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Spatial transcriptomics data analysis workflow for cancer therapy resistance schematic outline of key computational steps in of spatial omics data analysis for CTR research. (A) Preprocessing: Multi‐cell resolution technologies (e.g., Visium, GeoMx DSP) typically require cell type deconvolution, whereas single‐cell or sub‐cellular resolution technologies (e.g., <t>MERSCOPE,</t> Xenium, Stereo‐seq) employ cell segmentation to delineate individual cells. (B) Data format and results: The spatial coordinates (X, Y) of cells are integrated with gene expression data to determine cell identity and spatial domain annotations. Interactions among cells are inferred to reveal tumour‐microenvironment crosstalk. (C) Spatial resolved biological tasks: Multiple downstream analyses, including cell state trajectory analysis, identification of spatial domains, interaction among cells and detection of spatially variable genes (SVGs), can be used to provide insights into potential spatial heterogeneity and crosstalk associated with CTR.
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Spatial transcriptomics data analysis workflow for cancer therapy resistance schematic outline of key computational steps in of spatial omics data analysis for CTR research. (A) Preprocessing: Multi‐cell resolution technologies (e.g., Visium, GeoMx DSP) typically require cell type deconvolution, whereas single‐cell or sub‐cellular resolution technologies (e.g., <t>MERSCOPE,</t> Xenium, Stereo‐seq) employ cell segmentation to delineate individual cells. (B) Data format and results: The spatial coordinates (X, Y) of cells are integrated with gene expression data to determine cell identity and spatial domain annotations. Interactions among cells are inferred to reveal tumour‐microenvironment crosstalk. (C) Spatial resolved biological tasks: Multiple downstream analyses, including cell state trajectory analysis, identification of spatial domains, interaction among cells and detection of spatially variable genes (SVGs), can be used to provide insights into potential spatial heterogeneity and crosstalk associated with CTR.
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Spatial transcriptomics data analysis workflow for cancer therapy resistance schematic outline of key computational steps in of spatial omics data analysis for CTR research. (A) Preprocessing: Multi‐cell resolution technologies (e.g., Visium, GeoMx DSP) typically require cell type deconvolution, whereas single‐cell or sub‐cellular resolution technologies (e.g., <t>MERSCOPE,</t> Xenium, Stereo‐seq) employ cell segmentation to delineate individual cells. (B) Data format and results: The spatial coordinates (X, Y) of cells are integrated with gene expression data to determine cell identity and spatial domain annotations. Interactions among cells are inferred to reveal tumour‐microenvironment crosstalk. (C) Spatial resolved biological tasks: Multiple downstream analyses, including cell state trajectory analysis, identification of spatial domains, interaction among cells and detection of spatially variable genes (SVGs), can be used to provide insights into potential spatial heterogeneity and crosstalk associated with CTR.
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Spatial transcriptomics data analysis workflow for cancer therapy resistance schematic outline of key computational steps in of spatial omics data analysis for CTR research. (A) Preprocessing: Multi‐cell resolution technologies (e.g., Visium, GeoMx DSP) typically require cell type deconvolution, whereas single‐cell or sub‐cellular resolution technologies (e.g., MERSCOPE, Xenium, Stereo‐seq) employ cell segmentation to delineate individual cells. (B) Data format and results: The spatial coordinates (X, Y) of cells are integrated with gene expression data to determine cell identity and spatial domain annotations. Interactions among cells are inferred to reveal tumour‐microenvironment crosstalk. (C) Spatial resolved biological tasks: Multiple downstream analyses, including cell state trajectory analysis, identification of spatial domains, interaction among cells and detection of spatially variable genes (SVGs), can be used to provide insights into potential spatial heterogeneity and crosstalk associated with CTR.

Journal: Clinical and Translational Medicine

Article Title: Cancer therapy resistance from a spatial‐omics perspective

doi: 10.1002/ctm2.70396

Figure Lengend Snippet: Spatial transcriptomics data analysis workflow for cancer therapy resistance schematic outline of key computational steps in of spatial omics data analysis for CTR research. (A) Preprocessing: Multi‐cell resolution technologies (e.g., Visium, GeoMx DSP) typically require cell type deconvolution, whereas single‐cell or sub‐cellular resolution technologies (e.g., MERSCOPE, Xenium, Stereo‐seq) employ cell segmentation to delineate individual cells. (B) Data format and results: The spatial coordinates (X, Y) of cells are integrated with gene expression data to determine cell identity and spatial domain annotations. Interactions among cells are inferred to reveal tumour‐microenvironment crosstalk. (C) Spatial resolved biological tasks: Multiple downstream analyses, including cell state trajectory analysis, identification of spatial domains, interaction among cells and detection of spatially variable genes (SVGs), can be used to provide insights into potential spatial heterogeneity and crosstalk associated with CTR.

Article Snippet: , Imaging based , Vizgen MERSCOPE , FF, FFPE , 0.1 μm , 1 cm × 1 cm , 1000 , –.

Techniques: Gene Expression

Spatial transcriptomics data analysis workflow for cancer therapy resistance schematic outline of key computational steps in of spatial omics data analysis for CTR research. (A) Preprocessing: Multi‐cell resolution technologies (e.g., Visium, GeoMx DSP) typically require cell type deconvolution, whereas single‐cell or sub‐cellular resolution technologies (e.g., MERSCOPE, Xenium, Stereo‐seq) employ cell segmentation to delineate individual cells. (B) Data format and results: The spatial coordinates (X, Y) of cells are integrated with gene expression data to determine cell identity and spatial domain annotations. Interactions among cells are inferred to reveal tumour‐microenvironment crosstalk. (C) Spatial resolved biological tasks: Multiple downstream analyses, including cell state trajectory analysis, identification of spatial domains, interaction among cells and detection of spatially variable genes (SVGs), can be used to provide insights into potential spatial heterogeneity and crosstalk associated with CTR.

Journal: Clinical and Translational Medicine

Article Title: Cancer therapy resistance from a spatial‐omics perspective

doi: 10.1002/ctm2.70396

Figure Lengend Snippet: Spatial transcriptomics data analysis workflow for cancer therapy resistance schematic outline of key computational steps in of spatial omics data analysis for CTR research. (A) Preprocessing: Multi‐cell resolution technologies (e.g., Visium, GeoMx DSP) typically require cell type deconvolution, whereas single‐cell or sub‐cellular resolution technologies (e.g., MERSCOPE, Xenium, Stereo‐seq) employ cell segmentation to delineate individual cells. (B) Data format and results: The spatial coordinates (X, Y) of cells are integrated with gene expression data to determine cell identity and spatial domain annotations. Interactions among cells are inferred to reveal tumour‐microenvironment crosstalk. (C) Spatial resolved biological tasks: Multiple downstream analyses, including cell state trajectory analysis, identification of spatial domains, interaction among cells and detection of spatially variable genes (SVGs), can be used to provide insights into potential spatial heterogeneity and crosstalk associated with CTR.

Article Snippet: , Vizgen MERSCOPE ULTRA , FF, FFPE, adherent or suspended cells , ≤0.02 μm , 1.25 cm 2 /3 cm 2 , 1000 , –.

Techniques: Gene Expression