Sequoia LISST-Deep User Manual
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Sequoia LISST-Deep User Manual

Particle size analyzer
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LISST-Deep
Particle Size Analyzer
User's Manual
For serial numbers 4056 and higher
Built March, 2022 and later
Version 5.02
January, 2023
Store Software
USB Card Here
2700 Richards Road, Suite 107
Bellevue, WA 98005
USA
Telephone: (+1) 855-753-3313

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  • Page 1 LISST-Deep Particle Size Analyzer User’s Manual For serial numbers 4056 and higher Built March, 2022 and later Version 5.02 January, 2023 Store Software USB Card Here 2700 Richards Road, Suite 107 Bellevue, WA 98005 Telephone: (+1) 855-753-3313...
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  • Page 3 © This document is copyrighted by Sequoia Scientific, Inc. LISST-Deep User’s Manual Page iii...
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  • Page 5 4056 or higher. Warranty See the product warranty at: http://sequoiasci.com/support/warranty Technical assistance For technical assistance please contact your local Distributor or Sequoia. Please include the instrument serial number with any correspondence. Sequoia Scientific, Inc. contact information: Telephone: (+1) 855-753-3313 Email: support@sequoiasci.com LISST-Deep User’s Manual...
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  • Page 7: Table Of Contents

    Data Quality Control ..................... 36 Real-Time Data Processing with LISST-200X Software .......... 38 Autonomous Real-time Data Processing ..............40 Collecting Data from External Analog Sensors ............42 Configuring the LISST-Deep as a Sensor for a CTD ..........43 ..................... 44 TART AND ONDITIONS .....................
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  • Page 9: Introduction & Quick Start

    36 size classes of particles. This is called the particle size distribution (PSD). To measure scattering at multiple angles, the LISST-Deep sends a collimated beam of light into the water. Laser light scattering at an angle from the beam arrives, through a daylight rejection filter, at the focal plane of a receive lens at the same angle from lens axis (see figure).
  • Page 10 Because the LISST-Deep physically shields the detector from most ambient light, and because ambient light is not a factor over most of the LISST-Deep’s range of operating depths, ALR is turned off by default. For more about ALR, see Ambient Light Rejection on page 58.
  • Page 11 LISST-Deep’s auxiliary connector; see Configuring the LISST-Deep as a Sensor for a CTD on page 43.) The quick estimates are based on weighted sum of the net scattered light. One set of weight factors yields the total volume concentration;...

  • Page 12: General Description

    In addition to its primary scattering measurements, the LISST-Deep measures optical transmission, depth, and temperature, at depths up to 4,000 meters. The LISST-Deep is capable of autonomous operation when used with external batteries. Windows software is provided to program the instrument for a specific sampling schedule.
  • Page 13 Both values are stored automatically in the LISST-Deep data file. External I/O Port The LISST-Deep also has an auxiliary 6-pin connector for interfacing to other devices This port can be configured to produce analog outputs, or to receive analog inputs.

  • Page 14: Quick Start Tutorial

    C. Quick Start Tutorial This section gives quick instructions for getting started, with references to more detailed information in section II. Contents of When opening the LISST-Deep shipping case for the first time, you will Shipping Case find: • LISST-Deep instrument, •...
  • Page 15 Software the newer LISST-Deep version described in this document. It is supplied with the LISST-Deep on a USB memory card (about the size of a credit card). It is also available for download from Sequoiasci.com. This installation process is similar to that of most other Windows software.
  • Page 16 Application The LISST-200X software will automatically detect and connect to a LISST-Deep instrument if it is connected to the computer. The light blue tab in the lower left corner of the window should show that the instrument was found and connected.
  • Page 17 For example, when a ‘Sample to be Average of’ value is entered, the minimum sample interval is computed. If this value is less LISST-Deep User’s Manual Introduction & Quick Start...
  • Page 18 For this tutorial select the External Switch Start Condition. AutoStart If the AutoStart check box is selected, the LISST-Deep will start the sampling program whenever power is first applied to the instrument. NOTE: for AutoStart to detect the application of power, all power sources (including the USB cable) must first be disconnected for at least 6 seconds.
  • Page 19 For this example, choose External Switch as the Stop condition. Step 9: The accessories tab allows you to select which LISST-Deep Configure accessories are connected to the instrument. The accessories must be Accessories selected here for them to function properly. If there are no accessories, select ‘None’.
  • Page 20 Install the chamber by sliding the hose clamps over the end of the installation LISST-Deep, wrapping the plastic sheet as shown in the photo below. Tighten the clamps only enough to make a leak-proof seal. Overtightening could damage the inter-housing cable.
  • Page 21 High values on the inner rings combined with a lower transmitted laser power value can also be an indication of optical misalignment. LISST-Deep User’s Manual Introduction & Quick Start...
  • Page 22 If you want sampling to begin immediately, select a start condition of “Delay” with zero as the delay time. LISST-Deep User’s Manual Introduction & Quick Start...
  • Page 23 Due to mechanical constraints, the actuator for the magnetic switch is not permanently attached to the LISST-Deep. It attaches to a patch of Velcro fastener, at the location shown below. To improve its visibility, it is attached to a white lanyard.
  • Page 24 Choose the files to offload by clicking on them while holding down the CTRL key. The Shift key can also be used to select a range of files. Choose a location to offload the files to on the right side. LISST-Deep User’s Manual Introduction & Quick Start...
  • Page 25 ASCII .BGT Background ASCII Every LISST-Deep data file contains all the necessary information to process the file. Therefore, the software will automatically determine the instrument serial number, factory background, current background and other instrument specific parameters. A raw data file display will be generated for your selected data file.
  • Page 26 .CSV file is displayed automatically. You can Results also open any LISST-Deep .CSV file by selecting the View Process File button from the home page. A display similar to the one below will open. A list of available parameters is displayed on the left.
  • Page 27 A list of available parameters is displayed on the left. Clicking one of the parameters will open a new window where the parameter will be displayed. The parameter windows can be reorganized by dragging and dropping. LISST-Deep User’s Manual Introduction & Quick Start...

  • Page 28: Operation Details

    WARNING-Class 3R laser – AVOID DIRECT EYE EXPOSURE The LISST-Deep uses a laser diode emitting a maximum of 1 mW of visible (red) light at a wavelength of 670nm. Under normal circumstances the laser travels only within the 2.5 cm sample volume.

  • Page 29: Step By Step Procedures

    Software for Windows is used to configure the LISST-Deep and for downloading and processing the size distributions. The software is called LISST-200X, but also supports the revised version of the LISST-Deep described in this manual (it does not support older LISST-Deeps).

  • Page 30: Establishing Communication With The Lisst-Deep

    Establishing Communication with the LISST-Deep Establish communication with LISST-Deep using the supplied software and USB cable. Communicating with the LISST-Deep via the software should be automatic. If you have trouble, try following these steps exactly. STEP ACTION RESULT • If the LISST-200X software is open, close the...

  • Page 31: Saving And Evaluating Clean Water Backgrounds

    LISST-Deep. • Connect the instrument to the computer and establish communication in the LISST-200X program (page 22) • Clean the windows of the LISST-Deep, and the areas Optics clean and sample chamber ready near the windows including the outer housing. This is...
  • Page 32 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 LISST-Deep User’s Manual Operation Details...
  • Page 33 • You also have the option, not required, to save the background to a file on your computer. After the background is saved, select the ‘Save as .BGT File’ button. LISST-Deep User’s Manual Operation Details...

  • Page 34: Configuring Data Collection

    Instrument Status Displayed. Instrument Configuration from the home page. • To set the LISST-Deep clock to the computer clock, open the status bar, click the wrench icon, and select ‘Set Instrument Clock’. • You can also zero the depth sensor from this same menu.
  • Page 35 Select the correct parameters as required. • If the AutoStart check box is selected, the LISST-Deep will start the sampling program when power is applied to the instrument. If this is not selected the user must send the LISST-Deep User’s Manual...
  • Page 36 Click on the ‘Upload to Instrument’ button to load the configuration onto the LISST-Deep. A confirmation message will be displayed when the upload is finished. LISST-Deep User’s Manual Operation Details...
  • Page 37 • When the sampling program is running, you will receive a confirmation message that the program has started, and the instrument will become disconnected from the computer. At this point the instrument is ready to be deployed. LISST-Deep User’s Manual Operation Details...

  • Page 38: Offloading And Deleting Data Files From Internal Memory

    Offloading and Deleting Data Files from Internal Memory Data collected using the LISST-Deep is stored on the internal data logger. This section describes how to offload and delete files from the internal data logger. STEP ACTION RESULT • Connect the instrument to the computer and establish...

  • Page 39: Processing A Single Raw Data File

    .RBN file. If you would like to use the data file or an a different background file than the one in the RBN external .BGT file file, or use a data record as a background, select the ‘View/Select Background’ button LISST-Deep User’s Manual Operation Details...
  • Page 40 Excel etc. • The RTX file is a space delimited ASCII file containing the raw data from the LISST-Deep data logger. This is useful for looking at the raw data in a spreadsheet such as Excel etc.

  • Page 41: Batch Processing Multiple Raw Data Files

    • Files will be named with the same name as the raw data files but with different extensions. Several files will be created. • The CSV file is a space delimited ASCII file containing all the processed data. LISST-Deep User’s Manual Operation Details...
  • Page 42 • The RTX file is a space delimited ASCII file containing the raw data from the LISST-Deep data logger. • Press the “Process Files” button. Process files • The files will be processed in order and the progress bars will indicate the status of each file LISST-Deep User’s Manual...

  • Page 43: View Processed Data File

    • When multiple tabs are open, the tabs can be dragged out into their own windows, allowing for easy comparison between files. LISST-Deep User’s Manual Operation Details...

  • Page 44: Data Quality Control

    0.98-1.0 range, your measurements are taken in noisy data. very clear water. • This means that the signal-to-noise ratio will be low, and the data may have a lot of noise in them, but can most likely still be used. LISST-Deep User’s Manual Operation Details...
  • Page 45 • Be wary of data collected at transmission values between 0.98 and 0.995 – low signal-to-noise ratio. • Be wary of data collected at transmission values between 0.30 and 0.10 – generally decreasing data quality as the transmission decreases below 0.30 (30%). LISST-Deep User’s Manual Operation Details...

  • Page 46: Real-Time Data Processing With Lisst-200X Software

    10. Real-Time Data Processing with LISST-200X Software This procedure covers the acquisition, display and storage of processed data in real time, using the LISST-200X software. For on-board processing by the LISST-Deep firmware, see Autonomous Real-time Data Processing on page 40.
  • Page 47 Select output • The RTX file is a space delimited ASCII file containing the directory and file raw data from the LISST-Deep data logger. name • Data will not be saved until the ‘Start Logging Data’ button is pressed.

  • Page 48: Autonomous Real-Time Data Processing

    PSD processing autonomously, without requiring a connection to a Windows computer. You may choose to save the processed data files (.CSV) in the LISST-Deep memory, or transmit them in real time through the serial port, or both. Note that processing slows the maximum sampling rate.
  • Page 49 • IMPORTANT: after you have selected the desired Configuration configuration, press the ‘Send Config. To Instrument’ uploaded to instrument. button to load the configuration onto the instrument. Configuration complete. • A message box will confirm the upload has been completed. LISST-Deep User’s Manual Operation Details...

  • Page 50: Collecting Data From External Analog Sensors

    12. Collecting Data from External Analog Sensors The LISST-Deep can supply regulated 12V power to external sensors, and measure one to three analog voltages, depending on its firmware settings. If the 12V power output is activated, it will turn on each time the 200X collects a sample or burst of samples, and turn off each time the 200X goes into a waiting state of more than a few seconds.

  • Page 51: Configuring The Lisst-Deep As A Sensor For A Ctd

    For highest-quality data you will still need to offload and process the detailed data from the LISST-Deep after deployment. The LISST-Deep updates its analog outputs each time it collects a sample, at a maximum of 1 Hz.

  • Page 52: Start And Stop Conditions

    (If the programmed time has already passed, it will start immediately.) External The LISST-Deep will wait until the white plastic lever on its endcap is moved to the “1” position. (If it is already in that position, it will start Mechanical Switch Start immediately.)
  • Page 53 For all other Start Conditions the when the current depth is less than the threshold the LISST-Deep will stop and go into deep sleep. If using depth for both start and stop conditions, consider whether the start and stop thresholds should be different, depending on your deployment scenario.

  • Page 54: Instrument Communication

    C. Instrument Communication Overview The cables Sequoia supplies with the LISST-Deep send data through a standard USB port. However, the LISST-Deep itself communicates through RS-232 serial protocol. The 5-pin male connector on the LISST-Deep carries the RS-232 signals (and power). The cables incorporate adapters that convert between RS-232 and USB.

  • Page 55: Direct Command Summary

    Reset depth sensor offset Acquisition/Action Commands DL filename Delete file Start data collection using current parameters Grab sample and transmit it Acquire 20 samples and evaluate them for quality. Go into deep sleep mode (minimum power consumption) LISST-Deep User’s Manual Operation Details...

  • Page 56: Command Details

    Display current disk directory in DOS type format. Includes total bytes used and bytes available. LDeep:> DD Example: <DIR> 2099-03-14 03:35:48 <DIR> 2099-03-14 03:35:48 L2390658.RBN 1,612,440 2019-08-29 14:55:28 L2411501.RBN 3,253,800 2019-09-03 07:58:20 L2480807.RBN 736,800 2019-09-06 09:40:14 3 file(s) 7,608,360 bytes 2 dir(s) 1,016,381,440 bytes free LISST-Deep User’s Manual Operation Details...
  • Page 57 Syntax: DS 1 Description: Instrument status displayed in simplified format for reading by software LDeep:> ds 1 Example: LISST-Deep Current Status and Settings SN = 0 OM = 0 ST = 5 TD = 0 SP = 6 PD = 0...
  • Page 58 HELP or ? Description: Displays the list of command to the screen. LDeep:> HE Example: LISST-Deep Commands ------------------------------------- [list of commands] Display current Magnetic Switch status Syntax: Description: The current status of the Magnetic Switch is displayed to the screen. A value of 0 means the magnetic actuator is present in its assigned place on the LISST-Deep housing.

  • Page 59: Setup Commands

    Available only in firmware 2.2 or later, this command returns a number indicating the configuration of the 6-pin connector used for interfacing with external devices. In the current LISST-Deep it will return either 5, 6, or 9, and will accept one of those values to set the configuration. For full details, see Viewing and Setting the Auxiliary I/O Configuration on page L200x:>...
  • Page 60 Depth stop at 3 meters If Stop Condition = 2 (Time/Date Stop): LDeep:> PD 2016/12/31 23:59:59 Time stop at 2016/12/31 23:59:59 If Stop Condition = 5 (Fixed Number of Samples): LDeep:> PD 100 Stop after 100 samples. LISST-Deep User’s Manual Operation Details...
  • Page 61 Each sample is taken at the sample interval (in seconds) set by the SI command. If no value follows command, prompts will be displayed for the value. LDeep:> SB 10 Example: New Samples per Burst: 10 Set Clock with time and date Syntax: SC yyyy/mm/dd hh:mm:ss LISST-Deep User’s Manual Operation Details...
  • Page 62 Syntax: SENSORWARM x, where x is in seconds Description: If SENSORPOWER is on, SENSORWARM sets the number of seconds the LISST-Deep will wait for external sensors to warm up before it proceeds with sampling. LDeep:> SENSORWARM 10 Example: Power output, when used, will turn on with 10 second warmup.
  • Page 63 TD x or STARTDATA x where x is the start condition data described below 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 as follows: LISST-Deep User’s Manual Operation Details...

  • Page 64: Acquisition/Action Commands

    Delete the file 'L3231513.RBN'? Y for Yes or N for No: [N] ? Y Deleting L3231513.RBN Deleted. Cautions: WARNING: Make sure the file being deleted has already been offloaded. Once the file is deleted it cannot be recovered. LISST-Deep User’s Manual Operation Details...
  • Page 65 Go into deep sleep mode (minimum power consumption) Syntax: Description: Sends LISST-Deep in to low power sleep mode. Instrument will send a message every 30 seconds to indicate it is sleeping. It can be wakened at any time by sending 2 control-C characters about ½ second apart.

  • Page 66: Performance Optimization

    However, a and its certain amount of scattering is also generated by pure water, and by the LISST-Deep’s own optics and windows. We call this the Importance background scattering. In order to determine the scattering contributed by particles, the background scattering must be accurately measured and subtracted from the total scattering measured.
  • Page 67 The background measurement (described step-by-step on page 23) is Alignment 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.
  • Page 68 All of the other possibilities must be eliminated before it can be concluded that the instrument is misaligned. If necessary, the LISST-Deep can be aligned by Sequoia Scientific or an authorized service representative. LISST-Deep User’s Manual...

  • Page 69: Mounting And Orientation, Storage

    Any contact with other metal can 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. Failure to properly isolate the instrument from all other metal will void the warranty.

  • Page 70: Appendix A: Technical Specifications

    • Dimensions: 12.6 cm (4.95”) diameter, 96.3 cm (37.9”) long (see dimensional drawing on following page) • Weight: 18.6 kg (41 lbs.) in air, 9.5 kg (21 lbs.) in water • Depth rating: 4000 m LISST-Deep User’s Manual Operation Details...
  • Page 71 LISST-Deep dimensions in inches [mm] LISST-Deep User’s Manual Operation Details...

  • Page 72: Appendix B: Particle Size Bins

    13.8 15.0 17.7 16.3 17.7 20.9 19.2 20.9 24.6 22.7 24.6 29.1 26.7 29.1 34.3 31.6 34.3 40.5 37.2 40.5 47.7 43.9 47.7 56.3 51.9 56.3 66.5 61.2 66.5 78.4 72.2 78.4 92.6 85.2 92.6 LISST-Deep User’s Manual Operation Details...

  • Page 73: Appendix C: Data File Formats

    Appendix C: Data File Formats File Types and Extensions Used by the LISST-Deep. Extension Description Format Comments Raw data file produced by the LISST-Deep. In addition to raw scattering data, RBN files contain a complete description of the .RBN Raw Data...
  • Page 74 Accelerometer Z [not presently calibrated or used] Raw pressure [most significant bit] Raw pressure [least significant 16 bits] Ambient Light [counts – not calibrated] External analog input 3 [V] Computed optical transmission over path [dimensionless] Beam-attenuation (c) [m LISST-Deep User’s Manual Operation Details...
  • Page 75 The values in the raw ASCII data file (.RTX extension) are stored in the Format order shown below. Each sample is stored in one row. RTX files are only useful for troubleshooting or special applications. Sequoia does not supply software for processing them. Column # Parameter 1:36...

  • Page 76: Appendix D: Matlab Data Processing

    RBNdata = L200X_LoadRBN(datafile) ‘Datafile’ is the path to a binary .RBN file downloaded from a LISST-Deep. Optionally, you may specify a different clean water background file (.BGT) as a second argument. The data will then be corrected using the specified background file instead of the background contained in the RBN file.
  • Page 77 (recommended). ShowProgressBar – If set to 1, a progress bar will display the processing status. The function will return the volume distribution in µL/L (vd) and the midpoint of each size bin in microns (dias). LISST-Deep User’s Manual Operation Details...

  • Page 78: Appendix E: Connectors

    • 5-pin male, the primary power input and serial data interface • 6-pin male, for auxiliary input/output functions • 6-pin female in the center of the end cap, for connections between the LISST-Deep’s two pressure housings. The factory-installed cable should never be removed during normal operation.

  • Page 79: Auxiliary I/O Connector

    Analog In #2 (0 to 5V) Dual Analog Input with Trigger: similar to triple analog input, but one input acts as a trigger that allows an external system to start and stop logging by the LISST-Deep. Connector Pin # Ground...

  • Page 80: Viewing And Setting The Auxiliary I/O Configuration

    Viewing and Setting the Auxiliary I/O Configuration To view the current configuration in the LISST-200X software, once connected (see Establishing Communication with the LISST-Deep on page 22) open the instrument status bar and press the ‘?’ icon next to ‘Auxiliary IO’, as shown below:...
  • Page 81 ‘Load New Configuration…’ button. We recommend that nothing be plugged into the connector when changing the configuration. The configuration can also be viewed through the instrument serial port command line using the CONFIG command (see page 48), and changed through the IOCONFIG command (see page 51). LISST-Deep User’s Manual Operation Details...

  • Page 82: Appendix F: Particle Shape Models

    (i.e. black). This is an obvious fudge with consequences! Which model should you use? Sequoia’s software allows you to use both, then compare the results. But in general, the random model is best for any in-situ application.

  • Page 83: Appendix G: Analog Outputs

    Appendix G: Analog Outputs Introduction The LISST-Deep includes two analog outputs for interfacing with CTDs or other data acquisition systems (see Configuring the LISST- Deep as a Sensor for a CTD on page 43). These produce voltages indicating the approximate total concentration and mean diameter of particles.

  • Page 84: Appendix H: Troubleshooting & Support

    .RBN file(s) that contain the raw data. Email the data to your local Sequoia distributor, together with a detailed explanation of what you were doing and how the data were collected. If you purchased the instrument directly from Sequoia, email the data to support@sequoiasci.com.

  • Page 85: Revision History

    Version 5.02 Delete obsolete XR command January 2023 Version 5.01 Add Appendix G: Analog Outputs. August 2022 Version 5 First version describing the updated design introduced in 2022, starting March 2022 with LISST-Deep serial number 4056. LISST-Deep User’s Manual Operation Details...

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