Towards Reliable AI-Based Histological Staining: A Systematic Study of Scaling and Uncertainty in Unpaired Generative Models

Despite years of methodological progress, how far AI has come in liver fibrosis staging has never been systematically evaluated under the heterogeneous, multi-center conditions that define clinical practice. To address this gap, we introduce LiFS, a large-scale dataset and benchmark derived from the MICCAI 2025 CARE-Liver challenge, comprising 610 patients across multiple centers and scanners with multi-sequence MRI. To the best of our knowledge, LiFS is the first benchmark providing complete gadoxetic acid-enhanced sequences with histopathology-confirmed annotations from diverse real-world scanners. Through systematic evaluation of 9 independently developed methods selected from 96 registered teams against in-cohort radiologist reference results, our findings address how far current AI has progressed toward clinical-level liver fibrosis staging from three complementary perspectives. First, against radiologists, the best AI methods were broadly comparable to the senior radiologist and significantly exceeded the junior radiologist in selected settings, while median AI performance generally approached junior-radiologist levels. Second, from a data perspective, cross-center heterogeneity, label imbalance, and contrast-enhanced sequence variability emerge as the dominant challenges for AI methods. Third, from a technical perspective, methodological design choices, including spatial registration, input dimensionality, multi-modal fusion strategy, and backbone architecture, appear to modulate cross-center robustness, although no single choice alone closes the gap. Overall, LiFS provides a rigorous real-world benchmark for positioning the current state of AI in liver fibrosis staging and for enabling future research on the key challenges that limit clinically reliable deployment.

Virtual immunohistochemistry (IHC) staining from hematoxylin and eosin (H&E) images can accelerate diagnostics by providing preliminary molecular insight directly from routine sections, reducing the need for repeat sectioning when tissue is limited. Existing methods improve realism through contrastive objectives, prototype matching, or domain alignment, yet the generator itself receives no direct guidance from pathology foundation models. We present UNIStainNet, a SPADE-UNet conditioned on dense spatial tokens from a frozen pathology foundation model (UNI), providing tissue-level semantic guidance for stain translation. A misalignment-aware loss suite preserves stain quantification accuracy, and learned stain embeddings enable a single model to serve multiple IHC markers simultaneously. On MIST, UNIStainNet achieves state-of-the-art distributional metrics on all four stains (HER2, Ki67, ER, PR) from a single unified model, where prior methods typically train separate per-stain models. On BCI, it also achieves the best distributional metrics. A tissue-type stratified failure analysis reveals that remaining errors are systematic, concentrating in non-tumor tissue. Code is available at https://github.com/facevoid/UNIStainNet.

Virtual staining aims to computationally generate target-stained histopathological images while reducing the cost and time associated with conventional staining procedures. However, existing methods rely predominantly on strictly paired and accurately registered training data, which are difficult and expensive to obtain in routine practice. To reduce this dependence, we propose a stable semi-supervised virtual staining framework that jointly exploits both limited paired data and abundant unpaired source images. Directly incorporating unpaired images is challenging because their generated results lack corresponding targets for supervision, potentially leading to unrealistic staining, morphological degradation, or even training collapse. To obtain reliable supervision from these images, Hessian-derived morphology preservation extracts structural cues from each source image and constrains the generated output to retain tissue morphology. Histopathological realism constraints further guide the output toward plausible target-stain characteristics, preventing the source-derived structural supervision from degenerating into contour enhancement or simple color transformation. Together, the two components suppress structural and appearance drift, stabilize semi-supervised stain translation, and promote the preservation of diagnostically relevant information. Extensive experiments on H&E-to-IHC translation for Ki67 and HER2, as well as FFPE-to-H&E translation, demonstrate consistent improvements in image quality, morphology preservation, robustness, and downstream diagnostic performance. Code will be available.