# How to convert gray values to nanometers at the z-scale in the Plot Profil

### Sample image and/or code

PINAR6.BMP (292.3 KB)

How do I get the z-scale to convert the gray values into nanometers and then show me the nanometers in the z-direction in the plot profile?

Please explain the source of the image.

I just guessing but it looks like some kind of projection with brightness proportional to thickness. If that’s true then a linear rescaling the image using the data from the color bar should do it. After converting your test image to 32-Bit and multiplying by 1994/255=7.819 the gray scale is converted to thickness.

This picture is taken from an atomic force microscope. Using this microscope, the height differences between the patterns should be determined. I only received this picture as a BMP file and should evaluate it. On the picture you can see the gray values in the Z direction. I will try this picture as indicated in the corresponding scale to convert. For now, thank you very much and I’ll try.

I don’t quite understand this multipling. Sorry! I have now uploaded a picture of my place here and would like to see the nanometers instead of the gray value!
I ask for a simple instruction because I don’t work very intensively with ImageJ

@GPossi The gray scale bar at the left of the image is the height calibration. If you get its profile “Ctrl-Alt-K” you will see that it is a linear ramp. The minimum value of the ramp is 10 and the maximum value is 237. Since the ramp is only 100 pixels high we can assume that it is a compressed representation of a pixel value range of 0 to 255 where 0 refers to a height of 0nm and 255 refers to a height of 1994nm. If you plot gray(0-255) vs nm(0-1994) you get a simple two-point calibration line with a slope of 1994/255 = 7.819 nm/gray-level and an intercept a 0. To convert the 0 to 255 image to nm convert it to 32-bit using the ImageJ menu “Image>Type>32-Bit” and multiply the 32-Bit image by 7.819 using the ImageJ menu “Process>Math>Multiply”. Select “Image>Lookup Tables>Grays” and then “Image>Adjust>Brightness/Contrast” and click “Auto” to improve the view of the image.

If you get the profile again the number will be height in nm. You can change the axis labels by clicking “More>Axis Options” in the plot window.7.819.

Using the profile tool I’m getting about 200nm for a typical height difference.

Thank you very much for the great help. You managed to record the representation in nanometers and micrometers for a layperson. That’s exactly what I wanted and I’m over the moon. Again thank you very much. I am really happy and my heart is overjoyed that there are such nice people on the net.