Configuring SpectrumAnalyzer

Program settings can be accessed in the toolbar as soon as the application is connected to a spectrometer or that a file has been loaded:

When clicking the toolbar button, the configuration panel will open:

Program settings are divided into different groups:

Acquisition Properties

Acquisition properties let you configure the camera settings such as exposure, gain, region of interest, number of average and filtering.

Exposure will control the camera exposure time. It is recommended to select the highest exposure possible without saturating the camera sensor. Saturation is discussed in details in advanced operations.

Gain will control the camera gain. When saturation has been set to its maximum value (either limited by the camera or by the experiment), increase the gain without saturating the camera. Saturation is discussed in details in advanced operations. Gain will increase noise but low ADC values will yield even more noise. A good strategy is therefore to first set exposure and only then increase gain such that the saturation of the camera goes to roughly 80%.

ROI will control the region of interest of the camera sensor. It is recommended to adapt the ROI value to image entirely the slit but no more than that to avoid accumulating noise in the spectra. Typical values are within 16-100 pixels for the Starter and Performance Editions. It is not recommended to use values larger than 128 pixels as it may strongly slow down the acquisition when median filtering is enabled.

Num Avg. controls the number of images taken for each spectrum. Increasing this number will decrease noise in faint spectra but will take a longer time to acquire the data.

Enable Median Filtering will remove hot and cold pixels of the sensor using a 3x3 median filtering kernel on the image data. It is recommended to keep this settings on.

Logging

The logging panel will enable you to automatically save spectra to your disk every time the single capture button is pressed. The data can be saved as either CSV or Spectre files.

Automatic logging needs to be enabled to run the timed acquisition program. Timed acquisition is described in advanced operations.

Plot Settings

Plot settings will let you configure the plot data.

Boxcar smoothing will apply a boxcar kernel to the data. Boxcar smoothing will reduce noise at the expense of resolution. We recommend using a value of 3 for the Performance Edition and a value of 5 to 7 for the Starter Edition as a good trade-off between SNR improvement and resolution losses.

Show plot axis as will let you change the x axis. You may choose between pixels, wavelengths and Raman shift. In Raman shift mode, you will also be able to select the wavelength of your laser source to correct the offset of your spectra. The wavelength and Raman shift axis types are only available once a calibration has been performed or imported.

Enable Blank Removal will let you select if you wish to disable blank subtraction. We recommend to leave this settings on unless you really need to. The option will be grayed-out when no blank data has been acquired.

Enable Baseline Removal will perform a baseline removal on your spectrum using the algorithm described in Schulze et al. paper. Baseline removal should be applied on a need-to basis and we discourage you to leave this setting on all the time. Typical applications of baseline removal are strong fluorescence background on faint signals. Baseline removal can introduce artefacts in your spectra or even remove large weak bands like –OH groups which is why we recommend to avoid using it when peaks are readily visible even if fluorescence signal is present in the data.

Enable Savitzky-Golay Filtering will perform Savitzky-Golay filtering on your data. Savitzky-Golay filtering is a popular technique in spectroscopy to either smooth data plots (“smooth” option in derivative order settings) or to compute derivatives of the signal. Application of second order derivate includes discrimination of two nearby peaks that have Gaussian shapes. As the results strongly depends on the window and polynom order settings, we recommend you to play a bit with these settings depending on your specific data.