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microprofiling:spectral_m_profiler_howto

Spectral-m-Profiler

This program allows automated measurements of vertical profiles of light spectra in samples such as sediments or microbial mats. It is a successor of the m-Profiler program, with additions that enable the spectral light measurements using the light microprobe.

What do you need

  1. Ocean Optics Spectrometer (tested for USB2000 or USB4000)
  2. DAQ-device from National Instruments (see here for supported hardware)
  3. Motorized stage, controlled by LINPOS-server (see here for details)
  4. Light microprobe (see Lassen et al. 1992, listed here for more information)

Before you start measuring light profiles

  1. Connect Ocean Optics Spectrometer USB2000/USB4000 to the USB port.
  2. Connect the pins “Trigger in” and “Ground” on the spectrometer to a digital output of the DAQ device (we assume that it is digital output 0).
  3. Open OOIBase32, which is the controlling software for the spectrometer.
  4. In Spectrum→Configure Data Acquisition, select External Trigger to None and click OK.
  5. In the main window of the OOIBase32, set various settings of the integration time and average so that
    1. the spectrum looks good (i.e., the highest spectral reading is not too low, not too high, the background is substracted, etc.)
    2. the acquisition of the average spectrum takes at least a second (e.g., by setting the integration time to 40 msec and average to 50, one spectrum will be acquired in 40×50 msec = 2 sec). Note this time (denoted as Ts).
  6. In Spectrum→Configure Data Acquisition, select External Trigger to Software Trigger. IMPORTANT: check the Automatically save file on trigger checkbox and click OK.
  7. In File→AutoIncrement Filenames, check on Enable, Show File and Configure. After selecting Configure, set the base filename of your spectra, and reset the starting index to whatever you prefer (say 0), click on OK. From now on, EVERYTIME a spectrum is taken, it will be automatically saved to a file with the base filename and an index which will automatically increase by 1 after each spectrum acquisition (starting from the specified starting index).

NOW YOU ARE READY FOR AUTOMATED SPECTRUM ACQUISITION USING SPECTRAL-M-PROFILER.

How to measure light micro-profiles

  1. Start LINPOSserver, establish connection with the motor and set the light microsensor to the initial position for the measurements.
  2. Start Spectral-m-Profiler.exe.

  1. Connect to the LINPOSserver, check that the connection is functional.
  2. In Spectral-m-Profiler's GUI, define parameters of the DAQ device:
    1. DAQ device type (see MAX);
    2. DAQ device ID (see MAX);
    3. Digital channel to which the Spectrometer is connected (e.g., DO 0);
    4. Spectrum acquisition period (in s). NOTE: Set this to an interval a little longer than the expected time of single spectrum acquisition (e.g, if Ts = 2s, set this to 2.1-2.2 s, depending on the speed of the PC)'
    5. Press accept.
  3. Define the timing parameters of the measurement:
    1. Number of readings = how many spectra will be acquired at each depth;
    2. Pause between readings = how long will the program wait until the next spectrum at the current depth is taken;
    3. Resting time at each depth = how long will the program wait after arriving to a specific position before the first spectrum at that position is taken;
    4. Number of profiles to be taken;
    5. Pause between profiles = how long will the program wait before the next spectral profile starts being taken.
  4. Define the spatial parameters of the measurement, i.e., from where to where and in which steps will the spectra be taken, and to where will the motor go after all measurements are finished (standby).
  5. Select output file basename. IMPORTANT: The output filename MUST BE IN THE SAME DIRECTORY AS THE BASENAME OF THE SPECTRAL FILES IN OOIBase (see points 6-7 in the section above). The measurement results will be saved in basename.MPR, while the spectra will be saved as basename-zX-sY-pW.dat for the spectrum number s = Y taken at z = X um in profile number p = W.
  6. Start the measurements and be patient.

Notes

  1. Observe how the spectrum is taken after the light-bulb in the toolbar switches on and off.
  2. Version 0.8+ of the Spectral-m-Profiler program implements server capabilities. Start the Spectral-m-Profiler server (by clicking on the earth icon), connect to it and type help; to see the list of available commands. For example, the measurement can be started by sending “go;” to the server, or stopped by sending “stop;” to the server (note the semicolons at the end of the command!!).
  3. The output filenames with the spectra increase and increase. There is no way (or at least I am not aware of any) to influence the filenames externally. This means that one has to rename the most recently stored spectrum to basename-zX-sY-pW.dat (see above). This is what the program does automatically.
  4. Any *.Master.* files remaining in the output directory from the previous measurement will be renamed to *.bak during subsequent measurements. This is to avoid overwriting/deleting of the files (and thus loosing possibly valuable data) in case the user made a mistake in filename definition.
  5. It seems that Spectral-m-Profiler and the way OOIBase takes the spectra cannot fully be synchronized. The spectra are basically stored whenever the total acquisition time exceeds the set Ts value, and the accumulated acquisition time cannot be reset to zero. This, in practice, means that the spectrum i+1 may carry information from the spectrum i. This is obviously unacceptable, especially if spectra i and i+1 correspond to different depths. It is therefore recommended to acquire at least 5 spectra at one depth, taking into account that the 1st one may be partially influenced by the 5th one from the previous depth and thus may have to be discarded (in the later data analysis).
  6. If you need to go to the manual (“normal”) mode of spectrometer operation, go to point 4 in the first section. Note that this operation may cause crash of the OOIBase32 program. This is a problem of the OceanOptics software, not yours. If this happens, you will most likely need to disconnect the spectrometer, kill OOIBase32, reconnect the spectrometer and restart OOIBase32.
microprofiling/spectral_m_profiler_howto.txt · Last modified: 2013/09/10 12:26 by lpolerec

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