OMNIC Software

 

Online Manuals:

 

The software that runs the Nicolet FTIR benches and microscopes on Beamline 1.4 is called OMNIC. There are detailed online and hard copy manuals available for this software (the hard copies can be found in the bookshelf beside the Beamline 1.4.3 hutch). Therefore, this manual will simply give you an introduction of how to start the software, setup your experiment, and acquire data. The OMNIC software is capable of doing many types of data analysis and manipulation that will not be covered here, so the reader is referred to the manuals above for more information.

We will assume that you have a reference sample in the IR microscope, it is visually in focus, the MCT detector is cooled down, and you are ready to start a measurement (see the Beamline 1.4.3 or Beamline 1.4.4 manuals). Start the OMNIC Software by double clicking on its icon from the desktop (shown above). You will be asked to input your user name. If you don't yet have a user name, please ask Mike or Hans to set you up with one.

Once you have entered a correct user name, the OMNIC main window will appear (see Figure 1). To check the signal strength and set the spectrometer parameters, go to the Collect Menu and choose Experiment Setup. This will open a window like the one shown in Figure 2. If you are not doing any mapping, the first two tabs, Collect and Bench, are the only ones you need to set up to collect data.

 

 

Figure 1. View of the main OMNIC software window.

 

 

Collect Menu >> Experiment Setup >> 'Collect' Tab

 

Figure 2. Experiment setup window with the 'Collect' tab selected.

 

  • No. of scans: set the number of scans to collect and co-add to obtain your spectrum (more scans will reduce any noise, but will add to the collection time).
  • Resolution: set appropriately for your sample. Most solid and liquid samples are fine with a resolution of 4 cm-1, but check your data to see if any sharp peaks are limited by this resolution setting in which case you may want to increase the resolution to 2 or 1 cm-1. The lower the resolution the faster the data collection time, so only use higher resolutions if you need to and are willing to spend more time collecting each scan.
  • Final format: select the way the data will be processed and presented to you. For example, %Reflectance will automatically divide your sample spectra by the reference spectrum and present the results in percentage reflectivity. Other typical selections are Absorbance, %Transmission, and Single Beam (this last one does not divide by a reference spectrum).
  • Correction : most users leave this on 'None'. It will select a method to automatically correct for using an ATR (attenuated total reflectance) sampling technique and a few other corrections not typically used with the microscope.
  • Automatic atmospheric suppression: check to have software remove any lines from residual H2O and CO2.
  • File Handling: Leave 'Save automatically' and 'Save interferograms' selected. This will automatically save each spectrum you acquire and by saving the interferogram you will have the ability to go back and reprocess your data using a different background or lower resolution at a later date. You may type a four character filename that will be incremented and saved in your autosave directory.
  • Background Handling: most users have 'Collect background after 120 minutes' selected. This will remind you that after 120 minutes have passed that your background spectrum is getting old and you should really acquire a new one. Selecting either of the top two choices will force you to take a new background before or after every sample spectrum you take. This is usually impractical.
  • Type in an experiment description and an experiment title that will be shown on the main OMNIC window.
Once all the parameters are set, you can click on the 'Save As…' button at the bottom of the window and save the experiment file. Give the experiment file a name starting with your name or something you can easily remember so you can next time find the experiment file easily. Whenever you want to go back to the saved experiment setup, just open the Experiment Setup window, click on the 'Open…' button and select the experiment file you want to open.

 

 

Collect Menu >> Experiment Setup >> 'Bench' Tab

 

Figure 3. Experiment setup window with the 'Bench' tab selected. Typical values and selections are shown.

 

This screen shows the real-time interferogram signal and allows the user to do some spectrometer configuration setup. Assuming you have a reference sample in focus in the microscope and that the MCT detector is cooled with liquid nitrogen, you should see a signal similar to the one shown in Figure 3. By adjusting the fine focus knob of the microscope, maximize the signal intensity (the IR focus is slightly off from the visual focus). In reflectance mode (15x objective) with a gold slide as the reference sample, a peak-to-peak value between 8 and 12 on Gain 1, is expected if the system is correctly aligned.

The parameters in this window are shown in Figure 3 with their typical settings.

  • Sample compartment: select the microscope in either reflection (%R) or transmission (%T) mode, or the main 760 bench sample compartment.
  • Detector: The microscope only has one internal detector, an MCT/A. The main bench is equipped with a DTGS detector. The DTGS is a slow room temperature detector that is not fast enough to measure the synchrotron light pulses, but it can be used with the internal IR source.
  • Beamsplitter: select one of multiple beamsplitters available, a germanium coated KBr crystal for the mid-IR (standard), a Quartz beamsplitter for the near-IR, and an extended KBr beamsplitter that covers a portion of the near-IR and mid-IR. In addition to changing the software parameter, you must also physically change the beamsplitter. Mike or Hans can show you how to do this.
  • Source: choose the synchrotron source (External), the internal IR source (IR), or the internal white light source (White light).
  • Accessory and Window: not used with our setups, so leave them set to None.
  • Spectral Range: Using the synchrotron and the microscope with the KBr beamsplitter, you can measure from ~ 8,000 to ~ 650 cm-1, but you can select a smaller range to match what you are looking for. A smaller range does not speed up the data acquisition, however, so it is suggested that you keep the range set to at least 4000 to 650 cm-1, and larger is certainly fine too!
  • Gain: set preamplifier gain to enhance small sample signals. The system will begin to saturate if the peak-to-peak signal is > 15, so make sure that you do not turn the gain up beyond these levels.
  • Velocity: set the mirror speed in the interferometer (measured in cm/sec). A speed of 1.8988 m/s is typically a good compromise between speed and signal to noise.
  • Aperture: used only with the internal IR source, so you can ignore it for synchrotron based experiments.

Once again, now that you have all these parameters set, you can click on Save As… (or Save) to save this experiment file so you won't have to reselect everything next time!

 

 

Collect Menu >> Experiment Setup >> 'Diagnostic' Tab

 

Figure 4. Experiment setup window with the 'Diagnostic' tab selected. The shown view is what you should see when everything is operating normally.

 

The Diagnostics tab window is where to go when something is not working. The five blue icons along the top of the window indicate the status of the power supplies, alignment laser, internal sources, spectrometer electronics, and IR detectors, respectively. If there is a problem with any of these, a diagonal red slash will appear over the appropriate icon. If you see any of these indications, please call Mike or Hans. If nothing appears wrong, but you still do not see an interferogram signal, you may try pressing 'Reset Bench'. This will re-boot the bench electronics and will cause the spectrometer to re-initialize its zero positions. On occasion when the spectrometer has not had a signal in a many hours, this button will make the spectrometer find the zero peak mirror displacement again and start functioning like normal. If you continue to have problems getting a signal, please contact us.

The 'Quality', 'Advanced', and 'Configure' tabs in the Experimental Setup window are generally not used at our beamline. The Quality tab allows you to set up spectral checks during data collection; this is usually done only in industrial processes where the samples are very well known and you are looking for deviations from a standard. The Advanced tab allows you to set some of the Fourier transform parameters. The default settings will work for just about everyone, but we would be happy to tell you more about them if you feel you want to get to this level of understanding with FTIR. The 'Configure' tab allows you to configure the FTIR bench. Please do not change anything here.

 

 

 

Data Acquisition

Now that the Experiment Setup is complete, the data acquisition can begin!

  • First you need to take a background spectrum. Once you are happy with the signal strength seen in the Bench tab of the Experimental Setup window, close that window by pressing 'OK'. Then in the main OMNIC window (Figure 1) select the Collect menu followed by Collect Background. The system may prompt you again to make sure you are ready, then it will acquire the number of scans you set in the Experiment Setup window. You can see the progress of the scans at the bottom left corner during data collection, and the screen will show you an occasionally updated average of the data you are collecting.
  • Once the background is complete, you are ready to measure your sample. Put the sample in the microscope and focus on it visually (make sure you have pushed the View button on the front of the microscope). Then open the Experimental Setup window with the Bench tab selected and check the IR signal strength. Adjust the fine focus knob for maximum peak-to-peak signal, and if your signal is small you can increase the preamplifier gain value. When you are satisfied, close the Experimental Setup window by clicking 'OK'. Select the Collect menu followed by Collect Sample. If you are setup to automatically divide by the background spectrum (that is to say the final format is set to %Reflectance, Absorbance, %Transmittance, 1/R…), OMNIC will automatically present you with the final formatted resultant spectrum.

Now that you have an IR spectrum, you can do a lot of different types of data processing and visualization using the Process and Analyze menus. These functions will not be covered here, but can be found in the extensive on-line help files for OMNIC and the OMNIC manuals.

To print your data, select Report >> Preview-Print Report. You will then be asked to enter some optional text (anything you type here will be displayed at the bottom of the printout so you can use this for any notes you’d like to add to the printout. If you don’t want to type anything, just leave it blank and hit OK.). The program will then show you a preview of what the printout will look like. If you are happy, select Print and it will be printed for you.



Atlμs Mapping Software

Figure 5. View of the main Atlμs window. The right side shows the live video image coming from the microscope. The numbers on the axes are the absolute position of the x-y stage in microns. The left side is capable of showing the entire area of the x-y stage, composite images (mosaics), and can be zoomed in and out.

 

The software that automates spectral mapping of samples in the IR microscope is called Atlμs. To launch Atlμs from the main OMNIC window (Figure 1), go to the Atlμs menu and select 'Show Atlμs Window….' This will launch the program and you should see a window similar to to Figure 5. The image on the right is the live image coming from the microscope (if you don't see anything, make sure the microscope is in View mode.

calibration icon

The first thing to make sure is that the correct calibration is open. In the title bar of the screen shown in Figure 5, it states that the 15x objective calibration is open. If you are using a different objective with the microscope, click on the calibration bar icon (located in the middle of the lower Atlμs toolbar). There are calibration files for the 10x, 15x, and 32x objectives; select the correct one for what you are using. Now the scale on the video image will be correct and you can correctly set up mapping experiments.

The easiest way to begin setting up a mapping experiment is to use one of the blue colored tools at the bottom of the Atlμs window. They are, from left to right, pointer to select and move objects, a line map drawing tool, an area map drawing tool, a points map drawing tool, a background point selector, a target to move the x-y stage to a specific position, a rectangular aperture tool, a ruler, a way to add Text to the image, and a marker tool. Most people want to do line or area maps, so select the line or area map drawing tool and draw on the microscope image where you would like the software to acquire an IR map of your sample.

 

Line Map Area map

Figure 6. Examples of drawing a line map (top) and an area map (bottom) on the live microscope image (blue lines with step marks indicated).


Collect Menu >> Experiment Setup >> 'Mapping' Tab

 

Figure 7. Experiment setup window with the 'Mapping' tab selected. The shown view is what you should see if you are doing an area map.

 

Now that you have your map coordinates roughly drawn onto the microscope image, open the Collect menu, select Experimental Setup, and click on the 'Mapping" tab. This will open a window where you can specify the details of the map you want to collect. Under dimensions, you can change the step size for the x and y dimensions. Once you press apply, the program will calculate the estimated collection time for the map. If the time appears too long, you can decrease the dimensions of your map, change the step size, or change the number of averages. A word of caution: the estimated collection time is usually about half of the actual time to take the map!

The Collect button provides several more options. Typically 'Save Video Frames In Map File', and 'Store Map With Relative Coordinates' are selected. Only select 'Auto-Pause Before Each Spectrum' if you want the program to pause data collection at every map point to allow you to refocus or otherwise check on your samples (this takes a long time and you have to click OK over and over so choose this only if you really mean it!).

Now that you have completed the Map Setup, simply go to the Collect Menu and select Collect Map. You will be prompted for a file name and a place to save your map (the default is the Map directory in your folder). If you are using Beamline 1.4.3, make sure that the microscope is in 'View' mode before you press 'Save'; otherwise, the video capture will be of a very uninteresting black screen and not your sample!

 

 


Figure 8. Default profile of an area map.

 

 

Once the map is complete, the software will display a window that is split into several active areas as shown in Figure 8. The top left panel shows a contour map, and the top right panel displays the video image. The middle left panel shows the spectrum at the current cursor location in either of the top panels. The middle right panel will show a 3-D graph of the map, which can be rotated to obtain a better view. The lower panels include x and y profiles (only one-dimension for line maps), and a key for the colors of the contour map.

There are several additional tools associated with Atlμs that will allow you to analyze your maps. These include:

  • Profile Setup - allows you to select an entire band or ratio of bands to create a contour map
  • Principal Component Analysis - performs multivariate calibration for area maps
  • Image Analysis - lets you set up and perform "feature sizing"
Detailed explanations of these procedures can be found in the Atlμs manual.



 

 

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