Brent A. Orr

Jillur Rahman Saurav, Thuong Le Hoai Pham, Pritam Mukherjee et al.

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.

Md Zahangir Alom, Quynh T. Tran, Brent A. Orr

Histologic examination plays a crucial role in oncology research and diagnostics. The adoption of digital scanning of whole slide images (WSI) has created an opportunity to leverage deep learning-based image classification methods to enhance diagnosis and risk stratification. Technical limitations of current approaches to training deep convolutional neural networks (DCNN) result in suboptimal model performance and make training and deployment of comprehensive classification models unobtainable. In this study, we introduce a novel approach that addresses the main limitations of traditional histopathology classification model training. Our method, termed Learned Resizing with Efficient Training (LRET), couples efficient training techniques with image resizing to facilitate seamless integration of larger histology image patches into state-of-the-art classification models while preserving important structural information. We used the LRET method coupled with two distinct resizing techniques to train three diverse histology image datasets using multiple diverse DCNN architectures. Our findings demonstrate a significant enhancement in classification performance and training efficiency. Across the spectrum of experiments, LRET consistently outperforms existing methods, yielding a substantial improvement of 15-28% in accuracy for a large-scale, multiclass tumor classification task consisting of 74 distinct brain tumor types. LRET not only elevates classification accuracy but also substantially reduces training times, unlocking the potential for faster model development and iteration. The implications of this work extend to broader applications within medical imaging and beyond, where efficient integration of high-resolution images into deep learning pipelines is paramount for driving advancements in research and clinical practice.