Contains preprocessed single-cell data and metadata for feature selection. Preprocessed adata objects can be accessed using the read_h5ad function in anndata. Also contains the source data files for reproducing the Figures and Supplementary Figures referenced in the manuscript. The RPE iterative indirect immunofluorescence imaging dataset (adata_RPE.h5ad) from Ref. (https://doi.org/10.1016/j.cels.2021.10.007) was originally downloaded from the Zenodo repository (https://doi.org/10.5281/zenodo.4525425). The PDAC iterative indirect immunofluorescence imaging datasets (listed below) were originally downloaded from the Zenodo repository (https://doi.org/10.5281/zenodo.7860332). adata_PDAC_BxPC3_control.h5ad adata_PDAC_CFPAC_control.h5ad adata_PDAC_HPAC_control.h5ad adata_PDAC_MiaPaCa_control.h5ad adata_PDAC_Pa01C_control.h5ad adata_PDAC_Pa02C_control.h5ad adata_PDAC_Pa16C_control.h5ad adata_PDAC_PANC1_control.h5ad adata_PDAC_UM53_control.h5ad The CD8+ T cell differentiation dataset (adata_CD8.h5ad) from Ref. (https://doi.org/10.1126/sciimmunol.aaz6894) was originally downloaded from the Gene Expression Omnibus under the accession code GSE131847 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131847). The definitive endoderm differentiation dataset (adata_DE.h5ad) contains multiplexed single-cell RNA sequencing data profiling the differentiation of human embryonic stem cells into the definitive endoderm.