Strain Library Imaging Protocol: high-throughput automated single-cell microscopy for large bacterial collections arrayed on multi-well plates

摘要

Single-cell microscopy is a powerful tool for studying gene functions using strain libraries, but suffers from throughput limitations. Here we describe the Strain Library Imaging Protocol (SLIP), a high-throughput, automated microscopy workflow for large strain collections with minimal user involvement. SLIP involves transferring arrayed bacterial cultures from multi-well plates onto large agar pads using inexpensive replicator pins and automatically imaging the resulting single cells. The acquired images are subsequently reviewed and analyzed by custom MATLAB scripts that segment single-cell contours and extract quantitative metrics. SLIP yields rich datasets on cell morphology and gene expression, which illustrate the function of certain genes and the connections among strains in a library. For a library arrayed on 96-well plates, image acquisition can be completed within 4 min per plate.