title: Strain Library Imaging Protocol for high-throughput, automated single-cell microscopy of large bacterial collections arrayed on multiwell plates.
abstract: Single-cell microscopy is a powerful tool for studying gene functions using strain libraries, but it suffers from throughput limitations. Here we describe the Strain Library Imaging Protocol (SLIP), which is a high-throughput, automated microscopy workflow for large strain collections that requires minimal user involvement. SLIP involves transferring arrayed bacterial cultures from multiwell 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 data sets on cell morphology and gene expression that 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.
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, California, USA.
authors.forename: Handuo
authors.initials: H
authors.lastname: Shi
authors.affiliation: Biophysics Program, Stanford University, Stanford, California, USA.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Colavin
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, California, USA.|Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Timothy K
authors.initials: TK
authors.lastname: Lee
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, California, USA.|Biophysics Program, Stanford University, Stanford, California, USA.|Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Kerwyn Casey
authors.initials: KC
authors.lastname: Huang
mesh_terms: D001331:Automation; D001419:Bacteria / Q000166:cytology*; D007091:Image Processing, Computer-Assisted; D008853:Microscopy / Q000295:instrumentation*; D061848:Optical Imaging; D059010:Single-Cell Analysis / Q000295:instrumentation*; D057188:Workflow