Slide Set: Batch Processing for ImageJ
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Slide Set: Batch Processing for ImageJ

Slide Set is a framework for batch processing and analysis of image data using ImageJ. It simplifies image analysis by linking image files with important metadata like regions of interest, experimental conditions, and time point information, and automatically repeating analysis tasks across multiple regions in multiple images.

  • Avoid tedious and error-prone manual repetition without the effort of developing a scripted or fully automated solution.
  • Ensure the entire image analysis workflow is transparent and reproducible.

Slide Set is a plugin for ImageJ2. It works with Fiji, but not with “plain” ImageJ1.

More information, including installation instructions and documentation:

Comments, suggestions, and bug reports are greatly appreciated.


  • Organize data in tables
  • Simplify region of interest (ROI) selection
  • Save ROIs as SVG files for reference or reuse in multiple analyses
  • Flexible built-in analysis commands, including average pixel values, co-localization coefficients, region sizes, and image segmentation based on threshold values
  • Automate many general ImageJ2 plugins
  • Link analysis results to command inputs and track all command parameters to maintain transparency and reproducibility