ImageJ macros

Szu-Chin Fu

Some simple macros for ImageJ/FIJI that I used for quantitation of nuclear export activity in cells.

• [F1] Generating max intensity projection for z-stacks (total: 4 slices).
  • Input: the bottom stack.
• [F2] Generating average intensity projection for z-stacks (total: 4 slices).
  • Input: the bottom stack.
• [F3] Generating nuclear ROI(s) for DAPI/Hoechst stained nuclei images using Nuclei Watershed Separation.
• [F4] Generating cytoplasmic ring ROI(s) with a thickness of 150nm.

Steps:

1. Load you multichannel images e.g. YFP and Hoechest.
2. Select 4 nuclear z-planes spanning the middle of the nucleus.
3. Collapse into a single Hoechest (by average intensity projection using [F1]) and YFP image (by average intensity projection using [F2]).
4. Generate nuclear ROI(s) for DAPI/Hoechst stained nuclei images using [F3].
5. Remove unwanted nuclear ROIs e.g. untransfected cells.
6. Generate cytoplasmic "ring" ROI(s) using [F4].

7. Measure nuclear and cytoplasmic YFP intensity.
8. Correct for background noise by subtracting the intensity in a nearby region without any cell.