title: Using CellProfiler for Automatic Identification and Measurement of Biological Objects in Images.
abstract: Visual analysis is required to perform many biological experiments, from counting colonies to measuring the size or fluorescence intensity of individual cells or organisms. This unit outlines the use of CellProfiler, a free, open-source image analysis tool that extracts quantitative information from biological images. It includes a step-by-step protocol for automated analysis of the number, color, and size of yeast colonies growing on agar plates, but the methods can be adapted to identify and measure many other types of objects in images. The flexibility of the software allows experimenters to create pipelines of adjustable modules to fit different biological experiments and to generate accurate measurements from dozens or even hundreds of thousands of images.
authors.affiliation: Broad Institute Imaging Platform, Cambridge, Massachusetts.
authors.forename: Mark-Anthony
authors.initials: MA
authors.lastname: Bray
authors.affiliation: Broad Institute Imaging Platform, Cambridge, Massachusetts.
authors.forename: Martha S
authors.initials: MS
authors.lastname: Vokes
authors.affiliation: Broad Institute Imaging Platform, Cambridge, Massachusetts.
authors.forename: Anne E
authors.initials: AE
authors.lastname: Carpenter
mesh_terms: D057205:Automation, Laboratory / Q000379:methods*; D003470:Culture Media / Q000737:chemistry; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000254:growth & development
chemical_list: D003470:Culture Media
keywords: automatic image analysis; colony counting; open-source software; phenotypes; yeast colonies