[Gwyddion-users] Contrast level corresponding with height in Gwydddion exported RGB tiff file

[Witchukorn Phuthong]

Hi everyone,

Using Gwyddion, I do the basic leveling, scar removal and fourier noise
filtration, adjust the contrast and export my AFM image to RGB tiff file
and the contrast level has the height difference about 5 nm. Then, I would
like to associate the height and the brightness for further analysis in
imageJ. I also convert my RGB tiff file to 8-bit grayscale for this
analysis in ImageJ. So, I am wondering if it is valid to use the following
relationship: B = (255/5)*H; B = brightness (0-255 in grayscale) and H is
the height (nm) shown at a particular pixel of the original image after
contrast adjustment, when considering height threshold in ImageJ with
brightness?

For example, if I want to make the threshold height in imageJ to be 2.5 nm,
is it valid to set the threshold level for the brightness in imageJ to be B
= (255/5)*2.5 = 127.5 ~ 128.

Thanks,
Champ

[David Nečas (Yeti)]

Post by Witchukorn Phuthong
Using Gwyddion, I do the basic leveling, scar removal and fourier noise
filtration, adjust the contrast and export my AFM image to RGB tiff file
and the contrast level has the height difference about 5 nm. Then, I would
like to associate the height and the brightness for further analysis in
imageJ. I also convert my RGB tiff file to 8-bit grayscale for this
analysis in ImageJ.

I'm pretty sure ImageJ can read text data matrix. So save the data to
something.txt in Gwyddion and load that into ImageJ.

If you insist on a pixmap image format, use high-depth (16bit) greyscale
PNG. Or OpenEXR. Gwyddion saves the physical scaling info into all of
them, see

http://gwyddion.net/documentation/user-guide-en/pixmap-image-keys.html

In the case of PNG, any image software supporting the standard sCAL and
pCAL chunks should be able to open the image with the right scale
automatically (not sure if this applies to ImageJ or not).

Regards,

Yeti