Extended Data Fig. 2: Benchmarking results of neighborhood characterization methods in tonsil tissue.

(1A) Cellular composition-based neighborhood characterization. (1B) MESA: Protein-based neighborhood characterization. (1C) MESA: mRNA-based neighborhood characterization. (2A) BANKSY neighborhood characterization⁴⁵. (2B) CellCharter neighborhood characterization¹⁶. (2C) UTAG neighborhood characterization¹⁵. Each panel shows the full tonsil tissue sample (top) and a zoom-in view of a representative germinal center (bottom), with distinct colors denoting different neighborhoods. As compared to the approach based solely on cellular composition (1A), BANKSY (2A) and CellCharter (2B) showed finer-grained neighborhood characterization; however, MESA (1B and 1C) enables more granular neighborhood delineation. For example, in the germinal centers, BANKSY identified two distinct neighborhoods (labeled as 0 and 1); UTAG characterized a single neighborhood (labeled as 1); CellCharter produced results most similar to MESA, with three neighborhoods labeled as 0, 1, and 3. These comparative analyses highlight the advantage of incorporating multiomics information in niche identification. Methods leveraging the dynamic range of protein measurements as a proxy for cell states show enhanced sensitivity to spatially coregulated protein and mRNA expression patterns, enabling enhanced neighborhood identification.