Histopathology Image Segmentation

Whole-slide image (WSI) preprocessing, including tissue detection and patch extraction, is critical computational pathology, yet remains a major bottleneck for large-scale workflows. Existing methods often rely either on threshold-based heuristics that are sensitive to staining variations, tissue fragmentation, and artifacts, or on patch-wise deep learning pipelines with substantially higher computational cost. We present AtlasPatch, a scalable high-throughput WSI preprocessing method built around a foundation-model-based tissue detector that operates at thumbnail resolution: a single thumbnail-level forward pass yields a tissue mask that directly guides patch coordinate generation at the target desired magnification, avoiding repeated patch-level inference. The proposed detector's robustness and efficiency is driven by two coupled contributions: (i) a parameter-efficient adaptation of the SAM2 foundation model that updates only its layer-normalization parameters (0.076% of model weights), and (ii) a curated and semi-manually annotated multi-cohort dataset of 30,000 WSI thumbnail-mask pairs deliberately spanning multiple organs, scanners, tissue appearances, and artifacts. The detector is coupled with pyramid-aware contour mapping from thumbnail to full-resolution slide coordinates, enabling direct patch coordinate generation at the target magnification and parallelized high-throughput patch extraction. AtlasPatch's tissue detection achieves a precision of 0.986 and remains robust across slide variations. Compared with widely used deep-learning preprocessing methods, AtlasPatch is up to 16x faster while preserving downstream multiple-instance learning performance across six slide-level classification tasks. These results position AtlasPatch as a frontier of efficient preprocessing in large-scale computational pathology and pathology foundation models.

Drug-induced toxicity is a leading cause of preclinical and early-clinical failure, making early detection critical. Histopathology is the gold standard for toxicity assessment but relies on expert pathologists, creating a bottleneck for large-scale screening. We introduce an AI-based anomaly detection framework for whole-slide images (WSIs) of rodent liver that identifies healthy tissue and known pathologies (anomalies) and flags samples without training data as out-of-distribution (OOD). We evaluate OOD detection on two held-out categories: apoptosis (single-cell, near-OOD) and staining/processing artifacts (heterogeneous, far-OOD). We build a novel pixelwise-annotated dataset and fine-tune a pre-trained Vision Transformer (DINOv2) via Low-Rank Adaptation (LoRA) for segmentation, then use the Mahalanobis distance for OOD detection with class-specific thresholds. Optimizing the false positive rate subject to a predefined constraint on the false negative rate yields only 0.16% of pathological tissue classified as healthy and 0.35% of healthy tissue classified as pathological. Our false negative rate does not penalise cross-type errors, reflecting the safety-first objective of never overlooking a lesion; under the stricter correct-class criterion our method assigns 93.93% of ID and 89.38% of OOD findings to their own class. The study demonstrates technical feasibility of pixel-level anomaly detection for mouse liver histopathology, indicating possible applications in improving preclinical workflows and drug development efficiency.

Background and Objective: Precise and scalable instance segmentation of cell nuclei is a fundamental prerequisite for computational pathology, yet gigapixel whole-slide images (WSIs) pose significant computational challenges. While patch-based processing is standard during training, existing methods are often limited to small tile sizes during inference due to architectural bottlenecks or reliance on computationally expensive post-processing for instance separation. We introduce a faster, scalable, and end-to-end framework capable of processing large-scale image tiles while accurately modeling biologically realistic overlapping nuclei. Methods: We propose LSP-DETR (Local Star Polygon DEtection TRansformer). The model represents nuclei as star-convex polygons and employs a lightweight transformer with linear complexity, enabling the processing of high-resolution images in a single forward pass. A novel radial distance loss accommodates annotation uncertainty, allowing the segmentation of overlapping nuclei to emerge naturally without explicit overlap labels. Results: LSP-DETR achieves state-of-the-art efficiency, with an inference time of 0.45 s/mm^2, a 3.2x speedup over StarDist, the next-fastest method. On PanNuke, the model achieves competitive accuracy (67.5 bPQ), while yielding an F$_1$-score of 0.964 in polygon overlap when evaluated against consensus annotations from two expert pathologists. Furthermore, it outperforms larger models such as LKCell in generalization robustness, reaching an F1-score of 85.0 on MoNuSeg. Conclusions: LSP-DETR bridges the gap between high-fidelity segmentation and practical clinical requirements by eliminating heuristic post-processing. By providing a scalable, linear-complexity solution that naturally handles overlaps between nuclei, this framework sets a new direction for efficient high-throughput WSI analysis in digital pathology.