problem with the intensity in *.spc file tgspcread

I am using the tgspcread function to import *.spc files from a spectrometer.

The function reads everything fine, however the intensity of the spectra is much lower than it should be.

When I compare the intensity using the spectrometer program there is a difference of several orders of magnitude in the intensities and completely arbitrary. It appears that the tgspcread function is dividing the intensity of each spectrum by an arbitrary factor.

Does anyone have any idea what the function is doing?

below an example

[Alejandro Castro Alvarez]

I also found that the x-axis is slightly different from Matlab and spectrometer software. That moves the whole spectra

Answer 1

[Garmit Pant]

Hello Alejandro Castro Alvarez

I see that you are working with spectral data acquired from a spectrometer and saved as a Thermo Galactic GRAMS format SPC-file. You are trying to import the data to MATLAB using “tgspcread” function.

“tgspcread” function reads the raw binary data stored in the SPC-file and imports it into MATLAB in ‘double’ precision format. The function reads and converts the binary data as it is, without any post-processing like normalization.

I investigated the behaviour of the “tgspcread” function using a sample file that I have attached to the answer. On comparing the plots between MATLAB R2021b and Spectragryph v1.2.16.1, I found no discrepancy between the plots.

The following can be the reasons behind the discrepancy in the plots:

• The spectrometer software can be applying some post-processing steps like normalization or scaling while exporting the data to a SPC-file.
• The MATLAB script used to read and plot the data can be applying some normalization or scaling after using the “tgspcread” function.

You can refer to the documentation for the “tgspcread” function to understand how to refine your readings using input arguments:

https://www.mathworks.com/help/releases/R2021b/bioinfo/ref/tgspcread.html

I hope you find the above explanation and suggestions useful!

[Alejandro Castro Alvarez]

Hi Garmit,

Thank you for your response. I checked your file and it works properly (Spectragryph vs Matlab). However, I do not understand what happened to my files. I never use the equipment's software to treat the data; instead, I save it as it was measured.

I always check the files first before doing the analysis. Here a small script to check and plot the files.

[file,path] = uigetfile('*.spc','Select Raman');
filename    = fullfile(path,file);
SPCStruct = tgspcread(filename);
Freq=SPCStruct.X; % cm-1 or nm
Y   =SPCStruct.Y; % intensity 
plot(Freq,Y)

Do you have any idea what the problem could be?

I attach an example of the map.

Thank a lot for your help!