Tutorial: How To Evaluate A Raman Map With Origin Pro 9.0

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How

to evaluate a Raman map with Origin Pro 9.0

Niclas Mller

Tutorial: How to evaluate a Raman


map with Origin Pro 9.0
This tutorial intends to show you how to evaluate a Raman map, which you for
example recorded at the Raman XploRa. I will give an example how to create a
Raman map, which shows the 2D/G-peak intensity ratio of a graphene flake. You can
find the data which belong to the map below on my website1.

10m

1. Exporting data from the Raman-XploRa:


After recording the Raman map click on the window in which all the spectra are
displayed (in program Labspec). Click on File Split and type as a file name M.
The spectra will now be exported with the names M_x_y, with the coordinates x and
y.

2. Creating an analysis template in Origin:


If the spectra of your map contain similar peaks it is useful to create an analysis
template. One only has to fit one spectrum manually and saves the settings for the fit
as a template to fit all the other spectra.
As a first step import one spectrum of the map, which is representative. We do not
only want to import the data of the spectrum, but also the coordinates of the
spectrum, which are included in the file name. Click FileImportImport Wizard and
choose the file M_24_23.txt, or any other representative spectrum of the Raman
map. Click the button Next until the dialog window is titled Import Wizard
Variable Extraction. Here choose Specify location of variable names and values
using delimiters. Click Next and look in the top window for the line in which the file
name is displayed. Choose this name at Variable Line and choose Delimiter
Other _ as you can see in the picture below. Now you can choose the coordinates

1 http://niclasm.userpage.fu-berlin.de/Raman%20mapping%20tutorial/RamanMapping.html

How to evaluate a Raman map with Origin Pro 9.0

Niclas Mller

at Value, write a description at Enter variable name and click add. Do this to add the
x and y coordinate to the bottom window until it looks the same as in the picture
below.

Click Next to get to the dialog window Import Wizard Data Columns and make
sure that 1,000.00 is chosen as Numeric Separator. Then click Finish.
To fit the spectrum click on the column label B(Y) so that this column is marked. Now
choose AnalysisFittingNonlinear Curve FitOpen Dialog. Lets create a new
category (In the dialog box choose Category<New>) and name it Graphene.
Write as a function name G_2D_peak_fitting and choose Function Model Explicit
and Function Type Expression. We will only fit the G- and 2D-peak of the
spectrum for simplicity. If you want to evaluate the map more accurately you can fit
more peaks in the spectrum. Click Next and write the same parameters as in the
picture below. The abbreviations stand for y0 = Baseline, x = position of peak, A =
area of peak and w = width of peak.

How to evaluate a Raman map with Origin Pro 9.0

Niclas Mller

Click Next and fill in all the information as shown in the picture below. The
Function Body should be y0 + (2*A_G/PI)*(w_G/(4*(x-x_G)^2 + (w_G)^2))+
(2*A_2D/PI)*(w_2D/(4*(x-x_2D)^2 + (w_2D)^2)) which is a fit of the spectrum with
two Lorentz peaks.

Click Next and choose Always run Initialization Code before Fitting and Use Origin
C.
Click Next to set the upper and lower bounds of the parameters as shown in the
picture below.

How to evaluate a Raman map with Origin Pro 9.0

Niclas Mller

Finally click Finish.


Now we can use our defined function to fit the spectrum. Do this by choosing the
function and clicking Fit. Two new windows will appear in the workbook called FitNL1
and FitNLCurve1. In the window FitNL1 you will find all the values of the fitting
parameters. We need only a few of these information to create a Raman map and
the less information have to be generated for a spectrum, the faster the fit is.
Therefore the displayed information should be reduced to the necessary amount. To
do this click on the green lock (on the top, left side in the window) and choose
Change Parameters. At Settings Output deselect Optional Report Tables, at
Settings Advanced Quantities to compute Fit Statistics deselect all except Fit
status. Furthermore in the same window deselect Fit Summary and ANOVA. Finally
deselect Settings Fitted Curves Fitted Curves Plot and Residual Plots. If you
click on Fit now the window FitNL1 should only contain the information as in the
picture below.

These are the information we need for creating the Raman map. To list the fitting
results of all the spectra later in one table we have to create a result sheet in which
all the results of this one fit are listed in one line. Right click into an empty area if the
workbook and click Add New Sheet. Name the new sheet Results, create columns
and label them as shown in the picture below. You can also add a column, which is
named Fit Status. The x and y coordinates have units in m, because the step width
when recording the Raman map was 1m in x and y direction. If this is not the case
you can change the coordinate values with Set Column Values.

How to evaluate a Raman map with Origin Pro 9.0

Niclas Mller

Now the values from the sheet FitNL1 have to be copied into the result sheet. Do this
just by right clicking on the value and choosing copy. When pasting the value choose
Paste Link, which is necessary because the result sheet is used as a template later.
The peaks height can be calculated from the width and area with the formula
h_G=2*A_G/(PI*w_G). Right click on the column label D(Y) and choose Set Column
Values. One can type the formula into the window as shown in the picture below.
Make sure that Recalculate is set to Auto.

Do the same for the value of h_2D. Also use Set Column Values to calculate the
2D/G height ratio.
To insert the coordinates from the file name right click on the cell and choose Insert
Variable. Then click on the + sign beside USER.VARIABLES and the two coordinates
x and y will appear. When you insert them make sure that Insert as link is chosen.
The result sheet should now look like in the picture below.

Finally click File Save Workbook As Analysis Template and choose for example
G_2D_intensity_mapping.ogw as a file name. You should also save the project for
making changes later, if necessary.

3. Evaluating Raman map with batch processing in Origin:


Open a new project and click File Batch Processing. In the dialog window choose
Load Analysis Template and choose the link of the analysis template, which you
created before. Choose the text files from the Raman map which contain the spectra
in the File List. Furthermore choose:
Use Impost Setting in Workbook Yes
Dataset Identifier None
Data Sheet M_24_23
Result Sheet Results

How to evaluate a Raman map with Origin Pro 9.0

Niclas Mller

Output Sheet [Summary]Results!


Delete Intermediate Workbook Yes
Options Starting Row of Output Sheet 1
Options Clear Output Sheet on Start Yes
Options Append Label Rows No
Click OK.
Origin is now fitting all the Raman spectra of the map and creating a table with all the
results. This can take up to several hours, depending on the size of the map.
Now you should look over the result sheet and replace all unreasonable values for
the 2D/G height ratio with a default value, for example 0. The fastest way to control
whether a fit was successful is to look at the peak width of the G- and 2D-peak,
which should not be one of the boundary values.

3. Plotting a Raman map in Origin:


To plot the Raman map in Origin as a Contour Plot one has to convert the data into a
matrix. If the map has the same dimension in x-direction as in y-direction one can
convert the result data sheet into a matrix with xyz-gridding in Origin (Worksheet
Convert to Matrix XYZ Gridding Open Dialog). If this is not the case I did not
find any fast solution with Origin yet. We will therefore use Excel to convert the data
table into a matrix. Copy the three columns for x, y and 2D/G height ratio into an
empty Excel worksheet. Then create a Pivot Table out of these data, which is also
possible in Libre Office if you do not use Excel.
In Origin create an empty matrix and change its dimension by right clicking into the
empty cell on the top, left side (choose Set Matrix Dimension/Labels). Fill in the
values as shown in the picture below.

How to evaluate a Raman map with Origin Pro 9.0

Niclas Mller

Copy the values from the Excel worksheet into the matrix in Origin. You will see that
the value at coordinates x=1, y=1 is missing. Copy the correct value from the result
sheet into this cell. This corresponds to x=0, y=0 in the result sheet.
Plot the data in the matrix by marking all the values (click on the top, left cell) and
click Plot Contour Color Fill. If you want to see every pixel of the map, to get
more accurate information double click on the graph and choose Fill to Grid Lines. In
this case it is instructive to hide the contour lines (in the window Plot Details Plot
Properties click on the label Line, deselect Show Lines Show on Major Levels
Only and choose Hide All). Further increase the number of color levels to get more
information out of the map by changing the properties in the Plot Details Plot
Properties window. By right clicking on the map and choosing Axis make sure that all
the pixels are fully plotted (the pixels at the edges are usually not fully displayed).
Right click in the white area above the plot and choose Layer Management to resize
the map such that the aspect ratio is correct. Finally change the labels and add ticks
to all the edges and your map should look similar to the one shown in the picture
below.

If you have questions or suggestions please write me: [email protected]


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