Landmarks and angular measurements of maximum intensity projection of Z from confocal

I’m trying to place landmarks or beacons on a .tif (12 blue crosses in image) and either get locations (x,y) of those beacons or be able to measure multiple coordinates between them. Furthermore, I’m trying to find the angle of the line formed from each pair (yellow line and bracket) and a set 180 degree line (green dashed).

In short, I need three things:

  1. Set what horizontal or 180 degrees is.
  2. Place markers and output (x,y) or be able to measure many lines between all those 12 markers
  3. Find the angles of the 6 lines in relation to the preset horizontal

I’m happy to bounce in and out of various plugins or even programs and have about 300 images to measure. I do have the original .nd2 files from a Nikon A1, but doubt those will help in anyway.

Thank you for any assistance.


Hello Christian,

Did you try using the Angle tool from the main toolbar of ImageJ?

Here you are a video showing how to use it:

I hope it helps,