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Hematoxylin and Eosin (H&E) staining is widely regarded as the standard in pathology for diagnosing diseases and tracking tumor recurrence. While H&E staining shows tissue structures, it lacks the ability to reveal specific proteins that…
Cell detection, segmentation and classification are essential for analyzing tumor microenvironments (TME) on hematoxylin and eosin (H&E) slides. Existing methods suffer from poor performance on understudied cell types (rare or not present…
Chemical staining methods are dependable but require extensive time, expensive chemicals, and raise environmental concerns. These challenges highlight the need for alternative solutions like virtual staining, which accelerates the…
For invasive breast cancer, immunohistochemical (IHC) techniques are often used to detect the expression level of human epidermal growth factor receptor-2 (HER2) in breast tissue to formulate a precise treatment plan. From the perspective…
We present HistoAtlas, a pan-cancer computational atlas that extracts 38 interpretable histomic features from 6,745 diagnostic H&E slides across 21 TCGA cancer types and systematically links every feature to survival, gene expression,…
We present a self-supervised algorithm for several classification tasks within hematoxylin and eosin (H&E) stained images of breast cancer. Our method is robust to stain variations inherent to the histology images acquisition process, which…
Spatially Resolved Transcriptomics (SRT) is a cutting-edge technique that captures the spatial context of cells within tissues, enabling the study of complex biological networks. Recent graph-based methods leverage both gene expression and…
Hematoxylin and eosin (H&E)-stained slides are central to cancer diagnosis and monitoring, visualizing tissue architecture and cellular morphology. However, H&E lacks the molecular specificity needed to distinguish cell states and…
Spatial Transcriptomics (ST) is a technology that measures gene expression profiles within tissue sections while retaining spatial context. It reveals localized gene expression patterns and tissue heterogeneity, both of which are essential…
Spatial Transcriptomics (ST) provides spatially-resolved gene expression, offering crucial insights into tissue architecture and complex diseases. However, its prohibitive cost limits widespread adoption, leading to significant attention on…
Spatial transcriptomics offers spatially resolved gene expression profiling within tissue sections, but its cost and limited throughput hinder large-scale deployment. To extend this capability to routine practice, recent computational…
Spatial variable genes (SVGs) reveal critical information about tissue architecture, cellular interactions, and disease microenvironments. As spatial transcriptomics (ST) technologies proliferate, accurately identifying SVGs across diverse…
It is a critical task to evalaute HER2 expression level accurately for breast cancer evaluation and targeted treatment therapy selection. However, the standard multi-step Immunohistochemistry (IHC) staining is resource-intensive, expensive,…
Expression of human epidermal growth factor receptor 2 (HER2) is an important biomarker in breast cancer patients who can benefit from cost-effective automatic Hematoxylin and Eosin (H\&E) HER2 scoring. However, developing such scoring…
Advances in spatially-resolved transcriptomics (SRT) technologies have propelled the development of new computational analysis methods to unlock biological insights. As the cost of generating these data decreases, these technologies provide…
Recognition of Handwritten Mathematical Expressions (HMEs) is a challenging problem because of the ambiguity and complexity of two-dimensional handwriting. Moreover, the lack of large training data is a serious issue, especially for…
In computational pathology, automatic nuclei instance segmentation plays an essential role in whole slide image analysis. While many computerized approaches have been proposed for this task, supervised deep learning (DL) methods have shown…
Histological Tertiary Lymphoid Structures (TLSs) are increasingly recognized for their correlation with the efficacy of immunotherapy in various solid tumors. Traditionally, the identification and characterization of TLSs rely on…
Histopathology serves as the gold standard in cancer diagnosis, with clinical reports being vital in interpreting and understanding this process, guiding cancer treatment and patient care. The automation of histopathology report generation…
The spatial location of cells within tissues and organs is crucial for the manifestation of their specific functions.Spatial transcriptomics technology enables comprehensive measurement of the gene expression patterns in tissues while…