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. 2015 Jan 5:109:14.17.1-14.17.13.
doi: 10.1002/0471142727.mb1417s109.

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

Mark-Anthony Bray  1 , Martha S Vokes  1 , Anne E Carpenter  1
Affiliations

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

Mark-Anthony Bray et al. Curr Protoc Mol Biol. .

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.

Keywords: automatic image analysis; colony counting; open-source software; phenotypes; yeast colonies.

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Figures

Figure 14.17.1
Figure 14.17.1
An overview of the CellProfiler example pipeline. The names of the images created or objects identified appear in italics below each image, whereas the module names appear in a larger regular font.
Figure 14.17.2
Figure 14.17.2
(A) The original plate image. (B) The colonies identified. (C) The Subtracted Red image (or “the red channel”). (D) All identified colonies outlined. (E) The colonies classified by area. (F) The colonies classified by “redness”.
See this image and copyright information in PMC

References

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