Slide set: Reproducible image analysis and batch processing with ImageJ

Research output: Contribution to journalArticlepeer-review

16 Scopus citations

Abstract

Most imaging studies in the biological sciences rely on analyses that are relatively simple. However, manual repetition of analysis tasks across multiple regions in many images can complicate even the simplest analysis, making record keeping difficult, increasing the potential for error, and limiting reproducibility. While fully automated solutions are necessary for very large data sets, they are sometimes impractical for the small- and medium-sized data sets common in biology. Here we present the Slide Set plugin for ImageJ, which provides a framework for reproducible image analysis and batch processing. Slide Set organizes data into tables, associating image files with regions of interest and other relevant information. Analysis commands are automatically repeated over each image in the data set, and multiple commands can be chained together for more complex analysis tasks. All analysis parameters are saved, ensuring transparency and reproducibility. Slide Set includes a variety of built-in analysis commands and can be easily extended to automate other ImageJ plugins, reducing the manual repetition of image analysis without the set-up effort or programming expertise required for a fully automated solution.

Original languageEnglish (US)
Pages (from-to)269-278
Number of pages10
JournalBioTechniques
Volume59
Issue number5
DOIs
StatePublished - Nov 2015
Externally publishedYes

Keywords

  • Automation
  • Image analysis
  • Image processing
  • Reproducibility
  • Software

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry, Genetics and Molecular Biology(all)

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