tp81/imagej-countnuclei2d repository overview

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)

⁠Usage

docker run --rm tp81/imagej-countnuclei2d IMAGE_FILENAME

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

⁠Limitations

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