Advancements in Spatial Transcriptomics and Cell Analysis

The field of spatial transcriptomics and cell analysis is rapidly evolving, with a focus on developing innovative methods to enhance the resolution and accuracy of spatial transcriptomics data. Recent developments have centered around integrating histology images with spatial transcriptomics data to improve cell type annotation and uncover distinct microenvironmental niches. Additionally, there is a growing interest in learning adaptive cell graphs and topology-informed clustering methods to better model cell-cell relationships and spatial neighborhood information. These advancements have the potential to significantly improve our understanding of complex tissue ecosystems and cellular heterogeneity. Noteworthy papers include: HaDM-ST, which proposes a histology-assisted differential modeling framework for high-resolution spatial transcriptomics generation. scAGC, which introduces a single-cell clustering method that learns adaptive cell graphs with contrastive guidance. HistoPLUS, which presents a state-of-the-art model for cell analysis on H&E slides, achieving significant improvements in detection quality and classification score. CellSymphony, which leverages foundation model-derived embeddings to integrate spatial transcriptomics data with histology images at single-cell resolution. AtomDiffuser, which presents a time-aware degradation modeling framework for STEM imaging. SPHENIC, which proposes a novel topology-informed multi-view clustering method for spatial transcriptomics.

Sources

HaDM-ST: Histology-Assisted Differential Modeling for Spatial Transcriptomics Generation

scAGC: Learning Adaptive Cell Graphs with Contrastive Guidance for Single-Cell Clustering

Towards Comprehensive Cellular Characterisation of H&E slides

CellSymphony: Deciphering the molecular and phenotypic orchestration of cells with single-cell pathomics

AtomDiffuser: Time-Aware Degradation Modeling for Drift and Beam Damage in STEM Imaging

SPHENIC: Topology-Informed Multi-View Clustering for Spatial Transcriptomics

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