How to export AFM image to a data matrix?

I have exported .mi file of AFM data to .jpeg format using gwyddion software. I have attached the image. In this image, each pixel contains z-axis values or surface topography values (color coded). The maximum height of particles is 18 nm and minimum is 0. I would like to export this image into a 3D data matrix which contains information about X, Y and Z-axes values. Can anyone help to find a way?

Answer 1

[Amith]

Hi Bharat,

There is no direct way to import image data or AFM data into MATLAB, but it has options to import csv files using the csvread function or the readmatrix function.

Please refer to this MATLAB answer for more information: https://www.mathworks.com/matlabcentral/answers/575488-how-to-import-afm-data-to-matlab

Hope this helps!

Answer 2

[George Heath]

Hi Bharat,

There are MATLAB scripts avalible to open .gwy files, so I would export your .mi file from gwyddion as a .gwy image file and then use the open_gwychannel avalible here:

https://github.com/George-R-Heath/NanoLocz/tree/main/scripts

or

https://uk.mathworks.com/matlabcentral/fileexchange/154880-nanolocz

The open_gwychannel function will open files saved in gwyddion. If you download the script and then run:

[im, meta] = open_gwychannel(filename)

Replacing 'filename' with the filename eg:

[im, meta] = open_gwychannel('Testdata.gwy');

The output varible 'im' will be your image as a 2D matrix with z values in each field. Meta will list some meta data linked to the image.