Resources

Integration between single-cell genomics and spatial-omics

• MaxFuse github.com/shuxiaoc/maxfuse: cross-modality matching via fuzzy embedding
• MARIO github.com/shuxiaoc/mario-py: single-cell proteomic alignment pipeline

Expression and image fusion

• CellLENS github.com/sggao/celllens: cell neighborhood profiling with histology context

Tissue state analysis

• MESA mesa-py.readthedocs.io: multiomics + ecological spatial analysis

Spatial-omics × microbiome

• MicroCart-analysis github.com/BokaiZhu/microcart_analysis: Microbiome Cartography (Part 1)
• MicroCart-probe github.com/BokaiZhu/microbiomeFISH: Microbiome Cartography (Part 2)

Signal spillover correction

• REDSEA github.com/nolanlab/REDSEA: reinforcement-based bleed correction