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This is a simple script for ImageJ for quantifying separate cells in batch mode. Useful for sparse cells in tissue sections.

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mdepaco/ImageJ-Batch-sparse-cell-counting-script

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ImageJ Batch sparse cell counting script

This is a simple script for ImageJ for quantifying separate cells in batch mode. Useful for sparse cells in tissue sections.

Functions:

  • Open images one by one (in a user specified folder)
  • User draws ROI
  • Applies pre-set threshold (in this case 600, 65535)
  • Run particle analysis (in this case 60-1400 pixel size)
  • Closes images (NOT saving them)
  • Lets user choose where to save results/summary table

Hope it can be useful for someone else with similar needs :)

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This is a simple script for ImageJ for quantifying separate cells in batch mode. Useful for sparse cells in tissue sections.

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