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Sequoia LISST-VSF User Manual

Multi-angle polarized light scattering meter
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LISST-VSF
Multi-angle Polarized Light
Scattering Meter
User's Manual
Rev. B
Sequoia Scientific, Inc.
2700 Richards Road, Suite 107
Bellevue, WA 98005-4200
USA
Tel: (+1)(425) 641-0944 Fax: (+1)(425) 643-0595
www.sequoiasci.com
|
info@sequoiasci.com

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  • Page 1 LISST-VSF Multi-angle Polarized Light Scattering Meter User’s Manual Rev. B Sequoia Scientific, Inc. 2700 Richards Road, Suite 107 Bellevue, WA 98005-4200 Tel: (+1)(425) 641-0944 Fax: (+1)(425) 643-0595 www.sequoiasci.com info@sequoiasci.com...
  • Page 3  Approximately 4 sec per measurement set [involves 2 turns of Eyeball with vertical, and horizontal polarized laser].  Daylight rejection by laser modulation.  Data from small and large angles in a single data stream, including depth, temperature, date and time  This document is copyrighted by SEQUOIA SCIENTFIC, INC.
  • Page 5 Roving Eyeball and PMT for 15-150 (nominal) Mechanical and Electrical LISST-VSF Instrument Dimensions 13.3 cm (5.25”) diameter, 114.0 cm (44.9”) L Weight: 15.6 kg (34.4 lbs) in air; in water TBD Depth rating: 300 m survival depth (50 m operational depth)
  • Page 7 Welcome to the LISST-VSF! Using this manual This manual is divided into two sections. Section One contains an introduction to the LISST-VSF instrument and the principles of its operation. Section Two provides detailed instructions for operation Appendices provide further details …...
  • Page 9 Waste Electrical and Electronic Equipment Smaltimento di apparecchiature elettriche ed elettroniche da rottamare...

  • Page 11: Table Of Contents

    LISST-VSF C ................... 58 OMMAND UMMARY APPENDIX A: DETAILS OF LISST-VSF INSTRUMENT ............68 APPENDIX B: METHOD OF EXTRACTING P11, P12 AND P22 ..........72 APPENDIX C: MATLAB SOFTWARE ..................75 APPENDIX D: OBSERVATION ANGLES, DATA STORAGE FORMAT AND VARIABLE NAMES ...............................

  • Page 13: Section I: Lisst-Vsf Instrument

    Thank you for purchasing a LISST-VSF instrument, and congratulations on your new purchase. The LISST-VSF delivers a powerful suite of measurements for marine optical scientists, all from one package. It delivers the Volume Scattering Function (VSF) from small forward angles to wide angles, depolarization parameters, and the beam attenuation coefficient c.
  • Page 14 In the LISST-VSF instrument, the scattered light entering the eyeball is split into its two polarization components, and each is sensed with a dedicated photomultiplier (PMT). A set of measurements comprises the recording of these two PMT outputs over 2 rotations of the eyeball.
  • Page 15 Communication with this computer is over a serial line. The LISST-VSF instrument can be programmed from a PC to execute a specific data collection sequence. Software for programming the instrument and recovery of data is provided. Data download is also carried out using the provided software.
  • Page 16 A battery charger is provided. While the battery is being charged, it cannot power the instrument. A separate external power supply, with an underwater connector that mates with the instrument housing is provided for use in the laboratory. LISST-VSF User’s Guide...

  • Page 17: How It All Works

    Why is an ND filter used on the small-angle optics window? This is because Receive Window internal glow from the small-angle optics contaminates particle scattering at large angles, i.e. when the eyeball is viewing scattering at around 130 greater. The ND filter attenuates the glow. LISST-VSF User’s Guide...
  • Page 18 The expected measurement from, say, single size polystyrene beads can be computed using this function for comparison with actual data. Appendix B explains the methods. A listing of provided functions is in Appendix C. The use of MATLAB permits flexibility to the scientific user. LISST-VSF User’s Guide...
  • Page 19 It is not correct to use the same value of  at all times since it will depend on PMT voltage, and we do not know if it drifts significantly over time. NOTE: A version of the LISST-VSF MATLAB software tools that allows simple modification of  during data processing is under development!
  • Page 20 VSF derived from the ring detectors. Angle [deg] Angle [deg] -0.5 Angle [deg] Angle [deg] Figure 4 – Summary of LISST-VSF processed data See Appendix B for explanation of spikes in result and how to minimize them. LISST-VSF User’s Guide...

  • Page 21: General Precautions

    CAUTION light could be reflected into an eye causing permanent damage. LASER RADIATION Do Not Open You should never have to open the LISST-VSF or battery pack pressure Instrument Case cases. Doing so may void the Manufacturer’s Warranty! Connecting Cables Always connect this cable to the instrument first, then connect the other end to the battery pack, bench-top power source, or PC.

  • Page 22: Quick Start

    9. Manual 10. Sediment Samples 11. Spare O-rings 12. Mounting Clamps (4 sets) 13. Battery housing 14. LISST-VSF instrument 15. Test dusts in small quantities Set Up on the 1. First place the instrument stands approximately 1m apart. Bench Top 2.
  • Page 23 Simply insert the CD in your PC’s CD drive (or connect the USB disk) and follow along. A program icon will appear on your desktop and under the Sequoia folder in your All Programs menu. The MATLAB *.m files provided on the installation CD (or USB drive) will be copied to your working folder for data processing.
  • Page 24 Form the The LISST-VSF is provided with a bendable clear plastic sheet with sealing Laboratory Test gaskets and quick-release band clamps. This chamber has the advantages of Chamber quick and easy installation and the ability to inspect the sample being measured.
  • Page 25 A listing of stored files will appear. Select the ones to download and click OK. Cleaning the Before putting the instrument away, clean the inner endcaps and windows. Instrument Drain the test chamber, wipe and dry the windows. LISST-VSF User’s Guide...
  • Page 26 Wake up the instrument by clicking the adjacent button. Note that once put into sleep mode, it can take up to a minute to wake up the instrument. LISST-VSF User’s Guide...

  • Page 27: Section Ii: Operation

    1. Instrument mounting, storage and maintenance 2. Charging and Connecting the Lithium battery pack 3. Bench-testing and collecting background data 4. Offloading and erasing data files from instrument memory 5. Recording and storing a sample data file 6. Data Processing LISST-VSF User’s Guide...

  • Page 28: Ii.1 Instrument Mounting, Storage And Maintenance

    See Appendix H for: Accessories. Storage Notes The LISST-VSF is a sensitive instrument. When not in use, the instrument should be stored in its shipping case. Clean and dry the instrument before storage. Avoid storing the instrument in excessive heat or humidity. Do not store the instrument in freezing temperatures, or in environments with wide temperature fluctuations.
  • Page 29 Cleaning the The condition of the windows is critical to the performance of the LISST-VSF. optical windows Care must be taken when cleaning the windows. The windows and the instrument should be rinsed thoroughly with fresh water after each deployment to ensure that salts and sediments will not scratch the window during the cleaning process.

  • Page 30: Ii.2 Charging And Connecting The Lithium-Ion Battery Pack

    Weight: 10.3 kg (22.8 lbs) in air  Capacity: 14.8V, 39 A-hr. The battery pack connects to the LISST-VSF by way of a 3-pin wet mate-able connector (bulkhead connection is MCBH-3F). This same connector is also used to connect the battery pack to the charger.
  • Page 31 After charging is complete, the vent plug must be closed before the battery can be used. EXTREME CAUTION IS ADVISED IN CLOSING THE CHARGING PORT AFTER BATTERY CHARGING. FAILURE TO CLOSE PROPERLY CAN RESULT IN FLOODING, PERMANENT DAMAGE, AND EVEN FIRE. LISST-VSF User’s Guide...

  • Page 32: Ii.3 Bench Testing And Collecting Background Data

    II.3 Bench Testing and Collecting Background Data Bench Setup The LISST-VSF instrument should be set up on the two white plastic mounting blocks, placed roughly between the middle of each pressure case on either side of the eyeball. Make sure that you do not add bending moments on the pressure case.
  • Page 33 Water Clean water should reach a level approximately 1-2 cm above the optical windows. Sequoia recommends using distilled or reverse-osmosis water which has undergone 0.2 micron (or smaller) filtration. Superior lab results have been obtained by continuously circulating (pumping) the clean water contained in the sample volume through a 0.2 micron capsule filter (e.g.,...
  • Page 34 Check Instrument Alignment and Water Cleanliness (page 33). The LISST-VSF uses a dark ring detector reading to reduce sensitivity to ambient light. However, it is suggested that the sample volume be covered with a felt sheet or other opaque barrier during sampling.

  • Page 35: Ii.4 Offloading And Erasing Data Files From Instrument

    II.4 Offloading and Erasing Data Files from Instrument Connect Connect communications cable. Connect battery or benchtop power supply. Instrument and Run LISST-VSF software and open Terminal Window. Start LISST-VSF Software Connect to the instrument by clicking on the terminal window icon or selecting Terminal Window from the Communications menu.
  • Page 36 Baud Rate drop down menu, choose a lower baud rate and try again. Deleting Files When connected to instrument as described above: from LISST-VSF Memory Select Erase from the LISST menu or press the Erase button. list of files on the LISST-VSF datalogger will appear. LISST-VSF User’s Guide...
  • Page 37 Confirm the files to be deleted by clicking the Yes button. WARNING: Once a file has been deleted there is no way to recover the data. Make sure that the file has been properly offloaded before deleting any files LISST-VSF User’s Guide...

  • Page 38: Ii.5 Recording And Storing A Sample Data File

    Check Instrument Alignment and Water Cleanliness (page 33). The LISST-VSF uses a dark ring detector reading to reduce sensitivity to ambient light. However, it is suggested that the sample volume be covered with a felt sheet or other opaque barrier during sampling.
  • Page 39 LISST-VSF User’s Guide...

  • Page 40: Ii.6 Data Processing

    150 pairs of [angle PMT1on PMT1off PMT2on PMT2off] For more information, see Appendix D. Data The MATLAB functions provided for processing LISST-VSF data files will Processing prompt you for filenames. In addition to the background and data files, you will Sequence be prompted for a Factory background file, and a calibration factors file.
  • Page 41 The following command reads and displays a raw LISST-VSF data file. The raw data are also passed as output parameters from the function. view_rawfile.m [angles,rp,pp,rr,pr,rings1,rings2,LP,LREF,bat,PMT,depth,temp,date] = view_rawfile; When this script is run, a dialog box will appear for selecting the LISST-VSF Data File (*.DAT) downloaded from the instrument LISST-VSF User’s Guide...
  • Page 42 Saturation can be avoided by lowering the PMT control voltage. This is done by using the ~c command in the Terminal window. A lot of variables are displayed. When the PMT control is displayed, adjust is up or down in steps of 50. LISST-VSF User’s Guide...
  • Page 43 Auxiliary Data (i) Depth (top left), (ii) laser reference (red) and transmission (bottom, left), (iii) temperature (top, right) and (iv) the ratio of laser transmission/laser reference (bottom right). The last plot serves as indicator of homogeneity of the suspension. Figure 7 – Auxiliary data (top) and laser reference and transmission. LISST-VSF User’s Guide...
  • Page 44 5000 -500 -1000 -5000 Angle [deg] Angle [deg] Net Signal rp Net Signal rr 2000 15000 1500 10000 1000 5000 -500 -5000 Angle [deg] Angle [deg] Figure 8 – Outputs of two PMT’s for two laser polarizations. LISST-VSF User’s Guide...
  • Page 45 *.mat. The make_zsc function will prompt for the LISST-VSF raw data file to be processed. Only files matching Z*.DAT will be shown by default. All *.DAT files can be displayed in the Open Background Scattering File dialog by selecting it from the “Files of type”...
  • Page 46 LISST-VSF background scattering will be read from the input file and displayed. Four signals (rp, rr, pp, pr) are displayed, along with factory values for comparison. Current Factory Angle [deg] Angle [deg] Angle [deg] Angle [deg] Figure 9 – Comparison of current and factory eyeball background light.
  • Page 47 Binary Data File to Process: This is the raw file downloaded from the LISST-VSF containing scattering data. By default, files named (V*.DAT) saved from the GO command are listed. Use the Files of type dropdown box to select any file *.DAT.
  • Page 48 FACTORY Background Scattering File: This is the factory background scattering file provided by Sequoia, named Factory_ZSC_XXXX.mat, where XXXX is the serial number of the instrument. FACTORY Calibration Factors File: This calibration factors file provided Sequoia, named Cal_factorsXXXX.mat, where XXXX is the serial number of the instrument.
  • Page 49 A check of how well the chosen value of applies is shown next. How well the estimated  matches PMT’s at 45 and 135 (should be unity)  Figure 11 – How well PMT’s match at 45 and 135 with the selected LISST-VSF User’s Guide...
  • Page 50 VSF is top right, p12 is bottom left and p22 is bottom right. Figure 13 - Eyeball data after all corrections, before merging with rings. Note that p22 is unstable at 45 and 135 as explained in Appendix B. LISST-VSF User’s Guide...
  • Page 51 VSF and p12 and p22. The Composite VSF (rings and eyeball): log-log axis, and log-linear. Figure 14 –Composite VSF, combining rings and eyeball data on log-log and log-linear axes. Note: for small particles, rings data are noisy at smallest angles. LISST-VSF User’s Guide...
  • Page 52 In make_P, an automated procedure is used to find the relative gain () of the Relative Gain (α) two PMT’s. Noisy data may require adjusting the relative gain. This is the only adjustable parameter in the LISST-VSF instrument. “tweaking alpha” To adjust the relative gain, open make_P.m in the MATLAB Editor, and enable...
  • Page 53 2. It is possible to view each datafile using the view_file or read_file functions. Each displays raw data in different details. 3. The break in p22 at 45 and 135 is caused by the nature of these data with the rotating eyeball. LISST-VSF User’s Guide...

  • Page 54: Section Iii Instrument Programming And Command Details

    The transfer rate can be changed as described in Changing Offload Baud Rate in Section II.4. Communication Installing the LISST-VSF software will create an icon on your desktop to Software launch the software. Once connected, you will normally communicate with the LISST-VSF using this Windows software that also permits easy programming and data offload.

  • Page 55: Iii.1 Programmed Operation For Field Or Laboratory Use

    Time Delay. The details of each condition are described below. Depth Start The built-in depth sensor of the LISST-VSF is used to check the current depth to determine if the desired start depth has been exceeded. The instrument is powered up and 5 measurements of the depth are averaged over a two-second period.
  • Page 56 External The LISST-VSF has a white plastic lever on the endcap. This lever has Mechanical Switch a magnet imbedded in it. This magnet can activate a switch inside the Start pressure case. The base program looks at the status of this switch once a second.
  • Page 57 Stop battery voltage has dropped to less than 6 volts. The program will continue to sample until one of these conditions is met. It will then return to the L-VSF:> prompt. LISST-VSF User’s Guide...

  • Page 58: Iii.2 Lisst-Vsf Command Summary

    III.2 LISST-VSF Command Summary Display Commands Display Current Battery Voltage Display current Disk Directory Display current status information Display Current Time and Date Display general help messages and command list Setup Commands OM x Set Operating mode. ST x Set Start Condition.
  • Page 59 Syntax: DS or ds Description: The instrument settings and status are displayed to the screen. Example: input: DS output: LISST-VSF Current Status and Settings Serial number = 1425 Firmware Version 0.920 Jul 23 2012 17:34:17 Operating Mode: Fixed Rate Mode...
  • Page 60 Battery Voltage is 10.75 Current Date/Time: Tuesday, August 07, 2012 16:18:36 Current Day of the Year: 220 input: DS 1 output: LISST-VSF Current Status and Settings SN = 1425 OM = 3 ST = 5 TD = 0 SP = 5...
  • Page 61 Input: TD 2 (if Start Condition = 5 (Delay Start)) Output: New Start Condition data = 2 Start Condition: Delay Start with 2 minute delay Set Stop Condition Syntax: SP x or sp x, where x is the stop condition code described below LISST-VSF User’s Guide...
  • Page 62 Syntax: BI x or bi x, where x is the number of seconds between the start of 2 consecutive bursts, from 1 to 10,000 seconds. Description: In Burst Mode (OM = 2), the burst interval is the number of seconds between two LISST-VSF User’s Guide...
  • Page 63 Description: Issue the SD command to verify the current settings. Then confirm (1 = yes, 0 = no) that these settings should be burned into the EEPROM to be used with the AutoStart setting. Example input: SD output: LISST-100X Current Status and Settings LISST-VSF User’s Guide...
  • Page 64 0m at zero depth (in air). You must issue the ZD command, then select 1 (yes) or 0 (no) to reset depth sensor Example: input: ZD output: Depth Sensor Offset Reset Procedure Started. Instrument must be at zero depth and similar temperature to field conditions. LISST-VSF User’s Guide...
  • Page 65 Syntax: YS filename or ys filename where filename is the name of the file to be offloaded. Description: Offloads file from Compact Flash Module to PC using YMODEM offload at 115 Kbaud Example: Input: YS L1391205.dat Output: Starting… LISST-VSF User’s Guide...
  • Page 66 Example: Input: ZA Output: <Status information during sampling> Notes: The ZS command does not store the sample to a datafile, but average detector ring values may be written to a text file using the LISST-VSF software. Grab 20 samples and transmit Syntax: ZS or zs Description: Acquires 20 averaged sample and displays the result to the screen.
  • Page 67 LISST-VSF User’s Guide...

  • Page 68: Appendix A: Details Of Lisst-Vsf Instrument

    Appendix A: Details of LISST-VSF Instrument Fundamentals: The Volume Scattering Function (VSF) is an inherent optical property of water. It describes how an incident photon is scattered into different directions. The integral of the VSF produces the total scattering coefficient, usually denoted as b. The attenuation of light is described with a beam attenuation coefficient, c.
  • Page 69 16 bits. Simplified Optics Diagram: The LISST-VSF optical design consists of a 1 mm diameter green (532 nm) laser beam originating from a TEC laser module (1), then folded by a prism (3) onto the primary instrument optical axis. The default laser polarization is determined by rotation of the laser module and a polarizing beamsplitter (4).
  • Page 70 For each data acquisition sequence, a background scattering is measured. This is done with 0.2micron filtered water. This background is subtracted from particle data, to retain contribution of particles alone. The background from pure water was verified to appear similar to Rayleigh scattering. LISST-VSF User’s Guide...
  • Page 71 (11) through an ND filter (12) to ring detector (13). The large-angle scattering is sensed by the eye (14) and the scattered light beam is then steered to a polarization separator and twin-PMT assembly. This figure is out of date. LISST-VSF User’s Guide...

  • Page 72: Appendix B: Method Of Extracting P11, P12 And P22

    PMT2H: c = {P11 – P12 - cos(2) *[P12 - P22]} (B2b) where  is the relative gain of the two photomultipliers. is not known a priori, it is determined from data. Determining the Relative Gain of the Two Photomultipliers: LISST-VSF User’s Guide...
  • Page 73 This can be done within the make_P function. Experienced MATLAB users will know how. We will provide a description shortly. These equations are implemented in the MATLAB function make_P. LISST-VSF User’s Guide...
  • Page 74 VSF. The latter is absolutely calibrated as reported in: Agrawal YC, Mikkelsen O. A (2009): Empirical forward scattering phase functions from 0.08 to 16 deg. for randomly shaped terrigenous 1-21 µm sediment grains. Optics Express 17:8805–8814. LISST-VSF User’s Guide...

  • Page 75: Appendix C: Matlab Software

    Absolute sensitivity of PMT’s is adjusted to match the VSF estimated from ring 32. Estimates of the relative gain parameter  are obtained from data. The output is not averaged over scans. VSF and depolarization can then be plotted against depth. LISST-VSF User’s Guide...
  • Page 76 40 variables from 32 rings etc. for perpendicular laser polarization rings2 40 variables from 32 rings etc. for horizontal laser polarization temp Water temperature, 0.01 C steps, at endcap on ring-detector side. These variable names appear in data processing MATLAB software, and in function calls. LISST-VSF User’s Guide...

  • Page 77: Appendix D: Observation Angles, Data Storage Format And Variable Names

    3.2827 3.0229 3.2827 3.8703 3.5644 3.8703 4.5613 4.2016 4.5613 5.3731 4.9506 5.3731 6.3250 5.8296 6.3250 7.4384 6.8591 7.4384 8.7365 8.0614 8.7365 10.2430 9.4598 10.2430 11.9804 11.0777 11.9804 13.9674 12.9358 13.9674 16.2149 15.0493 Angles 33 to 182 6-155 LISST-VSF User’s Guide...
  • Page 78 Pressure, in digital counts; each count is 0.1m Temperature in units of 1/100 of 1 (Day*100 + Hour) at which data taken (Minutes*100 + seconds) at which data taken 41-790 150 sets of [ angle, PMT1_on, PMT1_off, PMT2_on, PMT2_off LISST-VSF User’s Guide...
  • Page 79 (laser power is recorded for each rotation of the eyeball) LREF N x 2 (laser reference output is recorded for each rotation of the eyeball) N x 2 (even though fixed for all rotations in a file) LISST-VSF User’s Guide...

  • Page 80: Appendix E: Connector Pinouts For Lisst-Vsf

    Appendix E: Connector Pinouts for LISST-VSF The LISST-VSF has 3 separate underwater connectors: A 5-pin, a 6-pin, and a 3-pin connector. The photograph shows the placement of each connector. The following text describes the detailed wiring for each connector. xxx...
  • Page 81 Connector Manufacturer: Impulse Enterprise, Inc. San Diego, CA, USA Connector Part Number (Bulkhead): MCBH (WB)-5-MP Stainless Steel Mating Cable Part Number: MCIL-5-FS xxx Connector Pin # Serial Ground No Connection Serial Ground Serial Out (to DB-9 Pin 2) Serial In (to DB-9 Pin 3) LISST-VSF User’s Guide...
  • Page 82 Connector Manufacturer: Impulse Enterprise, Inc. San Diego, CA, USA Connector Part Number (Bulkhead): MCBH (WB)-3-MP Stainless Steel Mating Cable Part Number: MCIL-3-FS xxx Connector Pin # Power Ground Custom Lithium Battery Charger Input, 14.8V nom. Power Out (12V nom. 9V-16.9V actual) LISST-VSF User’s Guide...

  • Page 83: Appendix H: Lisst-Vsf Accessories

    Appendix H: LISST-VSF Accessories a. Lexan ZSCAT Sheet b. ZSCAT clamps (2) c. Communications Cable d. Battery Cable e. Battery Charger f. Power Supply g. Stands (2) h. Installation Disk i. Manual j. Sediment Samples k. Spare O-rings l. Mounting Clamps (4 sets)

  • Page 84: Warranty

    If, during the twelve months after delivery (the “Warranty Period”), any Product does not comply with the warranties set forth in 1(a) and 1(b) above, SEQUOIA will, at its option, either (a) repair the Product, (b) replace the Product, or (c) refund the purchase price paid by Customer to SEQUOIA for the Product; provided that Customer gives SEQUOIA written notice of the noncompliance within the Warranty Period and ships the Product to SEQUOIA within one month after the end of the Warranty Period.
  • Page 85 SEQUOIA) will in no event exceed the purchase price paid by Customer to SEQUOIA for such Product. Further, SEQUOIA will not be liable for, or be in breach of or default on account of, any delay or failure to perform as a result of any cause, condition or circumstance beyond SEQUOIA's reasonable control.
  • Page 86 Document History Revision Date Description Author 2012/08/28 Draft document YCA/WHS/RS 2013/03/08 Updated for non-AOM units RS/WHS LISST-VSF User’s Guide...

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