Related papers: Multiscale topology classifies and quantifies cell…
Accurate detection of cancer tissue regions (CTR) enables deeper analysis of the tumor microenvironment and offers crucial insights into treatment response. Traditional CTR detection methods, which typically rely on the rich cellular…
The complex and dynamic crosstalk between tumour and immune cells results in tumours that can exhibit distinct qualitative behaviours - elimination, equilibrium, and escape - and intricate spatial patterns, yet share similar cell…
Conventional histopathology has long been essential for disease diagnosis, relying on visual inspection of tissue sections. Immunohistochemistry aids in detecting specific biomarkers but is limited by its single-marker approach, restricting…
Accurately modeling multi-class cell topology is crucial in digital pathology, as it provides critical insights into tissue structure and pathology. The synthetic generation of cell topology enables realistic simulations of complex tissue…
While pathology foundation models have transformed cancer image analysis, they often lack integration with molecular data at single-cell resolution, limiting their utility for precision oncology. Here, we present PAST, a pan-cancer…
Spatial transcriptomics (ST) provides essential spatial context by mapping gene expression within tissue, enabling detailed study of cellular heterogeneity and tissue organization. However, aligning ST data with histology images poses…
Accurate interpretation of histopathological images demands integration of information across spatial and semantic scales, from nuclear morphology and cellular textures to global tissue organization and disease-specific patterns. Although…
Spatial transcriptomics measures the expression of thousands of genes in a tissue sample while preserving its spatial structure. This class of technologies has enabled the investigation of the spatial variation of gene expressions and their…
Spatial transcriptomics has revolutionized tissue analysis by simultaneously mapping gene expression, spatial topography, and histological context across consecutive tissue sections, enabling systematic investigation of spatial…
The spatial distributions of different types of cells could reveal a cancer cell growth pattern, its relationships with the tumor microenvironment and the immune response of the body, all of which represent key hallmarks of cancer. However,…
A wide range of data that appear in scientific experiments and simulations are multivariate or multifield in nature, consisting of multiple scalar fields. Topological feature search of such data aims to reveal important properties useful to…
High-dimensional neural activity often reside in a low-dimensional subspace, referred to as neural manifolds. Grid cells in the medial entorhinal cortex provide a periodic spatial code that are organized near a toroidal manifold,…
Spatial transcriptomics is a technology that captures gene expression levels at different spatial locations, widely used in tumor microenvironment analysis and molecular profiling of histopathology, providing valuable insights into…
The cellular composition of the tumor microenvironment can directly impact cancer progression and the efficacy of therapeutics. Understanding immune cell activity, the body's natural defense mechanism, in the vicinity of cancerous cells is…
A long-standing challenge is designing multi-scale structures with good connectivity between cells while optimizing each cell to reach close to the theoretical performance limit. We propose a new method for direct multi-scale topology…
Spatial domain identification requires jointly modeling molecular signatures and physical coordinates, yet current tools frequently over-smooth biological boundaries, require user-specified cluster numbers, and lack principled multimodal…
The absence of a conventional association between the cell-cell cohabitation and its emergent dynamics into cliques during development has hindered our understanding of how cell populations proliferate, differentiate, and compete, i.e. the…
Recent advancements in spatial transcriptomics technologies allow researchers to simultaneously measure RNA expression levels for hundreds to thousands of genes while preserving spatial information within tissues, providing critical…
Understanding the intricate cellular environment within biological tissues is crucial for uncovering insights into complex biological functions. While single-cell RNA sequencing has significantly enhanced our understanding of cellular…
Spatial transcriptomics (ST) measures gene expression at a set of spatial locations in a tissue. Communities of nearby cells that express similar genes form \textit{spatial domains}. Specialized ST clustering algorithms have been developed…