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Thermo Fisher Scientific

Prepare Measurement Settings

OMNIC Paradigm software has basic and advanced settings for how you view and measure samples with your FTIR microscope.

Basic settings are used frequently and determine the type of analysis you are performing.

Advanced settings need to be adjusted less commonly and relate to how the instrument hardware is configured and how the data is processed to generate the sample spectrum.

Basic settings

Find the basic settings in the New Measurement pane after you set your sample location to the FTIR microscope.

Basic measurement settings for microscopy


Basic measurement settings for microscopy
Setting Description

Autofocus before capture

Select to automatically bring the sample into focus when starting the session.

If you do not select this option, you should either manually bring the sample into focus using the optional joystick and eyepieces before starting the session, or change your mosaic capture setting to Custom Mosaic. After starting the session, open the Camera View and bring the sample into focus manually before capturing a mosaic.

Session name

The name of the session data. This name is used in the saved data and, if you have Security Suite software installed, in the audit trail. The default name is the date and time the session was started.

Final format

Determines the units used for the collected data. You can convert to another Y-axis unit after collection by using the options in the Display menu.

Sample scans

The number of scans collected at each sample point. Fewer scans results in faster data collection but potentially noisier data.

Mosaic capture

Specify a mosaic type to capture automatically when you start the session.

To start the session without capturing a mosaic, select <No Mosaic>.

Extremely large mosaics require a large amount of hard-drive space to store and are time consuming to collect. To save disk space and measurement time, capture a mosaic of only the portion of the sample that you need for your analysis.

Camera profile

Select a camera profile to best fit the type of sample that you are analyzing. Camera profiles set the brightness, contrast, white balance, and more to provide the best image of the sample.

Many samples are prepared on highly-reflective backgrounds but are not highly reflective themselves. Make sure you select an option that best fits the sample surface and the area of interest.

  • High Reflective: Highly reflective samples usually visible reflections when they are exposed to a light source (such as nearby lights or sunlight). These samples include glass slides, glossy paper, and well-polished metals, for example.

  • Matte: Select this option for dark materials with rough surfaces that have low visible reflections, such as very dark plastics, rubber, cardboard or paper, or fabric.

  • Diffuse: Select this option for materials that have medium or low reflectivity and are light in color. Use “Diffuse” for samples such as light color plastics, non-glossy papers, pharmaceutical tablets, or similar materials.

Finding the right camera profile

To check if the camera profile setting is right for the sample material, bring the sample image into focus and adjust the illumination either automatically or by using the manual controls.

The illumination number should be between 15 and 70.

  • If it is less than 15, the camera setting should be adjusted to the high-reflective profile.

  • If the number is greater than 70, the camera profile should be adjusted to either diffuse or matte.


Add a tag to the session. Tags are useful for finding and filtering your saved sessions later.


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 better resolution but also takes longer to measure.


A default profile to use to display the chemical data after measuring a area, line, or set of points. You can change the profile after measuring data. For more on each profile, see Apply Profiles.

Analyze using

The technique used for measuring the sample. The selected technique determines what settings are available during the session.

  • Reflection

  • Transmission

  • ATR

Analyze particles

Select to analyze particles. If selected, particle analysis tools are available in the session view. This option must be selected before you start a session.

Enable Polarizer acquisition Select to use the polarizer and analyzer during data collection. You can also enable the polarizer during the session. 
Step size The distance that the stage moves between sample points, in micrometers. A smaller step size measures the sample at more points in an area but takes longer to measure and requires more space to save. 
Aperture height and width

The aperture is used to exclude unwanted parts of the sample from the measurement and to prevent unwanted light from reaching the detector. 

Imagine the aperture as a rectangular window that the infrared beam passes through during the measurement. 

You can also set the aperture height, width, and rotation angle in the camera view. 

Background and advanced settings

The background and advanced settings areas provide additional options for how your data is collected and processed.


Background settings for microscopy
Setting Description
Use the fixed reference location on the RaptIR sample holder

The RaptIR sample holder has built-in reference points for transmission and reflection analyses. Select
this option to automatically move the stage to the reference location after capturing your initial mosaic.
This option is not available if you selected Custom Mosaic in the Mosaic Capture list.

Match sample scans

If selected, the number of scans used for the background measurement will be the same as the scans used for the sample.

Set background scans

Select to choose a different number of scans for the background.

Measure background before each region

If selected, the software will measure a new background before each new region of the sample. For
example, if you have three area regions in your sample measurement, with this option selected, the
software collects a new background before each area.

Note that a set of points that use the same measurement settings is considered a single region.

Measure background once for entire sample

With the option selected, a new background is collected only when the measurement settings change. For
example, if you have this option selected, if you measure three areas in one sample collection and they all
use the same measurement settings, only one background is collected.

The following are advanced settings:

Advanced measurement settings for microscopy
Setting Description

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.

Collect your sample and background spectra using the same Zero Fill setting.


  • None: No zero filling is done.

  • 1: One data point is added between each collected data point

  • 2: Three data points are added between each collected data point

Optical velocity (cm/sec)

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.


Sets the amplification of the detector signal. Higher gain increases the signal but also increase the noise. The optimal gain depends on the experiment.


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"Apodization Functions" for a description of each of the options.


If your instrument has multiple beamsplitters installed, you can select one of them here. If you have the the ABX installed on your spectrometer, configure the ABX first and select your beamsplitter to use here.

Sample spacing

Sample spacing refers to how frequently the interferogram is sampled.

Lower sample spacing settings allow you to measure a more extended frequency range, and higher sample spacing settings are useful when measuring with very fast optical velocities, when the mirror is moving too quickly for the IR measurement to keep up.

  • 0.5: The IR signal is measured at every zero crossing and at the top and bottom of the laser signal wave. This setting allows a much wider data range.

  • 1: The IR signal is measured at every zero crossing of the laser wavelength. Use to extend the range beyond 7899 wavenumbers.

  • 2: The IR signal is measured at every other zero crossing. This is useful when using very fast optical velocities, but the maximum measured range must be below 7900.

Mapping speed

High speed is good for most applications, but you may want to try Normal if you need to improve the quality of your data. 


Displays the currently installed microscope detector.

Range limits

Sets the limits for the range of frequencies, in wavenumber, included in the collected spectrum.

Prompt for session name

If selected, the software presents a prompt to enter a new session name at the beginning of every new session.

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.

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