reading Ma-XRF mapped data cubes

I'm trying to import Bruker M4 Tornado ma-XRF maps into matlab for further processing.

I can read them in from a .raw file format, and convert this to a 3x3 data cube / hypercubes

data_cube = fread(fileID, [depth,width*height], 'uint8=>uint8'); %readable with cubeViewer

%% or

hcube = hypercube(data_cube,wavelengths); %readable with hyperspectralViewer

but when I read it in it looks like this: lines and dots and not a coherent structure that I imaged.

if anyone knows what im doing wrong, or how this might be corrected, I could do with any help.

[Abhishek Tripathi]

Could you provide the input image? This would greatly assist us in identifying the issue with the reading.

Answer 1

[Manikanta Aditya]

Hi Molly,

As per my understanding, you’re having trouble visualizing your data in MATLAB after importing it from a .raw file format. The image you’ve shared appears to show scattered white dots and lines, which suggests that the data might not be interpreted or visualized correctly.

Please try the following workarounds to see if you can resolve the issue at hand:

• Check the data import: Ensure that the data is being read correctly from the '.raw' file. The dimensions used in the ‘fread’ function should match the actual dimensions of your data.
• Data preprocessing: Depending on the nature of your data, you might need to perform some preprocessing steps before visualization. This could include noise reduction, normalization, or other transformations.

Please refer to the following references to know more about

• ‘fread’: https://www.mathworks.com/help/matlab/ref/fread.html
• Datapreprocessing: https://www.mathworks.com/help/matlab/preprocessing-data.html

I hope this resolves the issue you were facing.