Sequoia LISST-VSF User manual

LISST-VSF
Multi-angle Polarized Light
Scattering Meter
User’s Manual
Version 3.0
(December 2016)

ii LISST-VSF User’s Guide
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LISST-VSF User’s Guide iii
LISST-VSF

FEATURES:
In-situ measurements of P11 (VSF), P12 and P22 elements of the scattering Mueller matrix
from 0.1-155o(nominal) in water, to maximum depth of 50m.
Auto shut-off at depth greater than 50m, and auto resume when depth <50m.
VSF (P11) at small angles, 0.1 to 15o (nominal) in 32 logarithmic steps in angles
Integration of 0.1-155oVSF provides a good estimate of total scattering coefficient b.
Beam attenuation measured with LISST-100X optics.
EyeballTM optics permit 1oresolution in scattering angles between 15 -155o
Daylight rejection in eyeball data by laser modulation.
Data from small and large angles in a single data stream, including depth, temperature, date
and time.
Approximately 4 sec. per measurement set [involves 2 turns of Eyeball with vertical, and
horizontal laser polarization].
This document is copyrighted by SEQUOIA SCIENTIFIC, INC.

iv LISST-VSF User’s Guide
SPECIFICATIONS:
Parameters measured
Small-angle VSF in 32 log-spaced angles, from 0.1 to 15o(nominal)
VSF, P12 and P22 over 15-150oin 1osteps (nominal)
Beam attenuation
Temperature from –5° to 50°C with 10 mdeg resolution
Depth (50 m max operational depth; 8 cm resolution)
Operating Concentration range
Beam attenuation from 0.13 to 20 m-1 (based on 98%<transmission<30%)
Technology
Fiber Coupled TE-cooled Laser Diode @ 515 nm
Ring Detector for small-angle VSF
Roving Eyeball and Photomultiplier (PMT) for 15-150o(nominal)
Mechanical and Electrical
LISST-VSF Instrument
Dimensions 13.3 cm (5.25”) diameter, 86 cm (34”) L , plus 10 cm (4”) Standoff.
Weight: 13 kg (28 lbs) in air; 8 Kg (17lb) in water.
Depth rating: 300 m survival depth (50 m operational depth)
External power input: 12VDC nominal, max 20VDC
Sampling rate: 4 seconds for a full measurement of P11, P12, P22
Power drain: 700 mA measuring / 170mA quiescent
Data storage: 128GB, equivalent to 40,000? measurements
Battery Housing and Capacity
Dimensions 10 cm (4”) diameter, 52 cm (20.5”) long including handle
Weight: 6.5 kg (14.3 lbs]) in air; 2 kg (2.2 lb) in water
Voltage: 14.4 V nominal; 16 V fully charged; 12 V min. operating.
Capacity: 14 Ahr, 200 Whr.

LISST-VSF User’s Guide v
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 instructions for operation
Section Three provides instructions on programming.
Appendices provide further details …
Instrument Specific Constants
These are included in a MATLAB file, named lisstvsf_getcal.m.
Technical assistance
For technical assistance please contact your local Distributor or
Sequoia. Please be sure to include the instrument Serial
Number with any correspondence.
Sequoia Scientific, Inc. contact information:
Telephone: [phone]
Email: [email protected]

vi LISST-VSF User’s Guide
Waste Electrical and Electronic Equipment
Smaltimento di apparecchiature elettriche ed elettroniche da rottamare

LISST-VSF User’s Guide vii
Table of Contents
SECTION I: LISST-VSF INSTRUMENT....................................................................................1
I.1 INTRODUCTION .........................................................................................................1
I.2 GENERAL PRECAUTIONS ...........................................................................................6
I.3 QUICK START ...........................................................................................................7
SECTION II: OPERATION.......................................................................................................12
II.1 INSTRUMENT MOUNTING,STORAGE AND MAINTENANCE............................................13
II.2 CHARGING AND USING THE BATTERY PACK..............................................................14
II.3 BENCH TESTING AND COLLECTING BACKGROUND DATA............................................16
II.4 OFFLOADING AND ERASING DATA FILES FROM INSTRUMENT......................................19
II.5 RECORDING AND STORING A SAMPLE DATA FILE......................................................21
II.6 DATA PROCESSING.................................................................................................22
SECTION III: INSTRUMENT COMMUNICATION AND PROGRAMMING.............................30
III.1 PROGRAMMING.......................................................................................................31
III.2 COMMAND DETAILS.................................................................................................34
APPENDIX A: METHOD OF EXTRACTING P11, P12 AND P22...........................................42
APPENDIX B: MATLAB SOFTWARE....................................................................................45
APPENDIX C: OBSERVATION ANGLES, DATA FORMAT AND VARIABLE NAMES ......46
APPENDIX D: CONNECTOR PINOUTS FOR LISST-VSF ...................................................48
APPENDIX E: LISST-VSF ACCESSORIES ..........................................................................51
WARRANTY ............................................................................................................................52

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LISST-VSF User’s Guide 1
Section I: LISST-VSF Instrument
I.1 Introduction
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. An excellent estimate of the beam
scattering coefficient b, and by difference, the beam absorption coefficient a
can also be derived from the data. All properties are measured at a laser
wavelength of 515nm. The forward angles in water, from, 0.088 to 14.360at
which VSF is measured are spaced logarithmically. The intermediate and
large angles (>15-deg) are linear, with 1-deg resolution. The 10angular
resolution of this instrument permits examination of enhanced scattering by
bubbles in the ~80-deg region.
Light Scattering
and VSF
The Volume Scattering Function (VSF) describes the distribution of scattered
light energy as a function of scattering angle. VSF is defined for unpolarized
light source and no discrimination of polarization in the scattered light.
However, scattering of light by particles always produces changes in
polarization state of the scattered rays. The state of polarization is described
by the Stokes vector I, with elements I,Q,U,V. The Stokes vector of the
scattered light and that of the incident light Iiare related through a matrix
product:
Is= P Ii
where P is the scattering Mueller matrix. P is a 4 x 4 matrix. It contains
information regarding particle scattering characteristics. The elements of P
are often denoted by Pij. The first element, P11 is identical to the volume
scattering function, VSF. Elements [1,2] and [2,2] relate to changes in the
linear polarization properties I and Q. For example, element P12 produces
depolarization. Element P22 is known to be an indicator of sphericity of
particles; so that P22 =1 everywhere implies that particles are spheres. With
the LISST-VSF, it is assumed that symmetry forces elements P13 and P14 to
zero, and that P12 and P21 are equal. Thus only 3 unknowns describe the
Mueller matrix P.
At small forward angles, scattered light mostly maintains its original
polarization, so that depolarization is small. This instrument does not measure
depolarization at angles smaller than 15o, because there the VSF is measured
by a set of ring detectors, identical to our familiar LISST-200X instrument. A
different instrument, LISST-Stokes has been developed for small-angle
depolarization studies. If interested, please contact us.

2 LISST-VSF User’s Guide
Instrument
Overview
The small-angle part of VSF is measured using ring detectors, identical to the
ones used in our LISST-200X instrument. Each ring detector measures the
VSF into a small angle range. The range of angles covered by the rings is
0.088 to 14.80. (e.g. Agrawal & Pottsmith, 2000; included on the USB card)
For larger angles, and to measure the VSF and depolarization components, it
is necessary to measure the intensity and polarization state of the scattered
light. The LISST-VSF employs a single linearly polarized laser and two PMT
detectors. One PMT measures scattered light into perpendicular polarization
and the other into parallel polarization. The laser polarization is alternated
between vertical and horizontal by insertion or removal of a ½-plate. In this
way, a total of 4 measurements is made at each scattering angle, see Fig.1
Figure 1: Schematics of the optics. Top shows collimated laser (FCL) passing through
a polarization ‘purifier’ (GT), a beam-splitter (BS), ½-  plate (HWP), and pressure
window (W1). The eyeball (EYE) rotates and views scattering along the beam (SV).
An ND filter on the receive window (W2) is incorporated to reduce glow from the
receive optics. It is followed by receiving lens for the ring detector optics (RD), and
transmission sensor (LP). The lower figure shows the folded path of received light, a
spatial filter (SF), a laser line filter (LF) and polarizing beam splitter (PBS) which
delivers light to the two PMT’s.
Past VSF instruments have either employed a fixed set of detectors viewing a
common scattering volume, or a telescope that views a scattering volume and
rotates around it. These systems are not suitable for autonomous use. In
contrast, the LISST-VSF instrument uses a rotating eyeball. This eyeball is
placed to the side of the laser beam. As it rotates, it views different parts of
the laser beam (Fig.1, top), i.e. at different angles. At each angle, 4
measurements are made - scattering in two polarizations for parallel and
perpendicular polarization of the laser. This produces the desired VSF, P12,
and P22. The splitting of the received scattered light is shows in lower Fig.1.
The eyeball makes the LISST-VSF instrument compact, autonomous, and
manageable underwater. As a result, this instrument may be left on a tripod or
mooring.
As explained in Appendix A, due to the rotating eyeball receiver, the stored
scattered light signals are a mix of the 3 parameters P11, P12 and P22. The
convenience of the eyeball thus involves a price –solving for these quantities.

LISST-VSF User’s Guide 3
We provide software to perform this function. For details, please see
Appendix A. The physical layout of the instrument is shown in Fig.2 below.
The Instrument
Electro-Optic
Components
Figure 2: The internal arrangement and housing of the LISST-VSF. The endcaps on
this instrument are NOT to be opened without consent of the factory.
The instrument employs a single 515nm TE-cooled diode laser. Two
miniature, compact PMT’s are used to sense scattered light. Beginning with
SN 1660, firmware automatically controls the gain of these two PMT’s.
Alternately, the gain can be adjusted with software commands. The output of
PMT’s is digitized and stored in data files.
Depth and
Temperature
Sensors
A depth sensor is mounted to the instrument connector endcap. A
temperature sensor is also thermally bonded to this endcap. Please note that
the temperature sensor is therefore slow.
Communication
A cable is provided to connect the underwater connector on the instrument
endcap to a PC. Communication is at 9600baud, except when downloading
data, when it automatically switches to 115Kbaud.
Data Acquisition
sequence
When commanded to capture data, the following sequence begins: the laser
is turned on for a short period to reach stable power. After this warm-up, the
eyeball starts rotating. When the optical encoder, which reads eyeball position
reads 150, the two PMT data are captured at 10intervals. Between 150and
400of eyeball position, the laser is dimmed by the laser controller. This is
done because this scattering is stronger; dimming reduces demand on the
PMT dynamic range. At 410encoder position, laser power is returned to full.
Eyeball data are recorded till encoder reads 1500. For the duration of eyeball
data capture, the laser is chopped for ambient light rejection. After 1500, laser
chopping is turned off, laser power is set to full for ring data capture. When
ring data have been captured, the combined ring and eyeball data are written
to data file. Immediately thereafter, a half-wave plate is inserted in the laser
beam, so that during the next turn, PMT data would be captured with laser
polarization rotated by 90o. The measurement cycle repeats for the second
rotation, only now the half-wave plate is removed at end. This is illustrated in
Fig.3.

4 LISST-VSF User’s Guide
Auxiliary Data
and Checks
Background Data
One-step Data
Processing
Detailed Data
view
.
Figure 3 –Simplified description of timing of data acquisition. In each of 2 rotations of
the eyeball, laser is dimmed for 15- 40-degree positions of eyeball, then full power is
turned on. Shading represents chopping of laser power for ambient light rejection.
After eyeball data are acquired, rings are read at full laser power, following which the
½-  plate is inserted(arrows) for the second rotation, and the cycle repeats, ending
with removal of ½-  plate.
Also stored in each rotation are auxiliary parameters - depth and temperature,
battery voltage, date and time. Not shown in Fig.3. are two significant tests –if
current depth exceeds 50m, and if battery is depleted. If the depth is
exceeded, a new cycle of data collection pauses until depth is again less than
50m. If battery is depleted, the current cycle is completed, data saved, and
then instrument drops into low power mode.
The number of sets of data is controlled from PC commands.
As with our LISST-200X instruments, measurement of background light on
ring detectors from optics is an essential part of getting good data. Similarly,
background light from scattering by water molecules constitutes the
background for eyeball data. These backgrounds are saved prior to each use,
and subtracted from total scattering observed from particle laden water. Note
that eyeball background data depend on PMT control voltage. Consequently,
backgrounds are saved at a set of control voltages for use with corresponding
particle data.
Data processing is performed in MATLAB. A single function lisstvsf_makep
produces the desired end result: P11, P12, and P22, beam_c and beam_b.
For convenience, a few other functions are provided, e.g. lisstvsf_view to
view data files, and others to simulate the VSF from Mie theory. The expected
measurement from, say, single size polystyrene beads can be computed
using this simulation for comparison with actual data.
See the data processing section for detailed processing steps.

LISST-VSF User’s Guide 5
Example Results
Use in
Laboratory or
Field
PRECAUTIONS
We show below VSF obtained with 0.5 and 25-micron polystyrene spheres,
contrasted with Mie theory. Note that due to the 1-deg resolution of the
LISST-VSF, the very high resolution oscillations for 25mm particles are
averaged.
The instrument can be used in the laboratory, using a provided water
chamber, or in the field. It can be operated with an External Power Supply, or
using the supplied rechargeable battery. To become familiar with the
instrument, laboratory use is highly recommended first, before attempting a
field deployment.
In battery-powered field usage, the instrument can be used from a wire in a
profiling mode, or it can be mounted on a tripod or mooring for a time-series
observation.
NEVER INSERT ANYTHING REFLECTIVE IN THIS SPACE. THE LASER
POWER IS APPROXIMATELY 5mW. IT WILL DAMAGE EYES.
The windows and endcap faces should be clean if doing laboratory work. If
deploying in the ocean, make sure both windows are clean. Use lens cleaner
or soap and water. DO NOT USE ABRASIVE CLEANERS.
Rechargeable
NiMH Battery
Pack
External Power
Supply
The instrument power source is a rechargeable NIMH pack. With all systems
on, the instrument draws about 0.7 A current. The fully charged battery can
power continuous operation of the instrument for up to ~20 hours. Note that
the instrument checks the state of battery before capturing each set of data. If
the battery is low, a graceful shutdown is executed.
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.

6 LISST-VSF User’s Guide
I.2 General Precautions
Handling the
Instrument
The LISST-VSF is a delicate instrument. It contains precision, highly
aligned optics, and electronics. It is designed for the rigors of field use,
however it should be handled with care at all times.
Mounting the instrument, either in the laboratory or on a frame for
field use must make sure that the instrument is not subjected to
bending as that will cause loss of alignment.
AVOID SHOCK at all times.
Do Not Open
Instrument Cases
You should never have to open the LISST-VSF pressure case. Doing so
may void the Manufacturer’s Warranty!
Connecting Cables
Always connect cables to the instrument first, then connect the other
end to the battery pack, bench-top power source, or PC.
A BATTERY CHARGER IS PROVIDED WITH THE LISST-VSF.
NEVER USE ANY OTHER CHARGER FOR BATTERY CHARGING.
THIS MAY DAMAGE THE BATTERY AND VOID THE WARRANTY.
EXTREME CAUTION IS ADVISED IN CLOSING THE BATTERY
PRESSURE CASE AFTER BATTERY CHARGING.
CAUTION
LASER RADIATION
WARNING
The LISST-VSF uses a Class 3B green laser emitting a
maximum of 10 mW of visible light at a wavelength of 515 nm.
The laser beam under normal circumstances is not a threat.
However, if reflective objects are placed in the path of the laser
beam, the light could be reflected into an eye causing
permanent damage.
CAUTION
RISK OF FIRE

LISST-VSF User’s Guide 7
I.3 Quick Start
Section summary
In this section, we provide a condensed version of full operation, from opening
the instrument case as received, to data collection and processing. A detailed
description is included in Section II.
Contents of
shipping case
Let us see what is in the box!
Open the shipping case containing the instrument. You should see the
following items inside (see also Appendix H):
1. Lexan Sheet (for forming the water chamber in lab use)
2. Clamps to hold the lexan sheet wrapped aound the sample volume
(2)
3. Communications Cable (5-pin underwater female to USB)
4. Battery Cable (3-pin male to female underwater cable)
5. Battery Charger
6. Power Supply
7. Power Supply adapter cable (adapts to 3-pin underwater female)
8. Instrument Stands (2 for LISST-VSF, 2 for battery pack), for use on
laboratory bench.
9. USB memory card with software and electronic documents
10. Manual
11. Spare O-rings
12. Mounting Clamps
13. Battery housing
14.LISST-VSF instrument
Set Up on the
Bench Top
1. First place 2 instrument stands approximately 1m apart.
2. Remove the instrument and cradle it on these stands.
3. Similarly place the battery case on the two other stands.
Do not connect the two instrument cases with the power cable yet! It is
important to become familiar with the various parts first.
No LISST-VSF end-caps should be opened by the user. Only
recharging the battery requires opening one end of the battery
case. The user should never try to loosen or disassemble any of
the other components attached to either endcap. Doing so could
immediately void the warranty.

8 LISST-VSF User’s Guide
Connectors on
Instrument
Endcap
There are 3 connectors on the
endcap. The 3-pin connector is for
power (from battery or line power
supply). The 5-pin connector is for
communication. The 6-pin
connnector is for auxiliary use.
See Appendix D.
Battery Housing
Endcap
There is only one connector on the battery housing endcap. See Appendix D
for pin-outs.
Checking for
Clean Windows
In preparation for getting started, at this time, check the optical windows to
make sure that they are clean. There are three windows: Two are on the inner
endcaps, and one is on the eyeball.
The best way to check the windows is by using a flashlight. By shining light
from one side, almost parallel to the window surface, and viewing from the
other, the surface of the windows can be easily checked for cleanliness. If
there is dirt or fingerprints on the windows clean them first by rinsing them
with lukewarm water and a mild soap solution (e.g. mild hand soap, liquid dish
soap) and then rinsing off all soap residue with clean, particle-free water such
as de-ionized water, MilliQ water or distilled water. The windows can also be
wiped clean with a soft cloth (e.g. a lens cloth) and alcohol. It is not
recommended to use stronger solvents, such as acetone or toluene. Also, do
not use any abrasive cleaners or wipes. Treat the windows as you would an
expensive camera lens.
Attach
Communications
Cable
Remove the Communications cable from the
shipping crate. It is the 2 meter cable with the 9-
pin DB-9 connector on one end and the 5-pin
underwater connector on the other. Remove the
underwater cap from the Communications
connector. The connectors will all look similar.
The Communication connector is the only 5-pin
connector. It is located below the engraved
serial number. After removing the cap install the
cable making sure that proper alignment of the
cable is maintained, so that the connectors are
not bent.

LISST-VSF User’s Guide 9
Install LISST File
Transfer Software
An installer for the software is provided on the USB card that was shipped
with your instrument. Double click on ‘LISST File Transfer Setup.exe’ and
follow the onscreen instructions. A program icon will appear on your desktop
and under the Sequoia folder in your All Programs menu.
This software will allow you to download data files from the instrument. You
can also use this software to open a terminal window for direct communication
with the LISST-VSF.
The MATLAB *.m files provided on the USB card should be copied to a local
folder for data processing. Make sure this folder is in your Matlab path.
Form the
Laboratory Test
Chamber
The LISST-VSF is provided with a flexible clear plastic sheet with sealing
gaskets and quick-release band-clamps. This chamber has the advantages of
quick and easy installation and laboratory use. Install with rectangular
encoder housing facing up [ This is the bump above the eyeball in Fig. 2 (top)]
Fill with clean, particle-free water (0.2 micron filtered).
Check out the Sequoia Scientific YouTube channel for a video showing
how to assemble the flexible test chamber.
http://www.youtube.com/user/SequoiaScientific
NOTE: An improved test chamber for laboratory and flow-through use is in
development.
Connect Power
Connect the LISST-VSF to the battery pack with the supplied underwater
cable, or to the power supply provided with the instrument.
Start LISST-VSF
Program
Launch the software by double-clicking the icon on your desktop.
The software will automatically search and connect to the LISST-
VSF instrument. If the software fails to find your instrument, go to
Help menu and explore the LISST File Transfer Help document.
Open Terminal
Window
Under the Communications menu, select Open Terminal. This will open a
window within the software window. If you hit <enter> on the PC, the
instrument will respond with a LISST-VSF> prompt.
Note: The instrument communicates at 9600 baud through this window.
However, when downloading data, the transfer rate automatically changes
to 115k.
Basic Commands
Basic commands will be printed to the screen when the Terminal window is
opened. You can see a list of these commands again by sending an ‘HE’
command. [HE is for help]

10 LISST-VSF User’s Guide
Acquire
Background
Scattering File
Now try to acquire a background file. The Laboratory Test Chamber should
be nearly full with clean water (so that both of the windows on inner end-
caps are submerged, and the strut on which the eyeball encoder is
mounted is partially submerged). Make sure that the water is well-mixed
(give it a stir) else temperature variations or turbulent microstructure
(scintillation) will affect the small-angle measurements. At the L-VSF:>
prompt, type the command
L-VSF:> zs
and hit <enter>.
This command will initiate an approximately 10-minute sequence during
which backgrounds will be acquired at a discrete set of PMT gains. First,
the laser will turn on for about 15 seconds for power stabilization. Then, the
eyeball will start rotation and 10 sets of data will be collected (20 eyeball
turns). Next, the PMT gain setting will be changed, and approximately 10
sec will be allowed for the new gain to stabilize and 10 more sets of data
will be collected. Again, the PMT setting will be changed and so on. When
finished, the laser will turn off. This is the entire background data.
The instrument will save a background file with name ZDDDHHMM.VSF.
You can download this new file by closing the terminal window and
pressing the refresh button in the upper left of the LISST File Transfer
Window. Your new file should then appear in the list box under ‘Files on
LISST.’ Choose an offload directory using the controls on the right side of
the window. Then highlight the .VSF file and press the green arrow to
download the file.

LISST-VSF User’s Guide 11
Collecting Particle
Data
Drop some particles in the test chamber (use fine particles, e.g. 0.3 micron
or 1 micron polystyrene beads from Duke Scientific, Inc.). Mix the water
well to homogenize the suspension. Mixing particles is very important as
the method of using the eyeball assumes a homogeneous mixture!
In the command window, type the commands:
L-VSF:> pd 16
L-VSF:> go
The first command specifies to grab 16 sets of scans (again, recall each set
is two rotations of the eyeball). The second command means start data
acquisition. Note that PMT gains are automatically adjusted. PMT setting
for each data set of 2 eyeball turns is stored in the data file. When finished,
the instrument will shut down, and you will know that because the laser will
be out. The command window will return to the L-VSF:> prompt.
To collect data in a field deployment, you will need to program the
instrument, i.e. set the starting delay, sample rate, length of data collection
etc. This is explained in Section II.
Downloading Data
From the main window of the LISST File Transfer software you will see a
listing of files stored onboard the LISST-VSF and a listing of files in a local
directory. Use the controls on the right of the window to select an offload
directory. You can use the shift or ctrl keys to select multiple .VSF files to
offload. Once selected, press the green arrow to offload the files. Two
progress bars will keep you informed on the offload status.
Cleaning the
Instrument
Before putting the instrument away, clean the inner endcaps (with transmit
and receive windows) and also clean the windows. Drain the test chamber,
wipe and dry the windows.
Instrument stand-
by current drain
The LISST-VSF does not have a deep sleep mode such as is
provided in our LISST-100X/200X; as such when not taking data, it
is in the read and standby mode, with the screen showing list-vsf>
prompt.
In this standby condition, the instrument draws about 150mA
current. For this reason, if you do not intend to use the instrument
for an extended period, simply disconnect the power source.

12 LISST-VSF User’s Guide
Section II: Operation
Section Overview
This section contains detailed instructions for the operation of instrument and
collection and processing of data. Some of the information in Section I.3 is
repeated for completion and in greater detail.
Section
Organization
This section is divided into these subheadings:
1. Instrument mounting, storage and maintenance
2. Charging and Connecting the NIMH 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