Yimin Zheng

A single-cell view of human tissue aging reveals architectural decline beyond cellular composition

The paper analyzes single-cell data from human tissues to show that aging involves both cell loss and architectural remodeling, with structural decline independent of cell composition.

StainX: GPU-accelerated batch stain normalization for computational pathology at scale

StainX provides a GPU-accelerated framework for batch stain normalization in histopathology images, achieving significant speed improvements over CPU and other GPU implementations.

Spatially organized cancer-associated fibroblast subtypes partition cutaneous carcinomas into immune-active and contracted, immune-repressed niches

Tumor Heterogeneity Induces Pro- and Anti-metastatic Myeloid Cell Phenotypes in Breast Cancer Lung Metastasis

The paper profiles myeloid cells in breast cancer primary tumors and metastases to show how tumor heterogeneity drives shifts in myeloid cell phenotypes from anti- to pro-metastatic.

LazySlide: accessible and interoperable whole slide image analysis

LazySlide provides an open-source Python package for whole-slide image analysis and multimodal integration, enabling efficient histopathology workflows with minimal setup.

The Spatial Atlas of Human Anatomy (SAHA): A Multimodal Subcellular-Resolution Reference Across Human Organs

SAHA creates a multimodal, subcellular-resolution reference atlas of healthy human tissues, revealing spatial organization and disease-associated disruptions across multiple organ systems.

Histological aging signatures enable tissue-specific disease prediction from blood

This paper develops tissue clocks from histopathological images to predict biological age and disease risk from blood samples, showing non-uniform aging rates across tissues and associations with lifestyle and medical factors.

Marsilea: An intuitive generalized visualization paradigm for complex datasets

Marsilea provides a flexible visualization framework for complex datasets using a cross-layout paradigm, enabling intuitive and customizable visualizations with a Python library and web interface.