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Measure Samples
Select an article below to learn how to use Thermo Scientific OMNIC Paradigm Software to set up and measure a sample spectrum.
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Measurement settings allow you to specify how your sample is measured and how the data is processed after the spectrum is collected. Your settings control both how the instrument and sampling accessory measure the sample and how OMNIC Paradigm Software processes the data.
After adjusting your measurement settings, you can use them immediately or save them for later use.
This guide describes how to set, save, and use common measurement options. For a discussion of advanced settings, see “Advanced Measurement Settings.”
Set measurement options
Set and save your measurement settings or use previously saved settings before starting a measurement.
In OMNIC Paradigm Software for touchscreen, edit individual settings or import a settings file (.expx) before you measure your sample. To edit or review measurement settings, select an analysis type from the home screen.
Figure 1. Review measurement settings in the Summary, Details, and Background tabs
Set and save your measurement settings from the dashboard, or update a few options while previewing a sample spectrum.
Figure 1. Edit measurement settings in the New Measurement pane.
In OMNIC Paradigm Software for touchscreen, edit individual settings or import a settings file (.expx) before you measure your sample. To edit or review measurement settings, select an analysis type from the home screen.
Figure 1. Review measurement settings in the Summary, Details, and Background tabs
Set and save your measurement settings from the dashboard, or update a few options while previewing a sample spectrum.
Figure 1. Edit measurement settings in the New Measurement pane.
The following table describes the settings you will use most frequently.
| Option | Description | Default Setting |
|---|---|---|
| Measurement name | The name of your sample data. This name will appear when you save or open this data and in any reports you generate. The default name is the date and time of collection. | Date and Time |
| Number of sample scans | How many times the sample is scanned during 10 the measurement. The resulting data reflects the average of all the scans. More scans will result in more accurate data but will take longer to measure. | 10 |
| Resolution (cm-1) | Like the resolution of a photo or video, a better resolution will mean finer detail in your spectral data. For example, a better resolution will distinguish between two very close peaks while a poor resolution might combine them. A smaller value results in a higher (better) resolution, but also takes longer to measure. Typically, resolutions of 4 are used for solid and liquid samples. For gas samples, use a resolution of 1 or 0.5. | 4 |
| Analysis type | With OMNIC Paradigm for touchscreen, you select your analysis type from the home screen rather than selecting from a list. Allows you to automatically process your data after it’s collected. Use None to measure a sample without additional analysis. Search performs a correlation search. Use search to identify an unknown sample. Edit search settings in the Search Setup view. QCheck results indicate a match value between your sample and a reference. Use QCheck to verify the composition of a known sample. Edit QCheck settings in the QCheck Setup view. Quantify is used to quantify the components of a sample using a pre-selected quantification method. Select Identify > Quantify Setup to specify a quantification method. | None |
| Tag | Allows you to add a tag to the spectrum. Tags can later be used when searching for a spectrum. | |
| Final format | Determines the units used for the collected data. You can convert your data to another Y-axis unit after collection in the View/Display menu. | Absorbance |
| Sampling accessory | The sampling accessory used to measure the sample. Smart accessories are detected automatically. |
Save your measurement settings
Name and save your measurement settings so that you can easily select them from the dashboard for later use. Settings for Search, QCheck, and Quantify analyses are not saved in these settings.
To save your measurement settings
- Make any desired changes to the settings.
- Click New near the Settings menu at the top of the dashboard.
- Enter a new name for the settings and click Save.
Saved settings are added to the Settings list for later use.
Work with saved measurement settings
Once you have saved your measurement settings, you can edit or delete the settings.
To make changes to your saved settings
- Select the named settings that you want to update from the Settings menu.
- Edit the settings
- Click Save.
Your new settings are now saved under the old setting name and are available in the Settings menu.
To delete your saved settings
- Select the named settings you want to delete from the Settings menu.
- Click Delete.
- In the confirmation dialog, click Yes to permanently delete the named settings.
Save your measurement settings
Name and save your measurement settings so that you can easily select them from the dashboard for later use. Settings for Search, QCheck, and Quantify analyses are not saved in these settings.
To save your measurement settings
- Make any desired changes to the settings.
- Click New near the Settings menu at the top of the dashboard.
- Enter a new name for the settings and click Save.
Saved settings are added to the Settings list for later use.
Work with saved measurement settings
Once you have saved your measurement settings, you can edit or delete the settings.
To make changes to your saved settings
- Select the named settings that you want to update from the Settings menu.
- Edit the settings
- Click Save.
Your new settings are now saved under the old setting name and are available in the Settings menu.
To delete your saved settings
- Select the named settings you want to delete from the Settings menu.
- Click Delete.
- In the confirmation dialog, click Yes to permanently delete the named settings.
Import and export saved settings
Import a settings file to automatically update your current measurement settings to those you saved previously. When importing settings, you can import an OMNIC Experiment file (.exp) or an OMNIC Paradigm settings file (.expx).
OMNIC Paradigm software is compatible with .exp files that were created with OMNIC software. However, with OMNIC Paradigm, you can export only .expx files, which are not compatible with earlier versions of OMNIC software.
Importing an OMNIC Experiment file updates your measurement settings, but does not alter your analysis settings, such as Search Setup or QCheck Setup.
To import a settings file
- From the home screen, select an analysis type.
- While viewing the Summary tab, open the menu and select Open Settings.
- Select a .expx file to import and touch Open. Your settings will be updated to match the .expx file.
To import a settings file
- In the toolbar, click Settings.
- Select the .expx file you want to import and click Open.
- Your settings are updated to match the .expx file, and the named setting is now available in the Settings menu.
To export a settings file
- Choose the settings you wish to export from the Settings list
- Select Acquire Data > Export Settings.
- Enter a name for your settings file, select a directory to save the file, and click Save.
The settings file is now saved and ready for future use.
To import a settings file
- From the home screen, select an analysis type.
- While viewing the Summary tab, open the menu and select Open Settings.
- Select a .expx file to import and touch Open. Your settings will be updated to match the .expx file.
To import a settings file
- In the toolbar, click Settings.
- Select the .expx file you want to import and click Open.
- Your settings are updated to match the .expx file, and the named setting is now available in the Settings menu.
To export a settings file
- Choose the settings you wish to export from the Settings list
- Select Acquire Data > Export Settings.
- Enter a name for your settings file, select a directory to save the file, and click Save.
The settings file is now saved and ready for future use.
Accurate sample spectra require an accurate and current measurement of the background.
When you collect a background spectrum, you are collecting a measurement of the environment in the spectrometer without a sample in place, including characteristics of the detector and atmosphere inside the spectrometer. This background spectrum is then used to eliminate any signals in your sample spectrum that are due to the spectrometer or to the background environment. Without a measurement of the background, there would be no way to know whether you were seeing data from the sample you measured or from the background environment.
When to measure the background
Because the background environment in the spectrometer can change over time, you should update your background spectrum frequently.
In addition to collecting a new background spectrum periodically as the environment changes, collect a new background after any of the following circumstances:
- You have changed the hardware in your spectrometer, including changing sampling accessories
- You have changed the settings for measuring samples
Background settings
There are several options for when and how to measure the background. These options determine when and if you are prompted to collect a new measurement of the background.
To select a different background option, select an analysis option and open the Background tab.
Figure 1. Select a background setting in the Background tab.
To select a different background option, click More in the New Measurement pane of the dashboard and scroll to the Background group.
Figure 1. Select a background setting in the Background pane.
To select a different background option, select an analysis option and open the Background tab.
Figure 1. Select a background setting in the Background tab.
To select a different background option, click More in the New Measurement pane of the dashboard and scroll to the Background group.
Figure 1. Select a background setting in the Background pane.
The following table describes the background settings.
| Option | Description |
|---|---|
| Background scans | How many times the background will be measured. The resulting spectrum represents the average of all scans. More scans will produce a more accurate spectrum but will require a longer collection time. The default is 10. |
| Measure before every sample | If this option is selected, you will be prompted to collect a new background spectrum before every sample measurement. This is a good option when you are measuring only a few samples, as it ensures a current measurement, but it can slow down the measurement process. Allows you to measure many samples using the same background spectrum. You can enter any integer value between 1 and 1024, but note that the background environment may change over time and your sample spectra may become less accurate as time passes. |
| Smart background | Smart background measures the background automatically, so that you always have a current measurement without having to manually measure the background. |
| Use previous background | Allows you to select a previous background spectrum. This option should be used only rarely and under unusual circumstances (for example, if it would be impossible to load or remove the sample without changing the system environment). In this case, you would collect and save a background spectrum earlier, using conditions as close as possible to the conditions under which you will measure the sample. |
Measure the background
Measuring the background requires only a few simple steps. If you attempt to measure a sample without a current background spectrum, you will be prompted to measure the background before proceeding.
To measure the background
- From the home screen, select an analysis type.
- Open the Background tab to edit or review your background settings.
- To begin the measurement, touch Measure Background.
The Background Preview opens, and you can preview the background before proceeding. - To proceed, touch Start Background Measurement.
During the measurement, you can pause, restart, or stop the collection. If you stop the collection, the partial data will be used. For example, if you plan to collect 8 scans, but you stop after 4, the background spectrum will be available with 4 scans.
Once the background spectrum is measured, you can preview the sample spectrum and make any necessary changes to the sample measurement settings, or you can select Home in the menu to return to the home screen.
To measure the background
- Remove any sample from the sampling accessory.
- From the dashboard, select Preview and Measure Background.
The Background Preview window opens, and you can preview the background before continuing with the collection. - To continue, select Start Background Measurement, or click Dashboard in the toolbar to cancel and return to the dashboard.
During the measurement, you can pause, restart, or stop the collection. If you stop the collection, the partial data will be used. For example, if you plan to collect 8 scans, but you stop after 4, the background spectrum will be used with only 4 scans.
Once the background spectrum is collected, you can preview the sample spectrum and make any necessary changes to the sample measurement settings, or you can return to the dashboard.
To measure the background
- From the home screen, select an analysis type.
- Open the Background tab to edit or review your background settings.
- To begin the measurement, touch Measure Background.
The Background Preview opens, and you can preview the background before proceeding. - To proceed, touch Start Background Measurement.
During the measurement, you can pause, restart, or stop the collection. If you stop the collection, the partial data will be used. For example, if you plan to collect 8 scans, but you stop after 4, the background spectrum will be available with 4 scans.
Once the background spectrum is measured, you can preview the sample spectrum and make any necessary changes to the sample measurement settings, or you can select Home in the menu to return to the home screen.
To measure the background
- Remove any sample from the sampling accessory.
- From the dashboard, select Preview and Measure Background.
The Background Preview window opens, and you can preview the background before continuing with the collection. - To continue, select Start Background Measurement, or click Dashboard in the toolbar to cancel and return to the dashboard.
During the measurement, you can pause, restart, or stop the collection. If you stop the collection, the partial data will be used. For example, if you plan to collect 8 scans, but you stop after 4, the background spectrum will be used with only 4 scans.
Once the background spectrum is collected, you can preview the sample spectrum and make any necessary changes to the sample measurement settings, or you can return to the dashboard.
Measuring a sample requires you to prepare your sample, to set and save your measurement settings, to measure a background spectrum, and finally to measure the sample.
To measure a sample using OMNIC Paradigm Software
- Prepare your sample
How you prepare your sample will depend on your spectrometer and sampling accessory. For details on preparing and loading the sample, see your sampling accessory’s user guide. - Select the analysis type that reflects the analysis that you are performing. To measure a sample without performing additional analysis, select Measure.
After selecting an analysis type, the settings summary view opens.
Figure 1. The Summary tab displays common measurement settings.
- Review and edit your measurement settings.
Open the Details tab to review additional measurement settings or open the Background tab to adjust settings for how the background is measured. Depending on your background settings, you may be prompted to measure a new background before measuring the sample.
See “Measurement Settings” for a description of each setting.
For details on setting up your analysis, see “Identify an Unknown with ATR.” - When you are satisfied with your settings, touch Measure Sample. The sample preview opens and displays a live preview of the spectrum.
- To proceed, touch Start Sample Measurement.
During the measurement, you can pause, restart, or stop and save your measurement. For example, if you feel your data are sufficient and you do not want to wait for more scans, touch Stop to save and use the data as is. Touch Restart to clear all data and begin scanning from the beginning.
Once your sample is measured, you can process or analyze it in the spectral view, or you can measure another sample. To measure another sample from the Spectral view, touch Measure New Sample.
To measure a sample using OMNIC Paradigm Software
- Prepare your sample
How you prepare your sample will depend on your spectrometer and sampling accessory. For details on preparing and loading the sample, see your sampling accessory’s user guide. - To edit the settings for a Search, QCheck, or Quantify analysis, open the Identify menu and open the corresponding setup option.
- Set and save your measurement settings.
To use previously saved settings, select the settings from the Settings list.
Figure 1. The Settings list displays your previously saved settings - In the New Measurement pane, click Preview and Measure Sample
Depending on your background settings, you may be prompted to measure a new background. If so, follow the on-screen prompts to measure a new background. - While measuring the sample, you can pause, restart, or stop and save your measurement. For example, if you feel that your data are sufficient and you do not want to wait for more scans, click Stop to save and use the data as is. Click Restart to clear all data and begin scanning from the beginning.
See “Measurement Settings” for a description of each setting.
For details on setting up your analysis, see “Identify an Unknown with ATR.”
Once your sample is measured, you can process or analyze it in the Spectral view, or you can measure another sample. To measure another sample from the Spectral view, click More to review common measurement settings, and then click Measure New Sample to begin.
To measure a sample using OMNIC Paradigm Software
- Prepare your sample
How you prepare your sample will depend on your spectrometer and sampling accessory. For details on preparing and loading the sample, see your sampling accessory’s user guide. - Select the analysis type that reflects the analysis that you are performing. To measure a sample without performing additional analysis, select Measure.
After selecting an analysis type, the settings summary view opens.
Figure 1. The Summary tab displays common measurement settings.
- Review and edit your measurement settings.
Open the Details tab to review additional measurement settings or open the Background tab to adjust settings for how the background is measured. Depending on your background settings, you may be prompted to measure a new background before measuring the sample.
See “Measurement Settings” for a description of each setting.
For details on setting up your analysis, see “Identify an Unknown with ATR.” - When you are satisfied with your settings, touch Measure Sample. The sample preview opens and displays a live preview of the spectrum.
- To proceed, touch Start Sample Measurement.
During the measurement, you can pause, restart, or stop and save your measurement. For example, if you feel your data are sufficient and you do not want to wait for more scans, touch Stop to save and use the data as is. Touch Restart to clear all data and begin scanning from the beginning.
Once your sample is measured, you can process or analyze it in the spectral view, or you can measure another sample. To measure another sample from the Spectral view, touch Measure New Sample.
To measure a sample using OMNIC Paradigm Software
- Prepare your sample
How you prepare your sample will depend on your spectrometer and sampling accessory. For details on preparing and loading the sample, see your sampling accessory’s user guide. - To edit the settings for a Search, QCheck, or Quantify analysis, open the Identify menu and open the corresponding setup option.
- Set and save your measurement settings.
To use previously saved settings, select the settings from the Settings list.
Figure 1. The Settings list displays your previously saved settings - In the New Measurement pane, click Preview and Measure Sample
Depending on your background settings, you may be prompted to measure a new background. If so, follow the on-screen prompts to measure a new background. - While measuring the sample, you can pause, restart, or stop and save your measurement. For example, if you feel that your data are sufficient and you do not want to wait for more scans, click Stop to save and use the data as is. Click Restart to clear all data and begin scanning from the beginning.
See “Measurement Settings” for a description of each setting.
For details on setting up your analysis, see “Identify an Unknown with ATR.”
Once your sample is measured, you can process or analyze it in the Spectral view, or you can measure another sample. To measure another sample from the Spectral view, click More to review common measurement settings, and then click Measure New Sample to begin.
Next steps
Measuring a sample with OMNIC Paradigm Software requires only a few simple steps. Before measuring the sample, review your measurement settings and ensure that you have a recent background spectrum in use.
With your spectrum measured, you’re ready to identify, verify, or quantity the spectra. See “Identify an Unknown with ATR” for a guide to using a library search to identify your sample.
Use advanced measurement settings to control apodization, zero fill, range limits, instrument-specific settings, and more.
These advanced settings should typically be left in their default state. Only in rare or specific circumstances should you edit these settings.
To review or edit advanced settings, open the Details tab.
Figure 1. The Details tab displays advanced measurement settings.
To review or edit advanced settings, click More in the New Measurement pane.
Figure 1. Advanced measurement settings are available from the dashboard
To review or edit advanced settings, open the Details tab.
Figure 1. The Details tab displays advanced measurement settings.
To review or edit advanced settings, click More in the New Measurement pane.
Figure 1. Advanced measurement settings are available from the dashboard
Advanced measurement settings
The following table describes each of the advanced settings.
| Option | Description | Default setting |
|---|---|---|
| Detector | The detector is a device inside the spectrometer that produces an electrical signal in response to the infrared beam striking it.
| |
| Optical velocity | Determines the optical velocity in the interferometer. The default value is determined by the type of detector you are using, and can only be changed on certain spectrometers. On the Nicolet Summit spectrometer, the default value is 0.4747 and cannot be changed. | |
| Zero fill | Interpolates data points between the collected data points. This doesn’t increase the actual resolution of the data, but can smooth out sharp features and improve the line shape of a spectrum. Options
| 2 |
| Source | The component inside the spectrometer that emits the infrared radiation that travels to the detector. The source type is determined by your spectrometer setup. See your spectrometer user guide for details on the source. | |
| Apodization | Apodization refers to a mathematical function that is applied to the single beam data to reduce or remove peak side-lobes that can occur because the interferogram is not an infinite set of data. Strong apodization reduces more noise but can also reduce the resolution of the data and broaden peaks. You may want to consider weaker apodization, such as Boxcar, if you are measuring spectra with very narrow peaks, such as high-resolution gas spectra. See Apodization Functions for a description of each type of apodization. | Norton-Beer Strong |
| Automatic Atmospheric Suppression | Suppresses the effects of water vapor and carbon dioxide on the spectra you have collected. In general, it is better to control for atmospheric conditions using a current background spectrum. If you measure the background frequently or if atmospheric conditions change slowly, there is no need to use this feature. Use this feature only if you measure the background infrequently or when atmospheric conditions change rapidly. | Deselected |
| Range Limits | Sets the limits for the range of frequencies, in wavenumber, included in the collected spectrum. | Max: 4,000 Min: 400 |
| Aperture | Controls the intensity of the infrared radiation that reaches the sample. Aperture can only be changed when using spectrometers with adjustable apertures. In general, larger apertures will result in a better signal-to-noise ratio while smaller apertures result in better stability and accuracy. Small apertures are better for high-resolution measurements. You may need to use small apertures to acquire true high-resolution spectra. |
Apodization functions
Apodization refers to a mathematical function that is applied to the single beam data to reduce or remove peak side-lobes that can occur because the interferogram is not an infinite set of data.
Strong apodization reduces more noise but can also reduce the resolution of the data and broaden peaks.
See FTIR Spectroscopy Academy for a general introduction to apodization.
The following table describes the available apodization types:
| Option | Description |
|---|---|
| Boxcar | The interferogram is unweighted; that is, the data are simply truncated at the beginning and end. Use this type when you are measuring a gas sample, want maximum resolution and are not concerned about ringing effects (side lobes). The greatest amount of ringing will be present with this type. |
| Cosine | This setting suppresses side lobes and only moderately degrades the resolution of the spectrum. This setting is similar to the Happ-Genzel and Norton-Beer medium apodization. Cosine is normally used only to reproduce the results of other experiments that used it. |
| Happ-Genzel | Suppresses side lobes more effectively than the Triangular type and with less reduction in resolution than that type. (It results in more reduction in resolution than the boxcar type.) |
| Norton-Beer Weak | This setting has a less pronounced smoothing effect on data than do the Norton-Beer Medium and Norton-Beer Strong types and degrades the resolution less than those types. Side lobes appear on both sides of peaks and are more pronounced for sharper peaks. Use this setting only when the best possible resolution is required. This setting is generally not recommended and is normally used only to reproduce the results of other experiments that used it. |
| Norton-Beer Medium | This type has a smoothing effect on data which is between that of the Norton-Beer Weak and Norton-Beer Strong types. It suppresses side lobes as much as possible given that it only moderately degrades the resolution of the spectrum. The side lobe suppression is more significant than for Norton-Beer Weak apodization. This setting is suitable for most normal samples; it gives results virtually identical to those obtained with Happ-Genzel. |
| Norton-Beer Strong | Norton-Beer Strong is the recommended apodization for the Nicolet Summit and Summit Pro spectrometers. This setting has a greater smoothing effect on data than do the Norton-Beer Weak and Norton-Beer Medium types and degrades the resolution of the spectrum more. The side-lobe suppression is more significant than for Norton-Beer Medium apodization. |
| Triangular | Mathematically weights interferogram data to reduce ringing effects (side lobes), resulting in lower resolution than that obtained with the boxcar and Happ-Genzel types. Some ringing will usually be present with this type. This setting is normally used only to reproduce the results of other experiments that used it. |
| Blackman-Harris | The 4-term Blackman-Harris function is a strong apodization function that is better than any of the others at suppressing side lobes. However, it results in greater line broadening than any of the others. In practice this has the effect of reducing random noise in a spectrum while causing band broadening. |