3D Intensity Profile

Measurement of intensity profile in 3D space




Input: A text file and an active 3D image stack

Output: Values in results table.

Though intensity profile function is one of very popular function in ImageJ, tools for measuring intensity profile in 3D space is hardly found. This script loads a text file containing pairs of 3D coordinates and measures intensity profile between those two points.

The image at the top of this page is a schematic view of how 3D profile is sampled. Spheres are the two ends of sampling interval, and small spheres are the sampled points.


  • ImageJ
  • Apache Commons Math version 3.0 or later (preinstalled in Fiji)


Download K_3Dprofile.js and run the script in ImageJ or in Fiji.


Prepare a tab-delimited data text file with a pair of 3D coordinates per line (6 numbers per line). Run the script, and in dialog window choose the file, then 3D intensity profile in the top-image window will be calculated and shown in the Results table.