Public | Automated Build

Last pushed: a year ago
Short Description
Simplistic image to count nuclei in 2D using an imagej macro
Full Description

This small container is meant as a proof-of-concept for a simple object counter for 2D single channel images. It includes the following steps (see macro).

  1. Background subtraction (r=50px)
  2. Automatic Otsu thresholding
  3. Mask saving as TIFF
  4. Results saving as ROI collection
  5. Results saving as comma-separated values (CSV)


docker run --rm tp81/imagej-countnuclei2d IMAGE_FILENAME

This will spawn a new container, run ImageJ and call the macro CountFluoNuclei2D.ijm.


This is intended to be a proof-of-concept and as such has a few limitations:

  • it assumes the image is single channel, fluorescent (black background), single plane
  • the background subtraction is fixed at 50px
  • the minimum nuclei cutoff is fixed at 10px
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