First published: 2020-01-05 Sun
Last updated: 2020-01-05 Sun
ImageJ lookup tables (LUTs) map integer or floating point pixel values to colors. ImageJ comes with a lot of nice LUTs and there are many available on the internet as well (Christophe Leterrier has excellent ones available here https://github.com/cleterrier/ChrisLUTs). I recently wanted to make my own based on a colormap on an image exported from our microscope (myelin is the blue-ish color below that I wanted to use).
You can view the raw values of the LUT by clicking
Image>Color>Show LUT and clicking "List" on the resulting window.
Split the channels so only your channel of interest is showing (
Image>Color>Split Channels close all unrelated channels), and save this as a LUT by clicking
File>Save As...> LUT.... I saved mine as
Close and re-open Fiji and you should see your new LUT in the options menu