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multiscale cell cell interactive spatial transcriptomics analysis  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc multiscale cell cell interactive spatial transcriptomics analysis
Overview of MCIST workflow. Gene expression data are treated as a point cloud of cells, from which we construct a sequence of <t>multiscale</t> cell‐cell interaction graphs based on an affinity measure between expression profiles and k‐nearest neighbors (kNNs). These graphs give rise to an ensemble of low‐dimensional multiscale topological PCA representations of the gene expression data, each characterizing a specific combination of cell–cell connectivities. A latent space representation of the spatially resolved gene expression data is also constructed from a deep learning model to pair with the multiscale topological representation. These representations are then aligned for downstream ensemble clustering‐enabling spatial domain detection, residue‐similarity index (RSI)‐optimized trajectory inference, and differential gene expression analysis.
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Overview of MCIST workflow. Gene expression data are treated as a point cloud of cells, from which we construct a sequence of multiscale cell‐cell interaction graphs based on an affinity measure between expression profiles and k‐nearest neighbors (kNNs). These graphs give rise to an ensemble of low‐dimensional multiscale topological PCA representations of the gene expression data, each characterizing a specific combination of cell–cell connectivities. A latent space representation of the spatially resolved gene expression data is also constructed from a deep learning model to pair with the multiscale topological representation. These representations are then aligned for downstream ensemble clustering‐enabling spatial domain detection, residue‐similarity index (RSI)‐optimized trajectory inference, and differential gene expression analysis.

Journal: Advanced Science

Article Title: Multiscale Cell–Cell Interactive Spatial Transcriptomics Analysis

doi: 10.1002/advs.202508358

Figure Lengend Snippet: Overview of MCIST workflow. Gene expression data are treated as a point cloud of cells, from which we construct a sequence of multiscale cell‐cell interaction graphs based on an affinity measure between expression profiles and k‐nearest neighbors (kNNs). These graphs give rise to an ensemble of low‐dimensional multiscale topological PCA representations of the gene expression data, each characterizing a specific combination of cell–cell connectivities. A latent space representation of the spatially resolved gene expression data is also constructed from a deep learning model to pair with the multiscale topological representation. These representations are then aligned for downstream ensemble clustering‐enabling spatial domain detection, residue‐similarity index (RSI)‐optimized trajectory inference, and differential gene expression analysis.

Article Snippet: In this study, we present the MultiScale Cell‐Cell Interactive Spatial Transcriptomics Analysis method, which unites the strengths of spatially resolved deep learning techniques with a topological representation of multi‐scale cell‐cell similarity relations.

Techniques: Gene Expression, Construct, Sequencing, Expressing, Residue