The microscopic examination of surgical tissue remains a cornerstone of disease classification but relies on subjective interpretations and access to highly specialized experts, which can compromise accuracy and clinical care. While emerging breakthroughs in artificial intelligence (AI) offer promise for automated histological analysis, the growing number of proprietary digital pathology solutions has created barriers to real-world deployment. To address these challenges, we introduce OnSight Pathology, a platform-agnostic computer vision software that uses continuous custom screen captures to provide real-time AI inferences to users as they review digital slide images. Accessible as a single, self-contained executable file (https://onsightpathology.github.io/ ), OnSight Pathology operates locally on consumer-grade personal computers without complex software integration, enabling cost-effective and secure deployment in research and clinical workflows. Here we demonstrate the utility of OnSight Pathology using over 2,500 publicly available whole slide images across different slide viewers, as well as cases from our clinical digital pathology setup. The software's robustness is highlighted across routine histopathological tasks, including the classification of common brain tumor types, mitosis detection, and the quantification of immunohistochemical stains. A built-in multi-modal chat assistant provides verifiable descriptions of images, free of rigid class labels, for added quality control. Lastly, we show compatibility with live microscope camera feeds, including from personal smartphones, offering potential for deployment in more analog, inter-operative, and telepathology settings. Together, we highlight how OnSight Pathology can deliver real-time AI inferences across a broad range of pathology pipelines, removing key barriers to the adoption of AI tools in histopathology.

Three-dimensional X-ray histology techniques offer a non-invasive alternative to conventional 2D histology, enabling volumetric imaging of biological tissues without the need for physical sectioning or chemical staining. However, the inherent greyscale image contrast of X-ray tomography limits its biochemical specificity compared to traditional histological stains. Within digital pathology, deep learning-based virtual staining has demonstrated utility in simulating stained appearances from label-free optical images. In this study, we extend virtual staining to the X-ray domain by applying cross-modality image translation to generate artificially stained slices from synchrotron-radiation-based micro-CT scans. Using over 50 co-registered image pairs of micro-CT and toluidine blue-stained histology from bone-implant samples, we trained a modified CycleGAN network tailored for limited paired data. Whole slide histology images were downsampled to match the voxel size of the CT data, with on-the-fly data augmentation for patch-based training. The model incorporates pixelwise supervision and greyscale consistency terms, producing histologically realistic colour outputs while preserving high-resolution structural detail. Our method outperformed Pix2Pix and standard CycleGAN baselines across SSIM, PSNR, and LPIPS metrics. Once trained, the model can be applied to full CT volumes to generate virtually stained 3D datasets, enhancing interpretability without additional sample preparation. While features such as new bone formation were able to be reproduced, some variability in the depiction of implant degradation layers highlights the need for further training data and refinement. This work introduces virtual staining to 3D X-ray imaging and offers a scalable route for chemically informative, label-free tissue characterisation in biomedical research.

Accurate intraoperative diagnosis is essential for providing safe and effective care during brain tumor surgery.

Registration of histological and mass spectrometry imaging (MSI) allows for more precise identification of structural changes and chemical interactions in tissue. With histology and MSI having entirely different image formation processes and dimensionalities, registration of the two modalities remains an ongoing challenge. This work proposes a solution that synthesises histological images from MSI, using a pix2pix model, to effectively enable unimodal registration. Preliminary results show promising synthetic histology images with limited artifacts, achieving increases in mutual information (MI) and structural similarity index measures (SSIM) of +0.924 and +0.419, respectively, compared to a baseline U-Net model. Our source code is available on GitHub: https://github.com/kimberley/MIUA2025.

Despite the growing interest in designing truly interactive hyperparameter optimization (HPO) methods, to date, only a few allow to include human feedback. Existing interactive Bayesian optimization (BO) methods incorporate human beliefs by weighting the acquisition function with a user-defined prior distribution. However, in light of the non-trivial inner optimization of the acquisition function prevalent in BO, such weighting schemes do not always accurately reflect given user beliefs. We introduce a novel BO approach leveraging tractable probabilistic models named probabilistic circuits (PCs) as a surrogate model. PCs encode a tractable joint distribution over the hybrid hyperparameter space and evaluation scores. They enable exact conditional inference and sampling. Based on conditional sampling, we construct a novel selection policy that enables an acquisition function-free generation of candidate points (thereby eliminating the need for an additional inner-loop optimization) and ensures that user beliefs are reflected accurately in the selection policy. We provide a theoretical analysis and an extensive empirical evaluation, demonstrating that our method achieves state-of-the-art performance in standard HPO and outperforms interactive BO baselines in interactive HPO.

Simultaneous segmentation and classification of nuclei in digital histology play an essential role in computer-assisted cancer diagnosis; however, it remains challenging. The highest achieved binary and multi-class Panoptic Quality (PQ) remains as low as 0.68 bPQ and 0.49 mPQ, respectively. It is due to the higher staining variability, variability across the tissue, rough clinical conditions, overlapping nuclei, and nuclear class imbalance. The generic deep-learning methods usually rely on end-to-end models, which fail to address these problems associated explicitly with digital histology. In our previous work, DAN-NucNet, we resolved these issues for semantic segmentation with an end-to-end model. This work extends our previous model to simultaneous instance segmentation and classification. We introduce additional decoder heads with independent weighted losses, which produce semantic segmentation, edge proposals, and classification maps. We use the outputs from the three-head model to apply post-processing to produce the final segmentation and classification. Our multi-stage approach utilizes edge proposals and semantic segmentations compared to direct segmentation and classification strategies followed by most state-of-the-art methods. Due to this, we demonstrate a significant performance improvement in producing high-quality instance segmentation and nuclei classification. We have achieved a 0.841 Dice score for semantic segmentation, 0.713 bPQ scores for instance segmentation, and 0.633 mPQ for nuclei classification. Our proposed framework is generalized across 19 types of tissues. Furthermore, the framework is less complex compared to the state-of-the-art.

Histological staining of tissue biopsies, especially hematoxylin and eosin (H&E) staining, serves as the benchmark for disease diagnosis and comprehensive clinical assessment of tissue. However, the process is laborious and time-consuming, often limiting its usage in crucial applications such as surgical margin assessment. To address these challenges, we combine an emerging 3D quantitative phase imaging technology, termed quantitative oblique back illumination microscopy (qOBM), with an unsupervised generative adversarial network pipeline to map qOBM phase images of unaltered thick tissues (i.e., label- and slide-free) to virtually stained H&E-like (vH&E) images. We demonstrate that the approach achieves high-fidelity conversions to H&E with subcellular detail using fresh tissue specimens from mouse liver, rat gliosarcoma, and human gliomas. We also show that the framework directly enables additional capabilities such as H&E-like contrast for volumetric imaging. The quality and fidelity of the vH&E images are validated using both a neural network classifier trained on real H&E images and tested on virtual H&E images, and a user study with neuropathologists. Given its simple and low-cost embodiment and ability to provide real-time feedback in vivo, this deep learning-enabled qOBM approach could enable new workflows for histopathology with the potential to significantly save time, labor, and costs in cancer screening, detection, treatment guidance, and more.

Accurate intraoperative diagnosis is essential for providing safe and effective care during brain tumor surgery. Our standard-of-care diagnostic methods are time, resource, and labor intensive, which restricts access to optimal surgical treatments. To address these limitations, we propose an alternative workflow that combines stimulated Raman histology (SRH), a rapid optical imaging method, with deep learning-based automated interpretation of SRH images for intraoperative brain tumor diagnosis and real-time surgical decision support. Here, we present OpenSRH, the first public dataset of clinical SRH images from 300+ brain tumors patients and 1300+ unique whole slide optical images. OpenSRH contains data from the most common brain tumors diagnoses, full pathologic annotations, whole slide tumor segmentations, raw and processed optical imaging data for end-to-end model development and validation. We provide a framework for patch-based whole slide SRH classification and inference using weak (i.e. patient-level) diagnostic labels. Finally, we benchmark two computer vision tasks: multiclass histologic brain tumor classification and patch-based contrastive representation learning. We hope OpenSRH will facilitate the clinical translation of rapid optical imaging and real-time ML-based surgical decision support in order to improve the access, safety, and efficacy of cancer surgery in the era of precision medicine. Dataset access, code, and benchmarks are available at opensrh.mlins.org.

Linking phenotypes to specific gene expression profiles is an extremely important problem in biology, which has been approached mainly by correlation methods or, more fundamentally, by studying the effects of gene perturbations. However, genome-wide perturbations involve extensive experimental efforts, which may be prohibitive for certain organisms. On the other hand, the characterization of the various phenotypes frequently requires an expert's subjective interpretation, such as a histopathologist's description of tissue slide images in terms of complex visual features (e.g. In this paper, we use Deep Learning to eliminate the inherent subjective nature of these visual histological features and link them to genomic data, thus establishing a more precisely quantifiable correlation between transcriptomes and phenotypes. Using a dataset of whole slide images with matching gene expression data from 39 normal tissue types, we first developed a Deep Learning tissue classifier with an accuracy of 94%.