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LISST-Deep - Sequoia Scientific, Inc.

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1. Laser power iz too low compared to factory value Current laser power Factory laser power 1500 Average ring values exceed factory by a factor of at least 2 0 for 13 rina s 20 frames collected Frame Mum 20 BEGIN Collect Accept and Save Cancel When the BEGIN Collect button is pressed 20 samples will be displayed to the screen as they are acguired After all 20 are collected the average will be displayed If the values are acceptable the values can be saved to a file Enter the filename in the box and press the Accept and Save button 16 If there is a problem with the instrument or if the water or windows are not clean error messages will be displayed Dirty water or windows will generally cause higher values across the middle rings Large bubbles or particles in the water can cause higher values on the inner rings or left hand side of the display High values on the inner rings combined with a lower Laser power value can also be an indication of optical misalignment Step 11 The heart and soul of the LISST SOP software is the Operating Modes Configuring window This window is used to set all of the deployment parameters Instrument for To open the window choose Operating Modes from the LISST menu or Deployment press the button on the tool bar A window similar to the one shown below will appear LISST Instrument Operation Instrument Status Operating Mode Start Condition Stop Condition c
2. 60 LISST Deep Command Details Display Commands DB Display Battery Voltage The current battery voltage is displayed to the screen Example input DB output Current Battery voltage 8 90 volts DD Display Disk Directory Description Display current disk directory in DOS type format Includes total bytes used and bytes available Example input DD results L100x gt dd LISST 100X Disk Directory Volume in drive C is NONAME Volume Serial Number 1s 778B 155F Directory of CA L040305 BIN 4 136 03 05 04 6 30p L183705 BIN 1 672 03 05 04 6 37p 2 file s 5 808 bytes 0 dir s 15 933 440 bytes free L100x gt Display current status information The instrument settings and status are displayed to the screen Example input DS output LISST Deep Current Status and Settings Serial number 1004 Operating Mode Burst Mode Start Condition Time Start at 03 10 04 09 22 00 Stop Condition Fixed Number Stop at 1 samples Measurements per Average 10 Sample Interval 1 Burst Interval 1 Samples per Burst 0 Battery Voltage is 8 90 Current Date Time Wednesday March 10 2004 10 18 49 input DS I 61 LISST Deep User s Guide LISST Deep Current Status and Settings SN 1004 OM 2 5122 TD 03 10 04 09 22 00 SP 5 PD 1 MA 10 ST 1 BI 1 SB 0 BB 0 CT 0 IC 2 0 Current Time 03 10 04 10 18 49 Battery 890 Switch 0 Memory 15005640 Display general help messages and command list
3. View Rings Serial Port Output File Locations Aus Pars Realtime Instrument D ata Processing Existing Haw Data File 2 E Wild a binary raw data file ze ra wi Build an ASCII raw data file log v Build a binary particle size file pad p Build a binary particle size File ped Build an ASCII particle size file asc Build an ASCII particle size file asc Selections da NOT apply to data sources already oper Selections apply only to subsequent openings c Cancel Apply Help A binary PSD file must be selected before any other file type will be stored This is used to display the processed data to the screen The ASC type is a spaced delimited file containing all the processed data The LOG file is a space delimited file containing the raw data from the datalogger NOTE You should always check the Build an ASCII Raw Data file LOG when sampling in real time mode Sequoia Customer Support needs the LOG file in order to help you with data QC issues We cannot use the PSD or ASC file for troubleshooting the data LISST Deep User s D5 ST Deep User s Guide e Select Open Real Time Session from the File menu or press on Open Instrument selected the button e Choose the correct Background Scatter File and Select an Background and Output file Output file selected e A display will appear on the screen It is similar to the main Sample saved window of the View Processed
4. lt Prey Next gt Last lt Scale 0 0 Interval Sec 50 The left hand display 1s the volume distribution in units of micro liters liter in each size class The right hand display 1s the Cumulative Concentration Only a single sample is displayed at a time By using the buttons on the bottom of the display 1t 1s possible to manually or automatically step through the datafile The Timer button will step through the datafile by updating the display at a fixed rate The rate 1s set by the slider bar next to the Timer button 41 LISST Deep User s Guide e Additional information is stored in the processed datafile The Auxiliary parameter window displays these values for the current sample They will update as the Volume distribution is changed The window is opened by selecting Show Auxiliary Parameters Frame from the DataFrames menu An example of this window is shown below Auxihary Parameters FF Laser Power malt Battery volts External Instrument volts Laser Reference matta Depth meters Temperature deg L Aus 1 Aus 2 Li abit Transmission Warning Water too turbid Sample Number Show raw data 7 e The scale of the Volume Distribution plot can be changed by Display setting using the Scale button After selecting the button a modified display similar to the one shown below will prompt you for the maximum concentration for the Y axis of the plot Maximum Scale Setting Maxi
5. STEP BY STEP PROCEDURE RECORD AND STORE BACKGROUND SCATTERFILE Clean instrument and install Horizontal test Optics submerged in water assembly The Horizontal Test Assembly consists of a flexible plastic sheet which has a foam seal attached on two sides and two stainless steel metal clamps Wrap the sheet around the LISST Deep and clamp it on as shown in the picture below Fill with clean filtered water The water can be deionized water milli Q water steam distilled water or water from the water cooler The most important part is that the water be free of particles and bubbles Tap water is not recommended unless it has been outgassing in a beaker overnight as it typically has bubbles in it Connect communications cable and power and start Communications program the LISST SOP software started If the data acquisition program is still running stop L100X gt prompt showing its execution with a lt CTRL C gt Open the Collect Background Scatter Data from Background collected and saved the L SST menu or by pressing the m button on the toolbar LISST Deep User s Guide You will be prompted to select the factory background scatter file After selecting the file the window below will be displayed Collect Background Scattering Data 1000 O Output File Laser power is too law compared to factory value Current laser power Factory laser power 1500 Average ring values exceed factory by a factor
6. in Degrees for the VSF measurement in air are shown in the table below See also Sequoia s homepage http www sequoiasci com Articles ArticlePage aspx pageld 177 Type B Type C Ring Size bin Lower Upper Median Lower Upper Median MN N W W YW TWO OF N ABR DY R S so a u rw vn DDNDNDNDDNDM moor DD RU nd ON I 17 16 DD DD NN N ER EN EN bh EE O EN OO m NU BE yu UM O9 DNR WY E O EX OO N WN N D 0 Rua oS L UJ N LISST Deep User s Guide 82 Angles in water Angles in Degrees for the VSF measurement in water are shown in the table below See also Sequoia s homepage http www sequoiasci com Articles ArticlePage aspx pageld 178 Type B Type C Ring Size bin Lower Upper Median Lower Upper Median L B D W W YW LTL OF N ABR DYN BeoVAAADAAARWNY h2 t2 t2 l2 b2 P2 WD oo cO OO DD RUN ON I 17 16 DD DD NN N ER EN EN bh EE O EN OO m NU BE yu UM O9 DNR WY E O EX OO N WN N Nvv Rua UJ N 83 LISST Deep User s Guide Raw Data Storage Format The values in the raw data file are stored in the order shown in the table below Light intensity on detectors through 32 Temperature in units of 100ths of degrees C Day 100 Hour at which data taken Processed Data Storage Format Elements 1 32 33 34 35 36 37 38 39 40 41 42 LISST Deep User s Guide Minutes 100 Seconds at wh
7. la Lisst test File DataFrames LISST Communication Window Help Laser In Situ Scattering and Transmissometry LISST Particle Size Distribution Cumulative Concentration I I 1 17 250 1 17 250 microns microns BEL qum Sample Humber 0 Std Der 0 00 Total Vol Conc 0 00 Sequoia Scientific Inc Sequoia Scientific Inc Timer OFF gt gt Fist Prev 1 Last Scale 0 0 Interval Sarl A Ready NUM T To view the value of the auxiliary parameters such as time and depth select the View Auxiliary Parameter Frame from the DataFrames menu A display similar to the one below will appear showing the calibrated values 21 LISST Deep User s Guide Step 24 Opening RealTime Session LISST Deep User s Guide Auxiliary Parameters Laser Power fo rats Battery Do volts External Instrument oc volts Laser Reference rats Pressure D meters Temperature D deg L Aus 1 Do Aux 2 LN Transmission LN Warning Water too turbid Sample Number jo The LISST SOP software also supports the ability to acquire data process 1t and display 1t in Real time The Real time display of the processed data is very similar to the display of processed data The instrument can be configured for a Real Time session before data 1s collected but 1t 1s not required The current setting for Measurements per Average 1s used when acquiring the sample to display The recommend value
8. software is provided to program the instrument for a specific sampling schedule The primary measurements delivered by the LISST Deep are the small angle scattering properties of particles in water the laser optical transmission depth and temperature After recovery of the instrument small angle scattering data are off loaded from the instrument and subsequently inverted mathematically on a PC to produce the particle size distribution The inversion function is included in the software The principal measurement angular scattering distribution is obtained over 32 ring detectors whose radii increase logarithmically from 102 to 20 000 microns The detector is placed in the focal plane of the receiving lens The rings cover an angular range from 0 0017 to 0 34 radians Type B or 0 00085 0 17 Type C This angular range corresponds respectively to size ranges 1 2 to 250 microns Type B or 2 5 500 Type C General layout This self contained instrument consists of the following parts a solid state laser operating at 670nm wavelength and fiber optically connected to a laser beam collimating system a beam manipulation and orienting system a scattered light receiving lens the specially designed 32 ring detector preamplifier electronics a ring selecting multiplexer circuitry and a data logger 7 LISST Deep User s Guide Depth and Temperature External Sync Power Port Battery Life Auxiliary Equipment LISST Deep
9. thus reducing the importance of the background However Background Scatterfiles should always be done before an experiment Plastic bags Tupperware or clean containers of any kind can be used to acquire a background The instrument s optics end can be submerged in them vertically as long as the optics are completely submerged and there is no blockage of the windows by bubbles or other objects Backgrounds Scatterfiles should always be done before each data collection 68 Optical Alignment 69 The background scatterfile is the best source of information on the current health of the LISST Deep It provides information on the current functionality of all of the major systems including laser ring detector data collection electronics and optical alignment The LISST Deep is a sensitive optical device The laser must be aligned such that the focused spot is centered on the hole in the center of the ring detector If this alignment in not correct the instrument will not function correctly The background file can easily provide the user with information about the status of the alignment The first indicator of an alignment problem is a severe drop in the transmitted laser power The laser power and laser reference values will change over time but they should track together If the laser power drops to less than 50 of the factory value without a corresponding drop in the laser reference value misalignment may be occurring T
10. used as such for studies of underwater image propagation and beam spread A growing number of publications of measure ments using the LISST 100X instrument is available on our website http www sequoiasci com The conversion of the multi angle scattering to size distribution involves a mathematical inversion In this step a size distribution is found that would produce multi angle scattering that fits the observation There exists a vast literature on the subject of this inversion For the stout hearted user interested in learning all about it we recommend the most germane study of the subject Optimal scaling of the inverse Fraunhofer diffraction particle sizing problem The linear system produced by quadrature by E D Hirleman Particle Characterization 4 128 133 1987 The main conclusions are that the information content of the data is most stably retrieved by use of ring type detectors with each ring measuring the scattering over a sub range of angles and that the resolution is limited to relatively few size classes depending on the noise in the data For example for the dynamic range in scattering angles of 200 1 that is built into the LISST systems typically only 12 14 truly independent size classes can be resolved Simpler descriptions of principles and practice are offered in a separate study by Agrawal et al 1991 A more up to date description of the technology and its application is provided by Agrawal amp Pot
11. 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 If the unit is rotated so that the metal zinc anode s located at the top or North the Communications connector will be on the left or West After removing the cap install the cable making sure that the proper alignment is maintained Remove the Horizontal Test Chamber from the shipping case if not already installed on to the instrument This assembly consists of a flexible plastic sheet with seals glued to two edges Wrap the flexible plastic around the center section of the LISST Deep and secure it with the stainless steel clamps that have been provided The clamps only need to be tight enough to compress the foam seal lightly We can now fill the chamber with clean filtered water We use steam distilled bottled water filtered through a 0 2 micron filter Tap water may contain too many particles and may also contain dissolved gas that can release and form small bubbles on the optical surfaces Because the LISST Deep it typically used in very clean water applications it is very important that water that is as particle free as 12 possible be used for obtaining clean water backgrounds Step 5 Install the At this point instrument is ready to go Let s install the software that provided software is requi
12. ANY PRODUCT 6 No Consequential Damages SEQUOIA will not be liable for any indirect incidental special or consequential damages any cover or any loss of revenue profit data or use 7 Limitations of Liability SEQUOIA s liability whether in contract tort or otherwise and notwithstanding any fault negligence strict liability or product liability with regard to any Product including but not limited to any breach of or default by 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 93 LISST Deep User s Guide 8 Indemnification by Customer Customer acknowledges that the Products are designed and manufactured for use in non critical monitoring situations If Customer chooses to purchase a Product or Products for use in applications that could result in damages in excess of the price of the Product if the Product does not operate properly or otherwise fails Customer acknowledges and agrees that it is Customer s responsibility to provide for redundancy and or other safety or back up measures sufficient to assure that failure of a Product s will not cause such damages Customer agrees that it will defend and hold SEQUOIA harmless from any and all claims and costs including but not li
13. Deep uses a laser diode emitting a maximum of 1 mW of visible red light at a wavelength of 670nm The laser beam under normal circumstances is not a threat However if objects are placed in the path of the laser beam the light could be reflected into the eye causing permanent damage 9 LISST Deep User s Guide LISST Deep User s Guide 10 Getting Started This section is designed to give the user a quick introduction to the operating procedures for the LISST Deep It gives step by step instructions to unpack load software and acquire data in the lab Following the introduction are details on each step of the process Contents of Let s assume that you are opening the LISST Deep shipping cases for Shipping Case the first time Inside you will find the following User s Manual with software disk LISST Deep instrument Plastic Instrument stands and a Clear Tool Box with Communications and External Power cable Allen wrench set a small vial with Test Particles spare screws and a 110 220VAC power supply Contents of Tool Box Connector endcap Scrow 10 24X1 3 4 gt 4 E f 4 P 11 LISST Deep User s Guide Step 1 Remove Instrument from shipping case Step 2 Check for clean windows Step 3 Attach the Communications Cable Step 4 Install the Horizontal Test Chamber LISST Deep User s Guide Start by removing the white plastic instrument stands and set them on a flat work
14. Displays the list of command to the screen Example input HE output LISST Deep Commands followed by 30 lines of text Setup Commands Set Operating Mode Description Sets the Operating Mode to one of the following types 1 Real Time Mode 2 Burst Mode 3 Fixed Rate Mode OM command only without a parameter will initiate a prompt for the Operating mode Example input OM 3 output LISST Deep User s Guide 62 Set measurements per average MA x or max Where x number of samples per average Description Each recorded or displayed measurement is based on an average of measurements The number of measurements per average is set using the SA command If no value follows command prompts will be displayed for the value Cautions None Set Start Condition ST x or st x where x is the start condition code Description The ST command sets the start condition to be used when the GO command is issued The start condition options are 1 Depth Start 2 Time Date Start 3 Mechanical Switch Start 4 Digital Input Start 5 Delay Start If no value follows command prompts will be displayed for the value Set Start Condition Data TD x or td x where x is the start condition data Description The TD command sets the start condition data to be used when the GO command is issued The start condition data is used with the Start Condition setting For example if the Start Condition is Depth S
15. Factory Technical Service Representatives Chuck Pottsmith pottsmith O sequoiasci com 425 641 0944 ext 107 Doug Keir keir sequoiasci com 425 641 0944 ext 104 Table of Contents SECTION 15 INTRODUCTION TO THE LISST DEEP lt a iii 3 INTRODUCTION TO LASER DIFEFRACTION aa cies i sawn sions cal a o i a a a a i a a a a engen 3 GENERAL DESCRIPTION OF THE LISS DEEP une 3 7 SECTION 2 OPERATION 15 1 222 ios eat 9 GETTING STARTED ei 11 STEP BY STEB PROCEDURES 4 p estais Ras sea a a i a a I S a a a S a r i S i a a Os La 31 Step by Step Procedure Record and Store Background Scatterfile csse 33 Step by Step Procedure Offloading Deleting Data Files eese 35 Step Dy Step Procedure PTOCCSSING TOW Oldies on He D RH ER RE 37 Step by Step Procedure View processed datafile eese nnne enne 41 Step by step Procedure Real time data collection eese enne 45 Step by Step Procedure Configuring data collection eese 49 INSTRUMENT COMMUNICATION ze ae essen 39 LISS DEEP COMMAND SUMMARY asi siose tui obese A bue ir aM n DIN M o aS LP Deme Uc UM abe 59 LASS TSDEBPCONIMAND DB VAIS Laose iais ios oet ote een 61 PERFORMANCE OPTIMIZATION thee bct mi eoo i eui ede MM MC Me ees 67 INSTRUMENT MOUNTING aan Be a a i M LI cR EE a S mata Ier o LESS 71 INSTRUMENT STORAGE amp MAINTENANCE asien 13 APPENDIX A INSTRUMENT SPECIFIC DOCUMENTATION ssesssssss
16. Power Connector 5 pin connector 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 ConnectorPin Use o oo UE Power Serial Ground a Te External Power In 9V nom 6 12V Power Serial Ground Serial Out to DB 9 Pin 2 Serial In to DB 9 Pin 3 3 4 4 3 2 5 5 2 L 1 Bulkhead Endview Cable Endview 85 LISST Deep User s Guide Laser Controller Connector on Connector Endcap 6 pin connector Connector Manufacturer Impulse Enterprise Inc San Diego CA USA Connector Part Number Bulkhead MCBH WB 6 MP Stainless Steel Mating Cable Part Number MCIL 6 FS 5V Serial from Laser Module 5V Serial to Laser Module Ground Power Out to Laser Module Ground 2 6 1 1 5 3 3 5 4 4 Bulkhead Endview Cable Endview Laser Controller Connector on Laser Endcap 6 pin connector Connector Manufacturer Impulse Enterprise Inc San Diego CA USA Connector Part Number Bulkhead MCBH WB 6 MP Stainless Steel Mating Cable Part Number MCIL 6 FS 5V Serial to datalogger 5V Serial from datalogger Ground Power Out in from Main Electronics 9 12V Ground 6 2 2 6 1 4 5 3 3 5 4 4 Bulkhead Endview Cable Endview LISST Deep User s Guide 86 87 CTD Connector 6 pin connector Connector Manufacturer Impulse Enterprise Inc San Diego CA USA Connector Part Number Bulkhead AG 306 HP
17. User s Guide In addition to measuring the particle size and concentration the LISST Deep also has built in Depth and Temperature sensors The Depth sensor is a 5000 psi strain gauge sensor The stainless steel fitting on the Connector endcap is used for testing this sensor It is not required for normal operation However when not used for testing this fitting helps keep contamination out of the pressure sensor The temperature is measured using a high precision thermistor imbedded into the Connector end cap Both values are stored automatically in the standard format LISST Deep datafile The LISST Deep is also equipped with an external port for connecting the instrument to a SeaBird CTD Auxiliary input port The LISST Deep can obtain power from this port and it can output signals to the two CTD analog inputs that can be used for synchronizing the LISST Deep and CTD data files These ports are available on the 6 pin underwater connector on the Connector Endcap The connector is identical model and matching pinouts as the SeaBird CTD Auxiliary Input port Appendix C shows the connector pinouts Contrary to the LISST 100X the LISST Deep DOES NOT have an internal battery The LISST Deep must be powered at all times by external power at 12V For laboratory or tethered usage power can be applied through either the supplied Power and Communication cable or the optional SeaBird CTD interface Cables up to 50 meters can be provided to supply
18. at 9600 baud 8 data bits No parity and 1 stop bit Data file transfer is done using a YMODEM transfer at 115K baud Using the Opening the Terminal Window or alternate terminal software Terminal Window with the proper COM port and communications settings will allow the user to communicate with the instrument The LISST Deep should respond by either displaying text from a running program or echoing an L100X gt prompt If the instrument is in the Deep Sleep Mode it will only wake up every 30 seconds Print ZZZ to the screen and then return to sleep The instrument firmware is retained in on board flash memory and will start executing when power is applied After a power up pressing the ENTER key will cause an echo of the LIOOX gt prompt The Stop button will also send the commands to turn off the main power to the laser and electronics Pressing the Stop button when the instrument is not running will not hurt the instrument It is recommended to press the Stop button multiple times after stopping a running program to make sure that the main power is properly shut off Pressing the Start button will begin the collection of data using the current configuration Two Letter Under most situations the LISST SOP will be used to configure commands and operate the LISST Deep However there are times when it is useful to be able to talk to the LISST Deep at a lower level For this purpose a set of two letter commands is available to Operate the
19. example Depth Start and Depth Stop For all other Start Conditions the program will terminate and return to the L100X gt prompt 24 To stop a running program use the Stop button on the Terminal window or the e button on the tool bar This is particularly important of you have followed steps 17 18 and enabled autostart mode If you cycle power the instrument will simply start again and wait for the start condition to appear In this case you must always manually stop the program by clicking the Stop button on the tool bar Step 21 The instrument has now stored data on the on board Compact Flash card D loading dat 11 di i ownloading data Pressing the Instrument Query Button will display the instrument status including the number of samples saved Before you click the Query or Offload button you must stop the program by clicking the Stop button on the tool bar To offload the data select Offload from the L SST menu or choose the button from the toolbar A list of files will appear Choose the files to offload by clicking on them while hold down the CTRL key The Shift key can also be used to select a range of files Select OK and choose a location to save the files to The files will be saved with names in the following format Ldddhhmm dat where ddd is the day of the year hh is the hour and mm is the minute that the file was first written to As the data is downloading a Transfer Status window will app
20. external power and communication with the instrument This can allow Real Time observation of the Size Distributions Cables are also available for connecting the LISST Deep to SeaBird CTD Auxiliary inputs The instrument is shipped pre aligned and tested A communication cable is supplied so that a user need only provide a PC Software is provided to communicate with the instrument schedule an experiment offload the data and invert the measurements to obtain particle size distribution and volume concentration For laboratory use or for monitoring the progress of an experiment the software can be used for real time processing Section 2 Operation Section Section 2 1s divided in to two main sections The first section is Organization the Getting Started section This section will walk the user through using the instrument from opening the shipping case through processing downloaded data Reading the Getting Started section will give most users enough information to starting using the instrument Following the Getting Started section are detailed instructions for performing various procedures General LISST Deep is a sensitive optical instrument Please handle it Precautions gently Critical alignments may be disturbed if the instrument is subjected to shock or rough handling Evidence of shock rough handling will void the warranty Whenever in transit store the instrument in the provided padded shipping case WARNING The LISST
21. for the Measurements per Average is 10 Higher values can be used but the updating of the display will be reduced The Start and Stop conditions will not be used and therefore their settings are not relevant When exiting the Real Time session the power should automatically shut off Pressing the Stop button on the toolbar or the Terminal window will turn off the power Pressing these buttons when the instrument 1s already off will have no 1ll effects To open the Real Time session choose Open Real Time Session from the File menu or press the button Choose a background file to use when processing the data Choose an output PSD file A display very similar to the View Processed datafile will be displayed 28 29 bas Lisst Instrument File DataFrames LISST Communication Window Help Fal nae Laser In Situ Scattering and Transmissometry LISST Instrument Particle Size Distribution Cumulative Concentration 0 1 17 250 1 17 microns microns Mean 0 00 Sample Number 0 Std Dew 0 00 Total Yol Conc 0 00 Sequoia Scientific Inc Sequoia Scientific Inc Timer OFF a E gt Scale 0 0 Interval 5ec 50 Save Single Sample Use the Timer button to start and stop data collection The slider bar controls the data acquisition time The Scale Button adjusts the Particle Size Distribution scale The Save Single Sample button records a single sample to an ASCII file Note The main power and la
22. of the screen will show the current sample or frame e Pressing the Select First button will set the current cursor position as the starting point for processing Similarly selecting Select Last will set the end point for processing Use the Next and Previous buttons scroll through the complete datafile The Select First and Select Last points do not need to be on the same displayed plot 11 After selecting the range to process press the Process Processing Completed File button The display will show the processing progress and the Process File button text will change to Finished when the processing is complete The window can now be closed Notes LISST Deep User s Guide 40 STEP BY STEP PROCEDURE VIEW PROCESSED DATAFILE a Select Open Particle Distribution File from the File menu Open Particle Distribution File selected Processed datafile Select the processed data file from the file selection window selected Double click the file or type the file name and press Open After selecting the processed file a window similar to the one shown below will appear la Lisst test File DataFrames LISST Communication Window Help B test Laser In Situ Scattering and Transmissometry LISST Particle Size Distribution Cumulative Concentration 17 250 1 Wie microns microns Mean Sample Number 1 Sid Der Total Vol Conc 0 00 Sequoia Scientific Inc Sequoia Scientific Inc Timer OFF E gt gt Fist
23. scattering files can be collected in real time When the instrument communication has not been initialized the Connect Disconnect button will be a red light Pressing the button will Connect Disconnect toggle the communications status When the Connect Disconnect button is showing a green light the instrument communication has been initialized Pressing the button will disconnect the instrument Pressing the Open Terminal button will bring up the terminal window for Open Terminal ur l l p communication with the instrument including Start and Stop buttons The Program Settings button bring up the general settings windows for Program Settings setting display parameters and other software settings such as File Output Com Port settings and Plot When viewing processed data the Print button will be activated Pressing the button will send the current display to the printer 89 LISST Deep User s Guide Attempts to wake up instrument from low power sleep mode This may take up to 40 seconds Put LISST to sleep NOTE This feature should not be used with the LISST Deep as it has no internal battery Puts instrument into low power sleep mode a Us NOTE This feature should not be used with the LISST Deep as it has no internal battery LISST Deep User s Guide 90 Appendix E Comparison of LISST 100X and LISST Deep The LISST Deep and the LISST 100X are somewhat similar instruments They both measure the Same parameters an
24. the mean and standard deviation These features are located on the Display tab of the Settings window as shown below LISST Deep User s Guide 46 LISST Settings x Display View Rings Serial Port Output File Locations Aux Pars Header Text IESU eed C Es EE ST EUR Le Footer Text Sequoia Scientific Inc Maximum ordinate value 5 Animation frame interval 500 millisec Show mean on plot Save values as default Cancel The raw scattering values can be graphically display by Value of rings for selecting the View Rings command from the File menu An current frame example of this display is shown below displayed 30 Transmission Raw Ring Count 4095 100 O O Background Scatter Laser Power jo Factor Laser Power FOL A single sample may be saved to a separate file by pressing the Averaged data Save Single Sample button acquired and stored to an ASCII file When finished close the main window to stop communication Finished and with the LISST Deep shutdown CAUTION o The laser and Main power are on continuously while in the Real Time Session The program will stop and the power will be turned off when the window 1s closed However if the window is left open the power will remain on potentially draining substantial life from an external battery To turn off the power without exiting the Real Time session press 47 LISST Deep User s Guide on J button on the t
25. wake up Deep Sleep Enter zz to wake up Cautions The background scattering data and other settings are not affected by the ZZ command LISST Deep User s Guide 66 Performance Optimization This section contains information on optimizing the performance of the LISST Deep Background As was discussed in earlier sections the LISST Deep uses a Scatterfile and its custom detector to measure light scattered at small angles from Importance particles in water In order to measure only the scattered light contributed by the particles a measurement of the background scattering must be obtained This background scattering can come from a number of areas Scratches on the windows imperfections on the optics and other sources all contribute to the scattered light By subtracting this background scattering from the measured data a true measurement of the light scattered from only the particles can be obtained The measurement of background scattering has come to be called a ZSCAT The name comes from the fact that the measurement is obtained using water with zero scatterers or particles It is very important that clean and bubble free water is used The water can be fresh or salt water For most applications it has been found that steam distilled water is sufficient Steam distilled water is typically available in one gallon containers We have found that this distilled water tends to be a bit cleaner than typical bottled or
26. will indicate where in the complete datafile the currently displayed section is located The vertical cursor on the lower plot can be moved by clicking the mouse at the desired location Additional information is stored in the processed Auxiliary parameter window datafile The Auxiliary parameter window displays displayed these values for the current sample pointed to by the vertical cursor They will update as the cursor is moved Selecting the Show Auxiliary Parameter Frame from the DataFrames menu opens the window An example of this window is shown below Auxiliar Parameters EN Laser Power malt Battery volts External Instrument volts Laser Reference matta Depth meters Temperature deg L Aus Aus 2 Transmission Warning Water too turbid Sample Number 1 Show raw data FE LISST Deep User s Guide 9 e The raw scattering values can be graphically Value of rings for current displayed by selecting the View Rings command frame displayed from the DataFrames menu An example of this display is shown below As with the Auxiliary Parameters the vertical cursor indicates the sample currently displayed _ 100 2 L O r E LII L E EF Raw Ring Count Background Scatter Laser Power j Factory Laser Power 500 10 e To select the range of raw data to process position the Range to process selected cursor at the desired starting sample The display at the lower portion
27. 48 1 74 1 60 2 95 3 48 3 20 3 30 1 74 2 05 1 89 3 48 4 11 3 78 4 20 2 05 2 42 2223 4 11 4 85 4 46 5 28 2 42 2 86 2 63 4 85 512 3 07 6 27 2 86 3 38 3 11 23112 6 75 6 21 7 26 3 38 3 98 3 67 6 75 7 97 1 33 8 25 3 98 4 70 4 33 7 97 9 40 8 65 9 24 4 70 5 55 5 11 9 40 11 1 10 2 10 23 5 55 6 55 6 03 11 1 13 1 12 1 1 22 6 55 212 Pld 13 1 15 4 14 2 12 21 12 9 12 8 39 15 4 18 2 16 8 13 20 9 12 10 8 9 90 18 2 215 19 8 14 19 10 8 12 7 11 7 21 5 25 4 23 4 15 18 Di 15 0 13 8 25 4 30 0 27 6 16 17 15 0 17 7 16 3 30 0 35 4 32 5 17 16 17 7 20 9 19 2 35 4 41 7 38 4 18 15 20 9 24 6 22 1 41 7 49 2 45 3 19 14 24 6 29 1 26 7 49 2 58 1 53 5 20 13 29 1 34 3 31 6 58 1 68 6 63 1 2 12 34 3 40 5 372 68 6 80 9 74 5 22 11 40 5 47 7 43 9 80 9 95 5 87 9 23 10 47 7 56 3 51 9 95 5 113 104 24 9 56 3 66 5 61 2 113 133 122 25 8 66 5 78 4 222 133 157 144 26 7 78 4 92 6 85 2 157 185 170 2 6 02 6 109 101 185 218 201 28 5 109 129 119 218 258 237 20 4 129 152 140 258 304 280 30 3 152 180 165 304 359 331 3 2 180 2197 195 359 424 390 32 1 212 250 230 424 500 460 79 LISST Deep User s Guide Size Ranges for There are 32 size ranges logarithmically placed from 1 25 250 RANDOMLY microns in diameter type B or 2 5 500 microns type C In shaped particle both cases the upper size in each bin is 1 180 times the lower inversion method The table below shows the lower and upper limit of each size bin in microns together with the median size also in microns for each size b
28. Burst uaa Burst Interval f Sec m nm n Fixed Sample Rate sample to be Average ol measurements Time to get average 1 SBB Sample Interval fi Sec I I I I euor Cancel Apply Help The RealTime mode is used for real time size distribution displays This mode sends the raw data to the LISST SOP software for conversion to Size Distribution and displaying on the screen No data is saved in the datafile The Burst and Fixed Sample Rate modes are used to save data in the on board datafile The icons next to the various values give a better understanding of their meaning The software automatically checks the values entered to make sure that there is no conflict For example when a Measurements per Average value is entered the minimum sample interval is computed If this value is less than the minimum permitted the value will be changed to the minimum and the text will turn red A similar test is done on the Burst Interval setting For this example let s set the instrument to sample in the Fixed Sample Rate mode at a 1 Hz rate with 10 measurements per average After selecting the Operating mode the start and stop conditions can be selected Click the Start Condition tab to open up the Start Condition window shown below which is used to select the mode in which sampling will be started 18 LISST Instrument Operation Instrument Status Operating Mode Start Condition Stop Condition Depth Start when depth excee
29. Data function By selecting the Next button the window will be updated with the current size distribution Note that if the water is clean the display may not show any volume distribution The Sample Number value displayed underneath the plots will increment each time a sample is saved 7 The Timer button function is similar to its use in viewing Timer button processed data The timer will automatically acquire data at a pressed and samples fixed rate Note that this rate is limited to about 1 Hz due to the updating processing of the raw data into Volume distributions The slide automatically button next to the Timer button controls the sample speed If it is set too fast it will automatically reset to the maximum allowed rate The Auxiliary parameter window can be opened to display the Auxiliary Parameter current values of the auxiliary parameters such as pressure and window opened temperature Open the window by selecting the Show Auxiliary Parameter Frame from the DataFrames menu The scale of the Volume Distribution plot can be changed by Display setting using the Scale button After selecting the button a display modified similar to the one shown below will prompt you for the maximum concentration for the Y axis of the plot Maximum Scale Setting ES Maximum Scale Value E Cancel e Other options are also available for customizing the display such as changing the header and footer text or adding lines to show
30. ISST Deep and sampling will start if the start conditions have been met In order to save the program settings in the firmware open up the terminal window and type SD The current start and stop conditions 21 LISST Deep User s Guide LISST Deep User s Guide sampling mode sampling frequency etc for the LISST Deep firmware is listed Instrument SD Store current settings as defaults BO Set continuous binary output used with Autostart 2D Reset Depth Sensor DERSeL L100x gt AD LISST Deep Current Status and Settings Serial number 4006 Firmware Version 1 997 Jun 9 2011 13 50 46 Operating Mode Fixed Rate Mode Start Condition Delay Start with 1 minute delay Stop Condition Fixed Number Stop at l samples Measurements per Average 10 sample Interval 1 Battery Voltage is 23 98 Current Date Time Tuesday June 14 2011 10 03 07 Current Day of the Year 165 Da xou wish te set current settings to be defaults l yes U noj 0 2 l Send Tae Part open Stop Start If you wish to save the current settings as the default for the firmware type at the command line and click the Send button to save the current settings as displayed below 22 Step 18 Enabling Autostart 23 Instrument Ll00x gt SD LISST Deep Current Status and Settings Serial number 4006 Firmware Version 1 997 Jun 3 z ll 13 50 46 Operating Mode Fixed Rate Mode Start Condition Delay S
31. LISST Deep Particle Size Analyzer User s Manual June 2011 a 2700 Richards Road Suite 107 s Road Bellevue WA 98005 4200 Tel 425 641 0944 Fax 425 643 0595 B a m E f 2 se p E M c m P oo n o 5 om e m gt fe i pu a ee T e T E c gt 2 T Tw gn ae Tr gt at ar _ o A e 2 m r LISST DEEP PARTICLE SIZE ANALYZER Saeona Soari Ine I ET I 9 e S E U O I A I em gt te nd Pm SEQUOIA This document is copyrighted by SEQUOIA SCIENTFIC INC LISST Deep User s Guide Welcome to the LISST Deep Particle Size Analyzer Using this manual This manual is divided into two sections Section One contains an introduction to the LISST Deep instrument and the principles of its operation Section Two provides a detailed set of instructions for using and caring for the instrument Instrument specifications For a listing of instrument specific constants as used in the software for data processing refer to Appendix A Technical assistance For technical assistance please contact your local Distributor or a Sequoia Technical Service Representative listed below Please be sure to include the instrument serial number with any correspondence
32. SS Mating Cable Part Number AG 206 FS Connector Pin fe 1 PowrGrud 2 JDigtalSignllout 5i renal f Ground 4 SBigtaSignl2ou pS Signal Ground 6 BVinolIlSSTfromCTD Connector endview LISST Deep User s Guide LISST Deep User s Guide 88 Appendix D LISST SOP Software Button Description Runs the instrument for Real Time operation Open Real Time Note instrument must be already configured for real time sampling and Session be running i e not hibernating To wake from hibernation choose Wake Up LISST from LISST menu Open raw or processed file Depending on extension of file requested to open the appropriate procedure is started Queries instrument for it s current configuration and displays the information to the screen Offload Offloads stored data to a file for later processing Erase Erases the datafile by resetting the datafile pointer variable D in former versions to zero STOP Sto Sends a CTRL C to the instrument to stop a running program Also sends P PCLR 10 to turn off main power Set Instrument Sets the internal instrument clock to match the currently connected Clock computer clock Query Instrument Opens the Instrument Sampling Configuration window where operating Operating Modes mode and sampling schemes can be configured Opens the real time background collection windows where background iS EEUN
33. a different extension You can change this name if you wish Provide the file name and press Save If other output types are selected they will have the same base name with different extensions N ote e file types other than the default PSD file must have been selected before starting the Open Raw Data file command See step 2 A display similar to the one shown below will Main data processing appear selection window displayed to ha LISST C1039 03 the screen C1039 03 Laser In Situ Scattering and Transmissometry LISST 4095 0 Laser Power Battery Voltage Pressure Data File e The top portion of the display is a graphical LISST Deep User s LISST Deep User s Guide 88 38 39 representation of the raw data from the 32 rings The value of the 32 rings is represented as a vertical line with time moving from left to right The lower portion of the display shows the time history of some of the Auxiliary parameters This can be useful for determining when the instrument came out of the water when a particular profile was started or for determining what range of the datafile to process To change which Auxiliary parameters are displayed choose Auxiliary Parameter Display from the Options menu Note that only 400 samples of the Auxiliary Parameters are displayed at a time Use the Next and Previous buttons to move through the complete datafile The triangles on the lower edge of the upper display
34. 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 As to any Product repaired or replaced by SEQUOIA the Warranty Period will end upon the later of the end of the original Warranty Period or 90 days after SEQUOIA s delivery of the repaired or replacement Product to Customer Any Product component part or other item replaced by SEQUOIA becomes the property of SEQUOIA SEQUOIA may use refurbished components in the repair of Products supplied hereunder SEQUOIA s warranties shall be void and not apply if the Product has been subjected to misuse or alteration or repaired by a party not approved by SEQUOIA or the serial number on a product if applicable has been altered or defaced SEQUOIA shall not be liable for normal wear and tear such as replacement of consumables nor for defects or failure caused by maintenance misuse negligence or failure resulting from non compliance with SEQUOIA s specifications operating or maintenance manuals 3 Infringement Indemnification If any Product does not comply with the warranty set forth in 1 c above SEQUOIA will defend and indemnify Customer against any third party claim asserted in any proceeding against C
35. asc Build an ASCII particle size file asc Selections do NOT apply to data sources already oper Selections apply only to subsequent openings c Cancel Apply Help It is recommended that all file types be stored so that maximum flexibility in future processing of the data is maintained A binary PSD file is always created when processing raw data This 1s used to display the processed data to the screen in the LISST SOP The ASC type 1s a spaced delimited file containing the fully processed data The LOG file is a space delimited ASCII file containing the raw data from the datalogger Select Open Raw Data File from the File menu Begins process of specifying raw data file and all information needed for data processing 37 LISST Deep User s Guide e Choose the serial number of the instrument that Instrument serial number collected the data to be processed selected N ote e Only the serial numbers of the instruments that are loaded into the InstrumentData Txt file and have their calibration values stored in the LISST INI file in the Windows directory can be used Select Instrument Serial Number Select the background scatter data file from the file Background scatterfile selection window Double click the file or type the selected file name and press Open Select the output data file name The default file Output data file name name shown is the same as the raw data name but selected with
36. by the government is subject to restrictions as set forth in subparagraph c 1 ii of the Rights in Technical Data and Computer Software clause at 48 C F R 252 227 7013 or in subparagraph c 2 of the Commercial Computer Software Restricted Rights clause at 48 C F R 52 227 19 as applicable Portions of these items may be unpublished SEQUOIA reserves all rights under applicable copyright laws 12 Controlling Document In the event of any conflict or inconsistency between any provision of this Statement of Limited Warranty and any other provision of the Order the provision of this Statement of Limited Warranty will control 13 Controlling Law This Statement of Limited Warranty will be governed by the laws of the State of Washington without reference to its rules relating to choice of law for the purpose of applying another jurisdiction s law The U N Convention on Contracts for the International Sale of Goods will not apply Revised June 2011 LISST Deep User s Guide 94
37. d use the same LISST SOP software for configuring the instrument and for processing data The general setup and use is very similar Data are stored on a compact Flash Memory module and the data file formats are identical So is the external power requirement 12VDC for both instruments The differences are mainly related to the change in packaging required for the deeper depth rating of the LISST Deep Because the mechanical design and electrical design of the LISST Deep is VERY different from the LISST 100X most options available for the LISST 100X such as the Full Path Mixed Chamber will not work on the LISST Deep There are also a Start and Stop Conditions that are not available for the LISST Deep The table below briefly summarizes the differences between the two instruments SeaBird CTD connector for external power from SeaBird CTD Internal Battery for power External Digital Input for start stop of sampling External Analog port for logging data from OBS3 Turner Designs Cyclops 7 fluorometer or SeaBird MicroCat C T sensor l 7 Accessories for laboratory work BioBlock option to slow down fouling and extend deployments in productive waters LISST Deep has a special SeaBird CTD interface that allows the CTD to provide power to the LISST Deep The LISST Deep will output digital sync pulses to the CTD which can be used for synchronizing the LISST Deep and CTD data streams The LISST Deep does NOT have an internal batt
38. displays This mode sends the raw data to the LISST SOP software for conversion to Size Distribution and displaying on the screen No data is saved in the datafile e The Burst and Fixed Sample Rate modes are used to save data on the on board datalogger The icons next to the various values give a better understanding of their meaning The software automatically checks the values entered to make sure that there is no conflict For example when a Samples per Average value is entered the minimum sample interval is computed If this value is less than the minimum permitted the value will be changed to the minimum and the text will turn red A similar test is done on the Burst Interval setting LISST Deep User s Guide 50 Select Start Conditions tab to configure when the instrument will begin sampling e There are five options displayed Depth Time External Mechanical Switch External Digital Input and Time Delay Since the LISST Deep uses the same software as the standard LISST 100X there are some Start Conditions displayed that are not available on the LISST Deep The Start Conditions available on the LISST Deep are Depth Time Switch and Delay e The Digital Input is not available on the LISST Deep Selecting this option will cause an error message to appear in the terminal window when data collection is started with the GO command or when started through the LISST SOP software LISST Instrument Operation Instrument Statu
39. ds jo meters C Time Start Date 12 ZEN 2000 Start Time El s jo External Digital Input C Delay jo Hours 1 Minutes Auo Cancel Apply Help There are five options displayed Depth Time External Mechanical Switch External Digital Input and Time Delay Since the LISST Deep uses the same software as the standard LISST 100X there are some Start Conditions displayed that are not available on the LISST Deep The Start Conditions available on the LISST Deep are Depth Time Switch and Delay The Digital Input is not available on the LISST Deep Selecting this option will cause an error message to appear in the terminal window when data collection is started with the GO command or when started through the LISST SOP software Select the mode by clicking on the button next to its label Select the correct parameters as required For this example let s select the Delay Start Condition with the delay set to 1 minute Step 14 Setting Similarly the Stop conditions can also be selected Click on the Stop Stop Conditions Condition Tab to open the Stop Condition window For the LISST Deep the available stop conditions are Depth Time External Mechanical Switch Fixed number of samples and Maximum Memory or Low Battery The Digital Input Stop is not available on the LISST Deep 19 LISST Deep User s Guide Step 15 Saving the settings for future use Step 16 Starting the Data Collection LISST De
40. e Serial Port tab of the Settings window as shown below A baud rate of 38 400 is suggested for longer cables Please note that the download speed will be slower at the lower baud Open the Terminal window by choosing Terminal Window from the Communication menu or by pressing on the Terminal Window button At the Terminal Window enter the command DD in the command box and press the send button The DD command Display Directory will list all the files in memory to the screen To delete a file enter the command DL filename ext where filename ext 1s the file to offload Wildcards such as or L dat can also be used 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 Deep User s Guide 36 STEP BY STEP PROCEDURE PROCESSING RAW DATA is e Select Settings from the File menu and click on the Output Tab The window below will appear prompting for the desired output to use for the future data processing Note this selection must be made BEFORE starting the processing command LISST 100 Settings Display View Rings Serial Port Output File Locations AK Pars Realtime Instrument Data Processing Existing Raw Data File J FUE a binary raw data file zh raw Build an ASCII raw data file log IY Build a binary particle size file pad p Build a binary particle size File ped Build an ASCII particle size file
41. e display 49 LISST Deep User s Guide 3 To load a pre saved LISST Operating Procedure file LOP enter the file name in the file box or click on the Browse button to navigate to the correct file After the file is selected the appropriate settings will be made To apply these settings to the instrument press the Apply or OK buttons LISST Operating Procedure files can be saved by clicking the Save Summary to LOP button The setting must have first been sent to the instrument using the Apply button The Summary section will only update after the settings have been applied to the instrument 4 e By selecting the Operating Mode Tab at the top of the main Operating Mode window the screen below appears This screen is used to set the set type of sampling RealTime Burst or Fixed Sample Rate You can also select the samples per average and sample rates on this screen LISST Instrument Operation x Instrument Status Operating Mode Stark Condition Stop Condition Realtime Sample to be Average of measurements Time to get average Sec Burst Sample to be Average of measurements Time to get average Sec Sample Interval f CE HL uL I Samples Per Burst nui Burst Interval f Sec m np on eT f Fixed Sample Pate sample to be Average of measurements Time ta get average Sec Sample Interval f Sec L I I Moo Cancel Apply Help e The RealTime mode is used for real time size distribution
42. e spots finger prints etc alcohol may be used We recommend against the use of stronger solvents such as Acetone or Toluene Abrasive powders or tools must never be used near the optics windows they will scratch the windows and degrade instrument performance O rings that seal the mating parts of the instrument must be maintained and inspected regularly Whenever the end cap is removed check the o ring for any cuts or marks and clean and lightly grease the o ring before installing the end cap Spare end cap o rings have been provided O rings are inexpensive items that provide an invaluable service replace them if in any doubt about their condition When replacing the O ring be sure to clean the O ring groove thoroughly with cotton swabs etc making sure that no fibers or particles of dirt are left after the cleaning The LISST Deep should not require any adjustment or calibrations The pressure and temperature sensors can be re calibrated if desired The performance of the instrument can be checked with the use of a sample of particles of a known size distribution Comparison of the LISST Deep s performance with that of other particle size measuring devices that are not based on laser diffraction may result in inconsistencies because the instruments may measure different properties of the particles to interpret particle Size LISST Deep User s Guide LISST Deep User s Guide 74 Technical Specifications 10 96 Para
43. ear Transfer Status L The data is offloaded at 115K baud by default When using a cable longer than a few meters it may be necessary to reduce the transfer baud rate The File Download Baud Rate can be changed on the Serial Port tab of the Settings window as shown below A baud rate of 38 400 is suggested for longer cables Please note that the download speed will be slower at the lower baud rates 25 LISST Deep User s Guide LISST SOP Settings Display View Rings Serial Port Output File Locations AX Pars Serial Port comi vl Baud Rate a v Data Bits Parity Stop Bits Protocol File Download Baud Rate 115200 r 9600 13200 Save as default Fi 15200 Lancel Help Step 22 We now have the data transferred from the datafile of the instrument to a Processing Raw file on the PC To process the data file choose Open Raw Datafile or Data p press the Open button on the toolbar Select the instrument serial number raw data file to open and background scatter file to use when processing the data A display similar to the one shown below will appear bau Lisst test i IDE x Fille DataFrames LISST Communication Window Help exu 6 BS Data File Laser Power Battery Voltage Pressure O 0 Auxiliary Parameters Sequoia Scientific Inc 1 gt Fist lt Prev ge Next gt 2 Last sl Select Fis ii Select Last Process File Fram fro j fro The ran
44. ecause of the design of the pressure housing and optical path The U shaped mounting block provided with the instrument fits the diameter of the LISST Deep pressure housing and can be used for mounting the instrument To reduce the corrosion of the aluminum parts a zinc anode is attached to the Connector endcap This anode must be exposed to the water for it to be effective When mounting the instrument be sure to electrically isolate the instrument from all other metal Any contact with other metal will greatly increase the rate of corrosion Isolate the instrument with rubber or plastic to keep the LISST Deep from being the sacrificial anode for the mounting hardware LISST Deep User s Guide LISST Deep User s Guide 12 Instrument Storage amp Maintenance 73 Again it must be emphasized that the LISST Deep is a sensitive instrument When not in use the instrument should be stored in a well padded case For longer storage year or so the communication cable should be disconnected Never store the LISST Deep attached to an external battery pack As has been noted earlier the condition of the windows is critical to the performance of the LISST Deep Care must be taken when cleaning the windows The windows and the instrument should be rinsed thoroughly with fresh water after each deployment The windows should be cleaned with a soft cloth or lens tissue Liquid detergent soap and water may be used For removing greas
45. end Number 004 LISST Operating Procedure LOF File 9g Ready Browse C Running Sleeping Realtime Operating Mode Start at depth of 0 1 meters Samples Stored 0 Stop at depth of 0 1 meters Samples Remaining eeso Battery Voltage Tob Comments External Switch ON Date je 5 02 Time 13 40 57 Set Clock OF Cancel Apply Help The window has four tabs Instrument Status Operating Mode Start Condition and Stop Condition The Instrument Status page gives information about the current instrument It also allows previously saved instrument configuration files to be loaded on to the instrument The ability to save the current settings to a file is also available The Summary window shows the current deployment configuration Step 12 Setting By selecting the Operating Mode Tab at the top of the main window Operating Mode the screen below appears This screen is used to set the type of sampling RealTime Burst or Fixed Sample Rate You can also select the samples per average and sample rates on this screen 17 LISST Deep User s Guide Step 13 Setting Start Conditions LISST Deep User s Guide LISST Instrument Operation Instrument Status Operating Mode Start Condition Stop Condition C Realtime Sample to be Average of measurements Time to get average Gar Burst Sample to be Average of measurements Time to get average 1 Sec Sample Interval f Sec uL up gn Samples Fer
46. ep User s Guide LISST Instrument Operation x Instrument Status Operating Mode Start Condition Stop Condition Stop when depth less than o meters C Time Stop Date 12 JEN 2000 Stop Time 23 7 fo External Mechanical Switch C External Digital Input C Fixed Number of Samples Number of S amples to store fi Maximum Memory Battery suora For this example choose the Fixed Number of Samples as the Stop condition with the number of samples set to 10 After selecting the Stop Conditions return to the Instrument Status page by clicking on the Instrument Status Tab Once the settings have been sent to the instrument the Instrument Status Page will display the summary of the settings that have been selected These settings can be saved for later use by selecting the Save Summary to LOP A file name will be prompted for The file will be given an LOP extension which will identify it as a LISST Operating Procedure File Comments can be entered before saving in the box below the summary Previously saved LOP file can be opened using the Browse button Press the Apply button to configure the instrument This will cause the settings to be transmitted to the instrument The configuration will take about 30 seconds Once the configuration is completed we can return to the Instrument Status page to see the summary of the settings and save them for future use if desired Press the OK button to complete the configura
47. er LaserPower mw O Parameter2 Battery 001 0 volts Parameter3 External Instrument vos Parameter4 LaserReference mw ParameterS Depth 001 meters depth Parameter Temperature 001 O0 DegC Parameter Day 100 Houwr 1 0 Parameter8 Minutes 100 seconds 0 Volume Conversion Constant y O Constants for Firmware These constants are entered at the factory to be resident in the instrument firmware Parameter Battery Volts Parameter2 Dem Parameter Temperature o o y O Instrument Reference Data Ring Values 1 5 counts Laser Transmitted Power counts Laser Reference Power counts AAA Verified By 71 LISST Deep User s Guide LISST Deep User s Guide 78 Appendix B Size Ranges Angle Ranges and Data Storage Format Size Ranges for There are 32 size ranges logarithmically placed from 1 25 250 SPHERICAL microns in diameter type B or 2 5 500 microns type C In particle inversion both cases the upper size in each bin is 1 180 times the lower method The table below shows the lower and upper limit of each size bin in microns together with the median size also 1n microns for each size bin for type B and C instruments Type B Type Size bin Ring Lower Upper Median Lower Upper Median 1 32 925 1 48 1 36 2 50 2 95 212 2 31 1
48. ery It must be connected at all times to an external power source in order to work It is NOT possible to connect external instruments such as OBS s or SeaBird MicroCat CT sensors to the LISST Deep because of the missing External Analog Input 7 No flow through chambers mixing chambers or text chambers are available for the LISST Deep No BioBlock option exists for the LISST Deep because of the very different mechanical design of the LISST Deep optics 9 LISST Deep User s Guide LISST Deep User s Guide 92 Warranty STATEMENT OF LIMITED WARRANTY AND LIABILITY This Statement of Limited Warranty applies to all Sequoia Scientific Inc SEQUOIA products Products Any additional or different terms including any terms in any purchase order will be of no effect unless agreed to in writing by an authorized representative of SEQUOIA as reflected in a written SEQUOIA quotation 1 Limited Warranty SEQUOIA warrants that upon delivery by SEQUOIA a the Products will be free from defects in materials and workmanship b the Products will perform substantially in accordance with SEQUOIA s applicable specifications and c any Products or components or parts thereof that are manufactured by SEQUOIA do not infringe any U S patent or copyright 2 Correction of Non Compliance 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
49. estimates of Ne can be considered good Included with the LISST Deep instrument we have provided software that obtains the inverted volume distribution Ny We have also provided the matrix K for your instrument in ASCII and MATLAB formats in order for you to test your results A collimated laser beam enters water light is scattered by particles and sensed by a multi ring detector behind a receiving lens A photodiode placed behind a centered hole measures optical transmission 5 LISST Deep User s Guide LISST Deep User s Guide General Description of the LISST Deep The LISST Deep instrument is a laser diffraction device It consists of optics for producing a collimated laser beam a specially constructed detector array electronics for signal pre amplification and processing a data storage and scheduling computer and a small battery system The LISST Deep is somewhat similar to the LISST 100X particle size analyzer They share the same electronics and have very similar optics The software used to program the deployment and process the data into size distributions is exactly the same for both instrument However there are some very significant differences in the operation of the LISST Deep compared to the LISST 100X Therefore customers with experience using the LISST 100X are encouraged to read Appendix E to become familiar with these differences The instrument is capable of autonomous operation For such operation
50. estroy instrument performance Between individual casts if you do repeated profiles with the LISST Deep rinse the windows with clean particle free water to keep them clean so that salt is not drying on the windows A squirt bottle with clean particle free water will work very well for this If the windows and the optics end actually get dirty with sediment plankton oil etc the best way of cleaning them is to use a mild hand soap solution in lukewarm water Then gently rub the windows with a finger dipped in the soap solution until they are clean then rinse with lots of clean particle free water to get rid of soap residue Direct sunlight should also be avoided when obtaining a background The unit is relatively insensitive to sunlight however bright light can increase the noise in the measurement and give a false background scattering measurement It is recommended that the end of the instrument be shrouded with a dark cloth during the acquisition of the background In general the background should be taken in conditions that match the deployment conditions as closely as possible The low concentration limit of LISST Deep is very sensitive to the quality of the background scatterfile For this reason when working in near surface or mid depth water it 1s very important that a good background file be obtained with very clean water As particle concentrations increase the relative signal to background noise ratio also increases
51. ge of samples to process can be selected by entering values in the Select First and Select Last boxes The default selection 1s to process the LISST Deep User s Guide 26 complete file Press the Process File button to convert the raw file into processed size distributions For more details on the available options when this window is open please see the detailed Instruction for Processing Raw Datafiles For our example press the Process File button When the processing is complete the button label will change to read Finished Step 23 Viewing Processed data files are stored as ASCII files and as binary files with a Processed Results PSD extension The PSD files can be opened and viewed on the screen To open a processed Particle Size Distribution file choose Open Particle Distribution File or press the 44 button on the toolbar A display similar to the one below should open The left hand figure will display a bar chart showing the Volume concentration in each of the 32 log spaced size classes The right hand plot will be the Cumulative Concentration To view the samples as a movie press the Timer Off button The slider bar next to the button adjusts the refresh rate The First Prev Next and Last buttons allow you to step through the measurements one frame at a time When the last frame is reached the movie display will stop Use the First button to return to the first sample and press the Timer Off button to restart the display
52. he LISST menu or press on the Gets current directory of files Offload button from memory and displays the list Choose the files to be offloaded by clicking on the Files selected and path set file name on the list Multiple files can be selected by hold down the CTRL key while clicking on files Use the SHIFT key to select a range of files Press the OK button to accept the current selection A dialog box with a path for storing the downloaded data will appear Edit the path or press on the Browse button to select a new path The files names will remain the same as on the compact flash The file creation date and time will not be preserved Press OK to begin the offloading Data File Location Directory location For storing offloaded files MS equaiaS erverschuck PraductssLI85 T 10L0 E Engl Browse Cancel LISST Deep User s Guide A Status bar will be displayed for each file offloaded Offloading files from memory Text in the lower left corner will display the current to the PC file being offloaded LISST SOP Settings Display View Rings Serial Port Output File Locations Aus Pars Serial Port ICOM1 vl Baud Rate 3600 Data Bits Parity Stop Bits Protocol File Download Baud Rate Save as default Note The data is offloaded at 115K baud by default When using a cable longer than a few meters it may be necessary to reduce the transfer baud rate The File Download Baud Rate can be changed on th
53. he battery voltage has dropped to less than 6 5 volts The program will continue to sample until one of these conditions is met It will then return to the L100X gt prompt External Magnetic Switch The red external magnet is located close to the connector endcap When the magnet is placed on the instrument the magnetic switch is in the OFF position LISST Deep User s Guide LISST Deep User s Guide e Magnet is mounted ON the instrument e The internal switch is in the OFF position e The instrument will STOP sampling if the switch stop has been selected NOTE External Digital Input Stop is not available on the LISST Deep 58 LISST Deep Command Summary Display Commands DD Display current Disk Directory Display current status information DB Display Current Battery Voltage Display general help messages and command list Setup Commands SC mm dd yy hh mm ss Set Clock with time and date where mm month dd day yy year hh hour 24 format mm minute ss seconds Example ST 01 05 2005 21 05 03 Set Samples per Burst Acquisition Action Commands DL filename Delete file from Compact Flash Module ee Start Data collection using current parameters Grab sample and transmit it YMODEM offload of file at 115K Baud Go into deep sleep mode minimum power consumption ZS Acquire 20 samples and transmit them Used by SOP Acquire Background 59 LISST Deep User s Guide LISST Deep User s Guide
54. he second indictor of misalignment is high value on the inner rings The inner rings are shown on the left side of the background display As the focused laser starts to move away from the center of the ring detector it will scatter more light onto the inner rings This will cause the inner ring values to be much higher than the factory values It must be noted that low laser power or high inner rings may not always indicate misalignment Low laser power can also occur because the windows or water is dirty or if there are bubbles on the window Large particles or bubbles can cause the inner rings to be higher than factory values All of the other possibilities must be eliminated before the conclusion of misalignment can be reached Contact Sequoia at info O sequoiasci com or 425 641 0944 if in doubt LISST Deep User s Guide LISST Deep User s Guide 70 Instrument Mounting Mount the instrument Horizontal Isolate from all other metal 71 This section contains information on mounting of the LISST Deep The LISST Deep measures scattered light to obtain particle size distributions Therefore it is important to keep particles from sticking to the window surface The first line of defense it to keep the window surface vertical by mounting the instrument horizontally If the LISST Deep is mounted vertically so that the optical windows are horizontal sediment and particles can easily accumulate on the windows of the instrument b
55. hreshold the sampling will stop If the depth is not less than the threshold the program will continue sampling as per the configuration If the Start Condition is a Depth Start the program will wait 30 seconds and then return to looking for the Depth Start Conditions The delay is to keep the instrument from starting and stopping too quickly as the instrument is moving up and down If the Start Condition is Depth Start the program will return to checking for the Start Conditions For all other Start Conditions if the current depth is less than the threshold the program will stop and return to the L100X gt prompt Time Stop The program will check the current time after each sample or burst and compare it to the Start Time If the Start Time is equal to or later than the current time the program will stop and return to the L100X gt prompt Fixed Number of Samples The program will acquire a fixed number of samples before stopping For the Fixed Sample Rate mode the number of samples saved is checked after each sample is saved In the Burst mode the number of samples is checked only after each burst Therefore it may be possible to save more samples than specified When the number of sample to be saved has been reached the program will stop and return to the L100X gt prompt Maximum Memory or Low Battery The Maximum Memory or Low Battery Stop condition will continue to sample until the memory capacity has been reached or when t
56. ich data taken The values in the processed data file are stored in the order shown in the table below Each sample is stored in one row Parameter Volume concentration in ul l for size class 1 through 32 NOTE The volume concentration is computed under the assumption that the volume conversion constant was measured over a 5 cm path length If you are using a path reduction module PRM the concentrations in columns through 32 will not be correct However you can correct it simply by multiplying the volume concentration by a factor of 2 5 or 10 for data obtained with 50 80 and 90 PRM s respectively Laser transmission Sensor mW Battery voltage in calibrated units V External Auxiliary input in calibrated units mW Laser Reference sensor in calibrated units mW Pressure in calibrated units m Temperature in calibrated units C Day 100 Hour at which data taken Minutes 100 Seconds at which data taken Computed optical transmission over path Beam attenuation c m 84 Appendix C Connector Pinouts for LISST Deep The LISST Deep has 3 separate underwater connectors on the Connector Endcap and one on the Laser Endcap The Connector endcap has a 5 pin and two styles of 6 pin connectors The Laser EndCap has a single 6 pin connector a stainless steel fitting for the depth sensor and a zinc anode for corrosion protection The text below describes detailed wiring for each connector Communications and
57. id 150 rho 200 1732 1 25 Slower limit for first size range spherical particles 2 50 Slower limit for first size range spherical particles 1 00 Slower limit for first size range randomly shaped particles x 1 90 slower limit for first size range randomly shaped particles bins l x rho 0 31 slower limit Dins lt 3 2 x rho tiLL 32 3 7 gt upper Limit basto Sore bins 3 Li bDiasii 2 p M DOLOE The following lines of code in MATLAB will compute the lower upper and median angles in degrees for the VSF measurement in air and water B all logspace 0 10910 200 33 0 1 create 33 logspaced angles over a 1 200 dynamic range starting at 0 ldegrees type B Blo51 B all B all ANGLES O2 1 B all 1 32 The lower limits are the first 32 Of 33 ANGLES O2 2 B all 2 33 The upper limits are the last 32 of 33 ANGLES O2 3 SgrPt iANGLES OZ f 1 ANGLES 0Z2 2 9M1dDpO2Hts C all logspace 0 10g10 200 33 0 05 create 33 logspaced angles over a 1 200 dynamic range starting at 0 05degrees type C Liso Dl C all 6 311 ANGLES O2 4 C_all 1 32 The lower limits are the first 32 of 33 ANGLES O2 5 C all 2 33 The upper limits are the last 32 Of 25 ANGLES O2 6 sqrt ANGLES O2 4 ANGLES O2 5 Midpoints ANGLES H20 ANGLES O2 1 33 Create angles in water using the refractive index of water 81 LISST Deep User s Guide Angles in air Angles
58. in for type B and C instruments Type B Type C Size bin Ring Lower Upper Median Lower Upper Median 1 32 1 00 1 18 1 09 1 90 225 2 07 2 31 1 18 1 39 1 28 2 23 2 65 2 44 3 30 1 39 1 64 1 51 2 65 3 13 2 88 4 29 1 64 1 94 1 79 3 13 3 69 3 40 5 28 1 94 229 ZH 3 69 4 35 4 01 6 27 2 20 2 70 2 49 4 35 5 14 4 73 7 26 2 70 3 19 2 93 5 14 6 06 5 58 8 25 3 19 3 76 3 46 6 06 7 15 6 59 9 24 3 76 4 44 4 09 T15 8 44 por 10 23 4 44 5 24 4 82 8 44 9 96 9 17 11 D 5 24 6 18 5 69 9 96 11 8 10 8 12 21 6 18 7 29 6 71 11 8 13 9 12 8 13 20 7 29 8 61 7 92 13 9 16 4 15 1 14 19 8 61 10 2 9 35 16 4 19 3 17 8 15 18 10 2 12 0 11 0 19 3 22 8 21 0 16 17 12 0 14 1 13 0 22 8 26 9 24 8 17 16 14 1 16 7 15 4 26 9 31 8 292 18 15 16 7 19 7 18 1 31 8 37 5 34 5 19 14 19 7 2952 21 4 219 44 2 40 7 20 13 23 2 27 4 223 2 44 2 322 48 0 21 12 27 4 32 4 29 8 522 61 6 56 7 22 11 32 4 38 2 32 2 61 6 12 1 66 9 23 10 38 2 45 1 41 5 227 85 7 78 9 24 9 45 1 232 49 85 7 101 93 1 25 8 25917 62 8 57 8 101 119 110 26 7 62 8 74 1 68 2 119 141 130 27 6 74 1 87 4 80 5 141 166 153 28 5 87 4 103 94 9 166 196 181 29 4 103 127 112 196 232 213 30 3 122 144 132 232 273 252 31 2 144 169 156 273 222 297 32 1 169 200 184 322 381 350 LISST Deep User s Guide 80 The following lines of code in MATLAB will compute the lower upper and median size in microns of each bin for both instrument types See also this article on Sequoia s homepage http www seguoiasci com Articles ArticlePage aspx page
59. ing surface Remove the LISST Deep from the case and set it on the stands The LISST Deep has two distinct ends that we will refer to as the Optics endcap and the Connector endcap The connector endcap has three underwater connectors that are used for communication external power and connecting to optional CTD interface The battery pack is attached to the inside of this endcap The optics endcap contains the optical windows that the laser beam passes through to make a measurement The internal optics and electronics are mounted to the inside of this endcap At this time let s check the optical windows to make sure that they are clean There are two windows The Receive window is mounted in the center of the optics endcap Transmit window is located in the Crossbar suspended above the endcap The best way to check the windows is by using a flashlight By shining light from one side 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 water and then by wiping them with a soft cloth and alcohol Stronger solvents such as acetone can be used if necessary but is not recommended as a general practice Liquid dish soap can also be used In general do not use any abrasive cleaners or wipes Treat the windows as you would an expensive camera lens Remove the Communications cable from the shipping crate It is the cable with the
60. instrument See the following section for detailed descriptions of each command Start Condition The LISST SOP software or two letter commands can configure the LISST Deep with one of five Start conditions Depth Time External Magnetic Switch and Time Delay The details of each condition are described below 59 LISST Deep User s Guide Stop Condition LISST Deep User s Guide Depth Start The built in depth sensor of the LISST Deep 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 If the depth exceeds the threshold the program will proceed to the data collection routine If the depth does not exceed the threshold the instrument will power down and wait 28 seconds before checking the depth again The program will continue checking until the depth is exceeded or until the program is stopped Time Start The program will check the current time every second and compare it to the Start Time If the Start Time is equal to or earlier than the current time the program will go directly to the data collection routine It will continue checking the time until the Start Time is reached or until the program is stopped Time Delay Start The time delay start condition will cause the program to wait the specified number of seconds before continuing on to the data collection routine External Magnetic Swi
61. ion before it is complete press the Stop button or CTRL C Grab sample and transmit it Acquires single averaged sample and displays the result to the screen Example Input GX Output 32 ring values 8 Aux parameters j The GX command does not store the sample to a datafile YMODEM Offload Syntax YS filename or ys filename where filename 1s the name of the file to be offloaded Offloads file from Compact Flash Module to PC using YMODEM offload at 115 Kbaud Example Input YS L1391205 dat Output Starting The YS will initiate the YMODEM offload on the instrument A YMODEM file transfer must be started on the PC to accept the data HyperTerminal can accept YMODEM file transfers at 1 15K baud 65 LISST Deep User s Guide Grab 20 samples and transmit it Description Acquires 20 averaged sample and displays the result to the screen The ZS command is used by the LISST SOP program when acquiring a background Example Input ZS Output 32 ring values 8 Aux parameters repeat 20 times The ZS command does not store the sample to a datafile Go into deep sleep mode minimum power consumption Description Sends LISST 25X in to low power sleep mode Instrument will wake up every 10 seconds and wait for a response If there is no response with in 2 seconds the instrument will return to sleep mode Example Input ZZ Output Deep Sleep Enter zz to wake up Deep Sleep Enter zz to
62. is observed at multiple small forward angles At these small angles light scattering is determined almost entirely by light diffracted by the particle The light transmitted through the particle makes only a weak contribution to the measured scattering Since the light transmitted through the particle would experience the composition of the particle i e its refractive index and since it makes only a weak contribution to the observed scattering the method of laser diffraction is mostly independent of particle composition In the aquatic sciences particle refractive index is poorly known Thus except for shape effects laser diffraction offers an excellent method for size distribution estimation Shape effects are a matter of continuing research and no definite generalized guidelines are available to account for them by any method Consequently laser diffraction methods deliver the equivalent spheres size distribution This method determines size distribution of an ensemble of particles as opposed to counting type devices that size one particle at a time By calibrating for concentration with ISO standard natural particles shape effects are empirically included 3 LISST Deep User s Guide The LISST Deep records the scattering intensity over a range of small angles using a specially constructed multi ring detector shown in the graphic above This measurement is also known to optical scientists as the volume scattering function and can be
63. les to collect before stopping The TD setting is ignored for Mechanical Switch Stop option 3 or Digital Input Stop option 4 input PD 12 31 05 23 59 59 or PD 3600 Set Samples per Burst SB x or sb x where x is the number of samples per burst Each sample it taken at the sample interval set by the SI command If no value follows command prompts will be displayed for the value Example input SB 10 Set Clock with time and date Syntax SC mm dd yy hh mm ss or st mm dd yy hh mm ss Where mm month dd day yy year hh hour 24 format mm minute ss seconds If no values follow the SC or sc command prompts for entering the time and date will be displayed input SC 01 05 2001 21 05 03 LISST Deep User s Guide 64 Acquisition Action commands Delete file from Compact Flash Module DL filename or dl filename where filename is the name of the file to be deleted Description DL command is used to delete file from the Compact flash module Wildcards such as can be used Example Input DL L159 dat Output Are you sure Y N Cautions WARNING Make sure that the file being delete has already been offloaded before deleting the file Once the file is delete it can not be recovered Start Data Collection using current Settings Syntax GO or go Starts Fixed Rate or Burst Mode Data collection using current settings Example Input GO Output Waiting for start conditions To stop acquisit
64. mary of the current settings If the OK button is pressed when the configuration is complete the user will be prompted to open the Terminal window to start the program The program on the instrument is configured but not running To start the program and have it start looking for the Start conditions press the Run button on the Terminal window The Run button is equivalent to typing RUN and pressing Enter from any terminal program The Base Program will display text to the screen as it is running to confirm that it is running and to indicate where it is in the sampling cycle Once the program is confirmed to be running and waiting for the correct start conditions the LISST SOP program can be closed and the communications cable can be disconnected Be sure to replace the connector cap before deployment Note that if you disconnect the external power after step 7 the LISST Deep will stop sampling and NOT start again when external power is re applied unless steps 17 18 in the Getting Started section has been followed LISST Deep User s Guide LISST Deep User s Guide 54 Instrument Communication Serial Port Communication with the LISST Deep is via an RS 232C link A Settings cable that connects the instrument to a PC has been provided This cable connects the 4 pin underwater connector on the instrument to a DB 9 serial port connector If required DB 9 to USB or DB 25 pin adapters are available The RS232 link communicates
65. meters measured derived Particle Size distribution Total Volume Concentration Optical Transmission Depth Temperature Two external digital output ports used for CTD sync 5V logic Optical path length 5 cm standard Optical transmission 12 bit resolution Particle size range Type B 1 25 250 micron diameter Type C 2 5 500 micron Resolution 32 size classes log spaced Data storage memory 1GB 10 million samples standard Maximum sample speed size distributions per second Temperature sensor range 10 to 45 C resolution 0 01 C Depth Sensor range 0 to 3000 m of H20 resolution 80 cm of H2O External power input 12V nominal 6 to 15V Dimensions 12 6 cm 4 95 dia x 96 3 cm 37 9 Weight in air 9 5 Kg 41 Ib Weight in water 18 6 Kg 21 Ib Depth rating 3000 m standard Connector Endcap screws Socket head cap screws 10 24 1 long Connector Endcap O ring Parker Part 2 236 radial and 2 240 face 37 92 963 30 69 780 278 126 1 25 32 Dimensions in inches mm 75 LISST Deep User s Guide LISST Deep User s Guide 76 Appendix A Instrument Specific Documentation EE Instrument Instrument Owner Auxiliary Parameters The table below lists the auxiliary parameter labels and calibration constants These values are saved in the LISST INI file They can be viewed and or edited using the Edit Calibration Constants from the DataFrames menu Paramet
66. mited to attorney s fees and other costs of defense against such claims in excess of the price of the Products arising directly or indirectly from such Customer s use of the Products Such indemnification is a critical part of the consideration being provided by Customer over and above the price paid for the Product s for the right to use the Products for such purposes and Customer shall not use a Product or Products for such purposes if it is unwilling or unable to provide such indemnification 9 Statute of Limitations Customer will not commence any action based on breach of warranty with respect to any Product more than 18 months after SEQUOIA s delivery of such Product 10 Software The Products may include or be delivered with certain computer programs databases or other software that is proprietary to SEQUOIA SEQUOIA hereby grants Customer a nonexclusive license to use such software solely for the purpose of operating Products Customer will not use any such software for any other purpose modify adapt translate or create derivative works based on any such software or disassemble decompile or reverse engineer any such software No title to or ownership of any software or intellectual property rights are transferred to Customer 11 U S Government Restricted Rights Notice All software data technical information and written materials provided by SEQUOIA are provided with restricted rights Use duplication or disclosure
67. mum Scale Value E cence e Other options are also available for customizing the display such as changing the header and footer text or adding lines to show the mean and standard deviation These features are located on the Display tab of the Settings window as shown below LISST Deep User s Guide 42 LISST Settings Display View Rings Serial Port Output File Locations Aus Pars Header Text EET DEL eer AE IAE Footer Text Sequoia Scientific Inc hM aximum ordinate value E Animation frame interval 500 millisec Show mean on plot Save values as default Cancel Apply Help The current display can be sent to the printer by choosing Display printed Print from the File menu Print Preview and Print Setup are also available When finished viewing the processed data close the window Viewing of data complete 43 LISST Deep User s Guide LISST Deep User s Guide 44 STEP BY STEP PROCEDURE REAL TIME DATA COLLECTION Connect the instrument to the PC and start the LISST SOP program Instrument configured for Real Time data collection Open the Operating Modes Window and choose the Real Time Operating Mode Before starting a Real Time session the output file options must be set This must be done before selecting Open Real Time Session Select Output from the Options menu The window below will appear Output file type selected LISST 100 Settings ES Display
68. of at least 2 0 for 13 rina s 20 frames collected Frame Num 20 BEGIN Collect Accept and Save Cancel Press the BEGIN Collect button 20 samples will now Background is being collected be displayed to the screen as they are acquired After all 20 are collected the average will be displayed If the values are acceptable the values can be saved to a file Enter the filename in the box and press the Accept and Save button If there is a problem with the instrument or if the water or windows are not clean error messages will be displayed Dirty water or windows will generally cause higher values across the middle rings Large bubbles or particles in the water can cause higher values on the inner rings or left hand side of the display High values on the inner rings combined with a lower Laser power value can also be an indication of optical misalignment LISST Deep User s Guide 34 STEP BY STEP PROCEDURE OFFLOADING DELETING DATA FILES 35 L1051528 DAT 04 14 04 4 28p 11051637 DAT 04 14 04 4 37p 04 16 04 10 48a 04 16 04 11 06a L1061146 0 4T 04 17 04 11 473 j L1051149 DAT 04 17 04 11 488 04 17 04 11 51a 0417 04 1 01p L1067 306 03 T 04 17 04 1 10p L1100847 DAT 04 19 04 8 473 04 19 04 8 48a 04 19 04 8 482 L1100850 DAT 04 19 04 5 50a L1100851 DAT 04 19 04 8 51a 04 19 04 9123 04 19 04 4 55p 1101832 DAT 04 19 04 6 35p L1101845 DAT 04 19 04 6 50p L1101305 DAT 04 19 04 7 07p Cancel Select Offload from t
69. oolbar To start data collection again press the Next button The instrument will power up and store a sample This will take more time that a normal sample Once powered up the instrument will perform as usual LISST Deep User s Guide 48 STEP BY STEP PROCEDURE CONFIGURING DATA COLLECTION e Connect the instrument to the PC and start the LISST SOP LISST SOP open program and communicating with LISST Deep 2 e Open the Operating Modes window by choosing Operating Modes from the LISST menu or by pressing the 22 button on the toolbar LISST Instrument Operation Instrument Status Operating Mode Start Condition Stop Condition I S nstrument status Sere sere 004 LISST Operating Procedure LOF File Displayed gs Browse o Running Summary Sleeping Realtime Operating Mode Start at depth of 0 7 meters Samples Stored Stop at depth of 0 7 meters Samples Remaining Battery Voltage 7 Bb External Switch DN Date ee b 2 Time fr 40 5 Set Clock Uoj OF Cancel Apply Help e When first opening the Operating Modes window the LISST SOP program will send a Ctrl C to the LISST Deep If a program is running it will be stopped This is required so that the LISST SOP program can get the status information from the LISST Deep e To set the LISST Deep data logger clock to the computer clock Clock set press the Set Clock button Press the Query Instrument button to refresh th
70. packaged water We buy steam distilled drinking water and use it right out of the container The background measurement is the only health check one has of the instrument prior to deployment so it should be done as often as is feasible Watch for Another consideration when acquiring a background is outgassing outgassing causing small bubbles to form on the instrument and windows Bubbles on the windows will greatly modify the scattering pattern rendering the background useless Be sure to remove any bubbles from the windows before acquiring a background scatterfile Use a squirt bottle or pipette to blow the bubbles off the window A small volume horizontal chamber has been provided for submerging the optics while acquiring a background It is inserted between the windows of the optics The instrument should be placed horizontally on the supplied white plastic supports Roughly 120 milli liters of water is needed to fill the chamber 67 LISST Deep User s Guide Clean optics end before acquiring a background Between casts Dirty Windows Avoid Direct sunlight LISST Deep User s Guide Because the area surrounding the windows is submerged it is important to thoroughly clean and rinse this part of the instrument before acquiring a background Toothbrush liquid soap and lukewarm water works well for cleaning the optical parts of the instrument DO NOT use abrasive powders or steel brushes They will scratch optics and d
71. red for operation of the instrument A software disk is included with each instrument In addition to the communication and processing program the disk also contains calibration files specific for your instrument Follow the installation instructions in the README TXT file on the disk to install the software The typical procedure is to run the Install program and follow the prompts Step 6 Start Start the LISST SOP software by selecting it from the Start menu LISST_SOP The name LISST SOP refers to the Standard Operating Procedure program functionality of the program Step 7 Open The LISST SOP has a terminal window that allows the user to Terminal window communicate directly with the instrument To open the Terminal window select Terminal Window from the Communications window or select the 8 button form the tool bar A window similar to the one shown below will appear Instrument OF gt OF gt OF gt y Port open Stop Start Commands can be typed into the box in the lower section of the window When the Enter key or the Send button is pressed the command will be sent to the instrument The Start button sends a GO command to the instrument to start the instrument sampling using the current settings The STOP button sends a CTRL C to stop the sampling and to turn off the main power Step 8 Apply The LISST Deep instrument does not have any internal batteries so Power to the before we can talk to the in
72. s Operating Mode Start Condition Stop Condition C Depth Start when depth exceeds jo meters Time Start Date 2 EN 2000 Stark Time a a jo C External Digital Input C Delay jo Hours 1 Minutes Mn Cancel Apply Help 51 LISST Deep User s Guide e Choose the Stop Conditions Tab to select the conditions when sampling should stop e The available Stop Conditions are Depth Time Fixed Number of Samples External Switch and Maximum Memory or Low Battery e The Digital Input stop is not available on the LISST Deep LISST Instrument Operation El Instrument Status Operating Mode Start Condition Stop Condition Stop when depth less than jo meters Time Stop Date 12 JEN 2000 Stop Time EN ss jo f External Mechanical Switch f External Digital Input Fised Number of Samples Number of Samples to store C Maximum Memory Battery a Cancel Apply Help e Ifthe Start Condition and Stop Condition are both set to Depth the instrument will return to waiting for the Start Depth condition This is useful when doing multiple profiles It eliminates the need to communicate with the instrument between profiles LISST Deep User s Guide 52 Select Apply or OK buttons to configure the instrument with the current settings If the Apply button is pressed the program will return to the current window Returning to the Instrument Status window will display a sum
73. ser will be on until this window is closed or until the Stop button is pressed Significant loss of battery life can occur if the instrument is left powered up for an extended period of time It is suggested that external power be used for extended real time data collection The Auxiliary Parameters window can be opened during the Real Time session so that the values of various parameters such as depth and transmission can be monitored The raw scattering values on the detector rings can also be viewed by selecting View Rings from the DataFrames menu A typical display is shown below LISST Deep User s Guide LISST Deep User s Guide Rings 100 Transmission Raw Ring Count Background Scatter Laser Power jo Factory Laser Power ADO The view rings display 1s also available when processing a Raw Data file However it is not available when viewing a processed Size Distribution file The above steps are meant to give a brief introduction to most of the procedures that are required to operate the LISST Deep Most of these steps are covered in detailed Step by Step instructions in the following sections 30 Step by Step procedures The following topics are covered with Step by Step instructions Recording and storing a Background Recording a background scatter file is the first step in Scatterfile Downloading raw data files and Deleting Raw files Process raw data View Particle size data Process da
74. sssssnsssssssssssssssssssssssnsnsnnssssssssssnese 77 APPENDIX B SIZE RANGES ANGLE RANGES AND DATA STORAGE FORMAT 79 APPENDIX C CONNECTOR PINOUTS FOR LISST DEEP cccccccccccccccccccccccccccsssscssssssssscccccccssssssseees 95 APPENDIX D LISST SOP SOFTWARE BUTTON DESCRIPTION ccccccccssssssssssssssssssccsccccccccccsscssees 99 APPENDIX E COMPARISON OF LISST 100X AND LISST DEEP ccccscccssssssssssssssssscccccccccccccccsccsess 91 WARRANTY ae titan lese es 93 1 LISST Deep User s Guide LISST Deep User s Guide Section 1 Introduction to the LISST Deep Introduction to Laser Diffraction Principle of The product name LISST is derived from the term that describes Operation its operation Laser In Situ Scattering and Transmissometry LISST is a Trademark of Sequoia Scientific Inc The LISST Deep instrument uses the technique of laser diffraction to obtain particle size distribution PSD also called volume distribution in this manual This section describes the principle of operation of your instrument The laser diffraction method for sizing particles was invented in the 1970 s and rapidly became the most widely used optical method for determining size distribution for the simple reason that for laser diffraction the composition or refractive index of the particles 1s not important The reason that laser diffraction is unaffected by composition of particles is that the scattering of laser light
75. strument we need to power it up Connect 13 LISST Deep User s Guide LISST Deep LISST Deep User s Guide the communication cable to the 5 pin connector on the LISST Deep endcap connect the communication cable to a PC plug in the jack from the AC power supply in the DB 9 connector and then plug in the power adapter to a 110 220VAC source as displayed in the sequence below 14 SERM Now turn on the power and watch the terminal window You should now see text displaying in the Terminal Window as shown in the example below Instrument System Clock Speed 16000 khz System baudrate not being checked LISST LOOX Firmware Version 1 997 Jun 2 011 13 50 46 Firmware Filename LlIU UX prompt c L100 gt 4 J Port open Stop Start If the cable connections are not correct or the serial port setting is not correct nothing will display Try hitting the lt enter gt button a few times the L100X gt prompt should show If not check the serial port settings by selecting Serial Port Settings from the Communication menu The default settings are COMI 9600 baud 8 data bits No parity 1 stop bit and no protocol Step 9 Intro tothe The datalogger inside the LISST Deep is similar to the one in the 15 LISST Deep User s Guide Datalogger Step 10 Acquiring Background Scattering LISST Deep User s Guide LISST 100X instruments The datalogger of the LISST Deep uses removable Compac
76. t Flash cards The LISST Deep comes standard with a IGb card During sampling raw data are stored onto the flash card Subsequently the data must be offloaded and processed using the LISST SOP software at 115K baud The LISST Deep now has standard two letter commands that can be used for interfacing the instrument with other dataloggers and sensors The commands are very similar to the commands used with the LISST 100X instrument A complete description of the commands is shown in the LISST Deep Command Summary section A feature of the LISST SOP is the ability to acquire background scattering in real time The background scattering measurement is critical to good instrument performance It is especially critical for clean water applications where the optical transmission is greater than 80 over the 5cm path The background scattering will also check the overall health of the instrument It will verify that all of the systems are functioning and that the optics are still in alignment The current background will be acquired and displayed relative to the factory background scattering for the instrument The image below shows an example of this display It 1s opened by either selecting Collect Background Scatter Data from the LISST menu or by pressing the m button on the toolbar After selecting the factory background scatter file to use for comparison the window will display Collect Background Scattering Data 1000 Output File
77. t from the terminal window Step 20 Collecting Data LISST Deep User s Guide The LISST Deep will now start the the sampling program every time the power is applied and start checking if the start condition has been met If it has sampling will begin If the instrument is programmed and connected to external power but not yet started the configuration of the instrument can be checked by selecting Query Instrument from the LISST menu or by choosing the button from the tool bar A window will appear showing the current status and configuration To start the program press the Start button in the lower right section of the Terminal window I Port open The program will start and display text to the screen as it 1s running Depending upon the Start Conditions text will be displayed approximately every 30 seconds At this point the user will know that the instrument is running and is ready to be deployed When the start conditions are met the instrument will start sampling For our example when the delay time has expired sampling will start If the Terminal window is still open text will be displayed as the instrument acquires data Data collection will continue until the Stop Conditions are met In our case until the 10 samples have been collected If the Start and Stop Conditions are set to Depth the program will return to checking for the Start Condition This will only be true if the Start and Stop conditions match For
78. ta in Real time Configuring Data Collection 31 acquiring data This step by step describes the proper procedure to record and download a background scatter file and save it for later processing Information on interpreting the Background Scatter file is also provided Each data collection sequence is stored to a separate datafile on the compact flash memory Files can be offoaded to the PC using the Download data function of the LISST SOP software After downloading the data files can be deleted from memory This step by step procedure covers offloading and deleting files Data that has been downloaded from the datalogger is in a raw binary file It must be processed into particle size by the LISST SOP program The processing steps including optional displays and procedures are described After processing of the data into a Particle Size Distribution PSD file the data can be viewed to the screen This step by step procedure covers the viewing of data and optional displays Real time processing of data requires configuring the datalogger to output the raw information to the LISST SOP program This step by step procedure covers the acquisition and storage of processed data The LISST SOP software allows the user to program the instrument with a number of start and stop conditions This step by step procedure lists the available options and the unique features of each LISST Deep User s Guide LISST Deep User s Guide 32
79. tart option 1 the input will be start depth in meters If the start condition is set to Time Date Start option 2 the input for TD will be the start date and time If the Start Condition is Delay Start option 5 the input will be time delay in seconds The TD setting is ignored for Mechanical Switch Start option 3 or Digital Input Start option 4 If no value follows command prompts will be displayed for the value input TD 12 31 05 23 59 59 or TD 3600 63 LISST Deep User s Guide Set Stop Condition SP x or sp x where x is the stop condition code Description The SP command sets the stop condition to be used when collecting data The stop condition options are 1 Depth Stop 2 Time Date Stop 3 Mechanical Switch Stop 4 Digital Input Stop 5 Fixed Number of Samples Stop 6 Maximum memory or Low Battery Stop If no value follows command prompts will be displayed for the value PDO oO Set Start Condition Data PD x or pd x where x 1s the start condition data Description The PD command sets the start condition data to be used when the collection data The stop condition data is used with the Stop Condition setting For example if the Stop Condition is Depth Stop option 1 the input will be stop depth in meters If the stop condition is set to Time Date Stop option 2 the input for TD will be the stop date and time If the Stop Condition is Fixed Number Stop option 5 the input will be the number of samp
80. tart with 1 minute delay atop Condition Fixed Number Stop at 1 samples Measurements per Average 10 sample Interval 1 Battery Voltage is 23 95 Current Date Time Tuesday June 14 2011 10 03 07 Current Day of the Year 165 Do vou wish to set current settings to be defaults l yes noj 0 1 Current Settings being saved to EEPR M Current Settings saved as defaults L100x gt El lli B Port open Stop Start Now enter AS at the command line and click the Send button You will be prompted to confirm that you wish to execute the autostart of the saved defaults upon power up Enter 1 and click the Send button to confirm as shown below LISST Deep Current Status and Settings Serial number 4006 Firmware Version 1 997 Jun 9 011 13 50 46 Operating Mode Fixed Rate Mode Start Condition Delay Start with 1 minute delay atop Condition Fixed Number Stop at l samples Measurements per Average 10 sample Interval 1 Battery Voltage ia 25 98 Current Date Time Tuesday June 14 2011 10 03 07 Current Day of the Year 165 Do xou wish to set current settings to be defaults l yez Uznej 0 2 I Current Settings being saved to EEPROM Current Settings saved as defaults L100x gt AS Execute Autostart issue Go command upon power up l yes U noj 0 2 L Autostart will occur upon power up Ll00x gt Send Stop Start LISST Deep User s Guide Step 19 How to start the instrumen
81. tch The red external magnet is located close to the connector endcap Remove the magnet in order to turn the instrument ON if the switch start has been selected e Magnet is OFF the instrument e The internal switch is in the ON position e The instrument will START sampling if the switch start has been selected NOTE The External Digital Input Start is not available on the LISST Deep The LISST SOP software can configure the Base program with one of six Stop conditions Depth Time External Mechanical Switch Fixed number of samples and Maximum Memory or Low Battery The details of each condition are described below The LISST SOP software can configure the Base program with one of six Stop conditions Depth Time External Mechanical Switch Fixed number of samples and Maximum Memory or Low Battery When storing data in the Fixed Sample Rate mode the Stop conditions are checked after each averaged sample has been saved 56 57 When storing data in the Burst mode the Stop conditions are only checked after a full Burst has been completed The Start and Stop conditions have no effect on the Real time sampling mode The details of each condition are described below Depth Stop The built in depth sensor of the LISST Deep is used to check the current depth to determine 1f it is less than the desired Stop depth The averaged depth from the last sample acquired is used as the current depth If the depth is less than the t
82. tion A prompt appear that says Instrument is now configured but not started Do you wish to start the Instrument You can also choose to open the Terminal window by selecting the check box 20 Start Instument AN Instrument is now configured but nat started Tal must start the instrument before data collection can begin Do vau want to start the instrument Open the terminal window Ho If you select No the instrument will be configured but not started Choose Yes if you wish to start the program right away This will start the program and it will begin to check for the desired start condition to occur Once the desired start condition has been met sampling will begin However Note that because the LISST Deep has no internal power the instrument will Stop sampling as soon as you disconnect the external power If you click Yes and then disconnect the external power the instrument will NOT sample even if you reconnect the external power In order to make sure that the LISST Deep Starts sampling with the programmed settings when external power is re applied to the instrument you MUST follow steps 17 and 18 below Step 17 Saving Because the LISST Deep does not have an internal battery it can be the Current useful to save the program settings in the firmware and then have the Settings firmware start automatically whenever power is applied In this manner all you have to do is to apply power to the L
83. tsmith 2000 We explain the inversion process as follows Let E be the 32 element data vector that contains the angular scattering energy sensed by the 32 silicon rings It is related to the volume distribution via Agrawal Y C I N McCave and J B Riley 1991 Laser diffraction size analysis in Principles methods and applications of particle size analysis J P M Syvitski editor Cambridge University Press pp 119 128 Agrawal Y C and H C Pottsmith 2000 Instruments for Particle Size and Settling Velocity Observations in Sediment Transport Marine Geology 168 pp 89 114 The volume distribution is related to the number distribution via Ny a n a It represents the volume concentration of particles of particles in the size range a to a da The results from the LISST instruments provide the volume concentration of particles in each of 32 size classes The size classes are log spaced from the range 1 25 250 microns Type B instruments 2 5 500 Type C or 7 5 1500 microns Type D LISST FLOC See Appendix B for further details LISST Deep User s Guide 4 E KNy where K is the scattering property kernel matrix and Ny is the volume distribution The volume distribution is obtained by inverting the above equation To test whether the estimated solution is a good one one may compute the prediction of a scattered energy estimate E as E IA Ne If the measurements E are consistent with E the
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