Academic and industry resources

Nolan lab GitHub [web]

  • Analyze CODEX and CyTOF dataset

IonPath data analysis, MIBI Tracker [web]

  • Process and visualize MIBI datasets

Bodenmiller lab GitHub [web]

Zhuang Lab GitHub [web]

  • Handle MERFISH datasets

Cai lab GitHub [web]

  • Process seqFISH image data

Publications for spatial data

InsituNet [link]

  • Network Visualization and Analysis of Spatially Aware Gene Expression Data with InsituNet, Cell Systems (2018)

HMRF [link]

  • Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data, Nat Biotech (2018)

Giotto [link]

  • Giotto, a toolbox for integrative analysis and visualization of spatial expression data, BioRxiv (2020)


  • Identification of spatial expression trends in single-cell gene expression data, Nat Methods (2018)

SPARK [link]

  • Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies