Spatial Transcriptomics Analysis

Comprehensive analysis of spatially-resolved transcriptomics data to understand gene expression patterns in tissue architecture context. Combines expression profiling with spatial coordinates to reveal tissue organization, cell-cell interactions, and spatially variable genes.

LOOK UP, DON'T GUESS

When uncertain about any scientific fact, SEARCH databases first rather than reasoning from memory. A database-verified answer is always more reliable than a guess.

When to Use This Skill

Triggers:

• User has spatial transcriptomics data (Visium, MERFISH, seqFISH, etc.)
• User has only an H&E histology image and no spatial assay at all -- DeepSpotM_predict_gene_expression (local model, no API/key) predicts spatial gene expression for a 224x224 H&E tile directly, a virtual readout when no real spatial data exists yet. Treat its output as a model prediction to guide follow-up (e.g. which region to actually assay), not a substitute for the platforms above when real spatial data is the goal.
• Questions about tissue architecture or spatial organization
• Spatial gene expression pattern analysis
• Cell-cell proximity or neighborhood analysis requests
• Tumor microenvironment spatial structure questions
• Integration of spatial with single-cell data
• Spatial domain identification
• Tissue morphology correlation with expression