A categorization of spatial transcriptomics methods for cell-cell communication analysis.

Spatial transcriptomics methods enable detailed analysis of cell-cell communication, with 33 recent approaches categorized into three key types for tissue-level insights.

• Why it matters: Understanding cell-cell communication is crucial for deciphering tissue behavior and disease mechanisms, but existing methods vary in focus and application, creating a need for clear guidance.
• What they did: The authors reviewed 33 methods and organized them into three categories: network inference at cell-type or single-cell resolution, modeling of microenvironment-driven variability, and spatially informed gene co-associations, providing a structured guide for researchers.
• The result: This framework helps researchers select appropriate methods based on their goals, highlighting each approach's strengths and limitations, thereby advancing spatial transcriptomics research in cell communication studies.