How to make the heatmap of fluorescent intensity ratio using ImageJ like the example?


I am working with subcellular localization of membrane protein in neuron. To show the distribution richness of our protein, I want to invert the fluorescent picture into ratio map like the right panel of the example picture.


For a simple calibration bar on an image with a pseudocolor look-up table (LUT), use Analyze > Tools > Calibration Bar…

The following macro illustrates this:

run("Blobs (25K)");
run("Calibration Bar...", "location=[Upper Right] fill=White label=Black number=3 decimal=0 font=12 zoom=1 overlay");

More complex cases can be solved by scripting, as discussed here:


I really appreciate your response, which is helpful for my ratiometric.