Using CellProfiler for Automatic Identification and Measurement of Biological Objects in Images

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. © 2015 by John Wiley & Sons, Inc.

[1]  Anne E Carpenter,et al.  Microarrays of lentiviruses for gene function screens in immortalized and primary cells , 2006, Nature Methods.

[2]  Anne E Carpenter,et al.  CellProfiler: image analysis software for identifying and quantifying cell phenotypes , 2006, Genome Biology.

[3]  Anne E Carpenter,et al.  CellProfiler: free, versatile software for automated biological image analysis. , 2007, BioTechniques.

[4]  Nikolaos Scarmeas,et al.  The good, bad, and ugly? , 2012, Neurology.

[5]  Jianhua Xu,et al.  Colony size measurement of the yeast gene deletion strains for functional genomics , 2007, BMC Bioinformatics.

[6]  Jostein Dahle,et al.  Automated counting of mammalian cell colonies by means of a flat bed scanner and image processing , 2004, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[7]  Anne E Carpenter,et al.  Genetic Architecture of Hsp90-Dependent Drug Resistance , 2006, Eukaryotic Cell.

[8]  Anne E Carpenter,et al.  The Spemann organizer gene, Goosecoid, promotes tumor metastasis , 2006, Proceedings of the National Academy of Sciences.

[9]  Anne E Carpenter,et al.  Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software , 2011, Bioinform..

[10]  Anne E Carpenter,et al.  A Lentiviral RNAi Library for Human and Mouse Genes Applied to an Arrayed Viral High-Content Screen , 2006, Cell.

[11]  Polina Golland,et al.  CellProfiler Analyst: data exploration and analysis software for complex image-based screens , 2008, BMC Bioinformatics.