Emanuel. G. et al. Nat. Methods 14, 1159–1162 (2017);

Lawson, M.J. et al. Mol. Syst. Biol. 13, 947 (2017).

Pooled screens have accelerated the rate of genetic discovery by allowing large libraries of diverse genetic variants to be screened together rather than individually. However, pooled screens typically require phenotypic enrichment or, if developed in single-cell format, use RNA sequencing as the only readout. Two methods now perform pooled screens for dynamic, image-based phenotypes. Single cells, each bearing a genetic variant or perturbation that is associated with an expressed sequence barcode, are imaged and then genotyped by reading out the barcode with multiplexed fluorescence in situ hybridization. Emanuel et al. use their approach to identify improved YFAST fluorescent proteins from among 60,000 variants screened in bacteria, and Lawson et al. develop dynamic u-fluidic microscopy-based phenotyping of a library before in situ genotyping (DuMPLING) to show that CRISPR-induced perturbations in multiple bacterial clones can be screened for gene-regulatory phenotypes.