Signal Processing

1. Make sure your spectrometer is plugged in and choose the “Reconnect the spectrometer(s)” button to make a connection between the program and your spectrometer.
2. A prompt will appear alerting to a successful connection. The serial number of the spectrometer will help to indicate which instrument is being connected.
   
3. Now that the software is connected to the spectrometer, click the “Capture Data” button once to collect one scan. The data collection panel will default to “Single” – do not use Loop or Episodic unless it is necessary for your application.
4. Prior to collecting a scan, the Scope mode graph will remain blank.
   
5. After collecting one scan a trace of the spectrum will appear. The above trace is not taking advantage of the signal to noise ratio – any data collected with it would be noisy and erratic.
6. To optimize the curve and adjust the signal-to-noise ratio of the spectrometer, choose “AUTO SET” and follow the prompts given by the program. Use this feature only if the desired integration time is less than 5000 ms. If a longer integration time is needed, manual adjustment is recommended.
   1. Make sure to align the reflectance probe with the reference sample before choosing “AUTO SET”
   2. Often the optimal reference sample used is the substrate without any coatings.
7. This feature will instruct the user to configure the system with the reference in place and the light source on. When the user clicks Yes, the software runs a series of tests to automatically set the integration time, then, once it has chosen an optimized integration time, it instructs the user to turn off the light source, once the light source is off, the user indicates to the software that it is okay to take a dark reference.
8. The first prompt instructs the user to place the reference object. Typical geometry for reflectance of thin film measurements is to hold the probe at a 90° specular angle to the sample. Click “Yes” once the sample is in place and the light is on.
9. Next, the software will collect a scan, displaying it on screen. A new prompt will appear over the spectrum.
10. The new prompt instructs the user to turn off the light source. Turn off the source and once it is off, choose “Yes” – this will take a dark reference and subtract out the baseline of the instrument.
11. Now the process is complete. Turn on the light source, and choose “OK” – this will collect another scan to display the optimized curve.
12. If the user is more familiar with spectroscopy and wishes to further optimize the spectrum, Integration Time, Pixel Boxcar Smoothing, and Scans to Average are all available for modification. The goal is to set the integration time so that your spectrum is not saturated but as close to 65,000 counts in SCOPE as possible. Enter the desired time in the integration time input box, then click on the “Int Time (ms)” button next to the input textbox to apply the entered time. This is also the point at which you should adjust the number of scans to average (more scans averaged will increase accuracy, but will take more time for each reading). You can also add smoothing controls at this time in the Device Settings block. A pixel box car set to 3 and averaging set to 5 often gives nice results.
    

    In the first picture below, the spectrum is correctly optimized to be just below the saturation limit (65,536 counts). In the second picture below, the spectrum have a flat line on the top, indicating the need to reduce the integration time.

13. Now it is time to take references using the dark reference and light reference icons.
14. Turn off the lamp and left click on the dark reference bulb. The baseline will subtract out and flatten at the bottom of the Scope mode graph. The subtracted spectrum will be counted as 0% transmission/reflectance for future calculations, until overwritten.
    1. Prior to left-clicking on the dark reference icon, the bulb will have rays coming out of it.
    2. After left-clicking the dark reference icon, the bulb’s rays will appear.
    3. A right-click will release the dark reference – this is often recommended to do before optimizing settings (Integration Time, Smoothing, Scans to Average).
    4. Hovering the mouse pointer over the icon will pull up a tool-tip indicating if the dark reference has been captured.
15. Turn on the lamp, make sure that the reference standard is in proper geometrical position and left-click on the “Take Reference” icon. This will set the upper boundary for transmission/reflectance measurement and count the spectrum as 100% for future calculations, until overwritten.
16. The upper left-hand corner has selectable tabs for the raw Scope mode display and the Reflectance mode display. The bottom left-hand corner displays the serial number of the device being used, integration time (1-65536), scan averaging (1-1000), pixel-boxcar smoothing (0-4), X-timing resolution control (should always be set to 3), temperature compensation (set to off unless operating in an environment with temperature drifts), and triggering timeout (on/off).
17. Now that the dark and light references have been taken, left click on the data collection icon and then choose the reflectance tab to view the reflectance plot.
18. The reflectance plot’s trace appears as a straight line at 100% while viewing the reference standard, but there will be noise in regions where there is little signal to noise due to a lack of light signal in the raw Scope data.
19. Toggling the raw Scope mode, it is evident that there is little signal near 300nm and beyond 1000nm for the following plot, which explains why there is noise in the reflectance plot.
20. To combat the noise, the user can increase the integration time even further to try to get closer to the saturation point without saturating. The closer the signal gets to the saturation point, the higher risk that the detector saturates. This is not a damage concern as much as it is a concern of data. The recommended setting is to be at ~90% of the maximum.
21. If the noise is present in the UV region and the spectrometer is capable of detecting signals in the UV range, a Deuterium lamp is recommended. StellarNet offers the SL1-SL3 Combo, SL3, and SL4 lamps for UV reflectance applications. The SL5-DH deuterium halogen lamp is only appropriate for transmission applications. If the noise is present in the NIR region, a halogen lamp should be used and it may become necessary to use an InGaAs detector for the 900-1700nm range or Extended InGaAs for 900-2500nm range as Si-CCD and CMOS detectors have limited sensitivity in the 900-1100nm range. Another way to stabilize data is to increase sample averaging, and increase smoothing of the data.
22. Now that settings have been configured, signal has been optimized, and references have been taken, it is time to perform some measurements.
23. Before a measurement is taken, a recipe must be loaded. Before a recipe can be loaded, a recipe must be created. Review the following Recipe Creation and Performing a Measurement sections.