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Plotting Many Spectra Together with the Overlay Manager

When an array of spectra is acquired as a single experiment, the spectrometer saves it as a matrix and you have, automatically, the same plotting options available for a 2-D spectrum. When, instead, the experiment is saved as a series of 1-D spectra, it's easy to combine them together with the Overlay Manager. This dialog can also be used to plot together two or more 2-D spectra (each one with a different color, possibly!).

How to Create a Stacked Plot with the Overlay Manager:

Step 1

Open and process all the spectra.

Step 2

Bring to the fore the first spectrum of the series.

Step 3

Choose Format > Overlay. The list of open windows appears (the foremost window is excluded).

Step 4

Select the spectra that you want to import as overlays: click into the boxes at at left of their names. To select all the windows at once, click “ALL”.

Step 5

Set the value (in screen points) for the progressive vertical offset between adjacent spectra. With the initial value of zero the spectra are perfectly superimposed.

Step 6

Click Apply to see the effect. You can try with different values. It is easier to adjust this offset when the overlay manager is closed: click on the first overlay (from the bottom) and drag to the new position.

Step 7

If the order of the spectra is not correct, try sorting them with a click into the column headers.
If you desire a different order, click ALL to remove the “overlay” check marks, then check them again in the desired order. The first item you check goes to the bottom of the logical stack; the last item goes on top. This logical stack is used to apply the progressive offsets. To synchronize the table with the internal stack, choose “List as Stacked” (on the Mac: under the “Order” pull-down menu).

Step 8

You can set the color for a single overlay: click the corresponding colored rectangle on the left. The “extend” button (on the Mac: an orange arrow) extends the change to the other spectra listed above. An article on the web describes how to create a color gradient.

Step 9

If the frequency scale of the overlays is not correct, click Force Same Scale (copies the frequency reference from the foremost document into the other ones).

Step 10

Close the Overlay Manager. The first document stores the links to the overlays: in this way they can remain linked forever, unless you rename or delete the files (broken links are immediately forgotten). If you move all the files together, the links remain valid.

In our example, it's not necessary to change the relative amplification of the overlays. If you need, you can press the button Fit: the highest peak of the last overlay will become as tall as the window; or you can enter an explicit value for the amplification. When the dialog is closed, you can use the keys * and / to obtain the same effect.


To change the amplification and the offset values you can move the cursor over it and rotate the mouse wheel.
When typing the offset values, you are allowed to enter them as percentages (of the window size).
On Windows, you have three fields where the values for the selected overlay are reproduced and can be edited.


If you double click a name into the table of the open windows, the overlay is transformed into an exact replica of the corresponding document, including its frequency scale, integrals, window size, etc...

Related Topics

Creating a Poster

Subtracting a Spectrum from Another One

Keyboard Commands to Manipulate the Overlays

Tabulating the Integrals of a Series of Spectra

Aligning the Overlays


Web Tutorial

The Automatic Labelling Machine