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Sequoia LISST-Holo2 User Manual

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LISST-Holo2
User's Manual
Version 1.0
January 2018
Sequoia Scientific, Inc.
2700 Richards Road, Suite 107
Bellevue, WA 98005
USA
Tel: (+1) 425-641-0944
Fax: (+1) 425-643-0595
info@SequoiaSci.com
www.SequoiaSci.com

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  • Page 1 LISST-Holo2 User’s Manual Version 1.0 January 2018 Sequoia Scientific, Inc. 2700 Richards Road, Suite 107 Bellevue, WA 98005 Tel: (+1) 425-641-0944 Fax: (+1) 425-643-0595 info@SequoiaSci.com www.SequoiaSci.com...
  • Page 3 Technical assistance To obtain technical assistance related to your LISST-HOLO2 , please contact your local distributor (a list of our international distributors can be found on www.SequoiaSci.com) or Sequoia Scientific, Inc. directly. Please be sure to include the instrument serial number with any correspondence.

  • Page 4: Table Of Contents

    Table of Contents Introduction to the LISST-Holo2 and In-Line Holography ............. 6 Overview—Using the LISST-Holo2 ..................7 Getting Started ........................... 8 Introduction ..........................8 Connect cables and power up ..................... 8 Take a hologram ........................10 Hologram Processing with Holo Batch and Holo Detail ............13 Intro ............................
  • Page 5 11.7 5-Pin Bulkhead Connector Pin Assignments ................53 11.8 6-Pin Bulkhead Connector Pin Assignments ................54 Warranty ........................... 55 Index ............................57...

  • Page 6: Introduction To The Lisst-Holo2 And In-Line Holography

    The following pages contain a Quick Start section and a Getting Started Section. The Quick Start section is a very brief introduction to the operation of the LISST-Holo2. It is intended for experienced user as a refresher or for people who do not want to read a manual.

  • Page 7: Overview-Using The Lisst-Holo2

    Overview—Using the LISST-Holo2 This is a very brief overview of LISST-Holo2 operation. For a more detailed introduction to the instrument, proceed to section 3, Getting Started. Unpack Open shipping case and remove the LISST-Holo2, white plastic stands, Wi-Fi router, blue 8-pin Ethernet cable, 5-pin Power and Communications Cable and External Power Supply.

  • Page 8: Getting Started

    3.2 Connect cables and power To program and offload data from the LISST-Holo2 you need a PC with a web browser (e.g. Firefox, Chrome, Edge) and access to a power source. The LISST-Holo2 contains internal batteries, however, for this tutorial we’ll demonstrate how to use the instrument with external power.
  • Page 9 A wireless router is provided with the LISST-Holo2 which allows you to connect your LISST-Holo2 to the internet or a local network. Most users will need the router to communicate with the LISST-Holo2. The LISST-Holo2 can be directly connected to a computer, however, this will require custom network settings on your computer.

  • Page 10: Take A Hologram

    The LISST-Holo2 will boot up. The endcap LED will flash yellow for approximately 40 to 60 seconds. When it is ready, the LED will blink green every 5 seconds. See section 10 for more information about the LED colors and status light indicators.
  • Page 11 The About page shows the FAQ where you can find more information about how to download, install, and use OpenSeeIt to view the unprocessed holograms. If you took a hologram without anything in the laser beam, your hologram will typically look something like this. LISST-Holo2 User’s Guide...
  • Page 12 U-shaped spacer. To put the LISST-Holo2 to sleep, click the Home button, then click the Sleep button. If the Sleep button is not present on the Home page, go to the Tools page and put the instrument to sleep using the Sleep button on the Tools page (see section 6.6).

  • Page 13: Hologram Processing With Holo Batch And Holo Detail

    The holograms are processed using two MATLAB-based programs called Holo Detail and Holo 4.1 Intro Batch. You do not need to be connected to the LISST-Holo2 to process previously offloaded holograms. 4.2 Install the hologram processing software To install the software, plug in the USB memory card that was shipped with your instrument and locate the LISST-Holo2 software folder.

  • Page 14: Holo Batch - Automated Batch Processing Of Multiple Holograms

    Reconstruction Parameters in the Options Menu. The Change ROIs and Advanced buttons then become active. Also, the three input boxes for selection of the minimum and maximum focal length, as well as the step size become active. LISST-Holo2 User’s Guide...
  • Page 15 Note that you can delete and add ROI’s using the Delete and Add buttons. In this example to the left, one of the 10241024 pixel ROI’s have been deleted. Subsequently the Delete button has been grayed out. LISST-Holo2 User’s Guide...
  • Page 16 HOLO2 this value is 28 mm. DO NOT CHANGE THIS VALUE. The Pixel Size is the size of each pixel in micro-meters (µm). For the LISST-HOLO2 the pixel size is 4.4 µm. DO NOT CHANGE THIS VALUE. The wavelength is the wavelength of the laser in nm. For the LISST-HOLO2 the wavelength is 658 nm.
  • Page 17 Min Depth indicates where to start reconstructing images. A value of 0 mm will start reconstruction at the receiving window of the LISST-HOLO2. Max Depth indicates where to stop reconstruction. A value of 50mm will stop the reconstruction at the opposite window (transmit window) of the LISST-HOLO2.
  • Page 18 Now click the Raw Holograms button in order to select the path from where Holo Batch will read your raw holograms. Select the folder where your raw holograms are stored and click LISST-Holo2 User’s Guide...
  • Page 19 ‘Raw Holograms’ will open in a browser window, you can now select which holograms you would like to process. If you would like to process all of the holograms in the directory, you can ignore this button. LISST-Holo2 User’s Guide...
  • Page 20 Click the Process button to process the selected holograms. One of the two screens on the left will appear, depending on if you chose to show data visualization or not. Press the ‘Go’ Button to start the processing. LISST-Holo2 User’s Guide...
  • Page 21 You will notice that several files have been created for each hologram. The exact number of files created depends on what you have selected for output options. These files are briefly described in the following sections. LISST-Holo2 User’s Guide...
  • Page 22 The table below shows the parameters in columns 1-75 of the .CSV file. Column # Value Unit Year (YYYY) Month (MM) Day (DD) Hour (HH) Minute (MM) Second (SS) 1/100s of a second (hhh) NOTE: Currently not available. NaN (Not a Number) displayed instead. LISST-Holo2 User’s Guide...
  • Page 23 Equivalent Convex Area Diameter μm Particle Volume The Convex Area is the area, based on pixel count, of all pixels within the convex hull of the particle. The convex hull is the smallest polygon that can contain the particle. LISST-Holo2 User’s Guide...
  • Page 24 If you selected to save particle vignettes, a small .tiff image of each particle will be saved in the reconstructed images folder. The Centroid X, Y locations specify where the particle is located. Together with the Focus Depth, these 3 numbers locate the particle in the 3-D space of the laser beam. LISST-Holo2 User’s Guide...

  • Page 25: Holo Detail - Processing Of Individual Holograms

    ‘Example Holograms’ folder located on the ship disk. Select a hologram from the list on left. The selected hologram will then be displayed. Only one hologram at the time can be selected, displayed, and processed in Holo Detail. LISST-Holo2 User’s Guide...
  • Page 26 The ROI box will appear as a blue square overlaid on the hologram. The ROI can be moved to another location by moving the mouse over the ROI, selecting it, and then moving it around to the desired location within the hologram. LISST-Holo2 User’s Guide...
  • Page 27 . The Z axis (the focus depth) is displayed above the reconstructed image. Clean Stack Slider The Clean Stack slider is used to reduce noise in the image. The slider can be moved from left to right to help remove background noise in the images. Improfile Button LISST-Holo2 User’s Guide...
  • Page 28 Click the Reset button to zoom out again. Grid Button The grid button draws a grid onto the slice. This makes it easier to determine the size of the particles in the slice. Click the grid button again to turn off the grid. LISST-Holo2 User’s Guide...

  • Page 29: Holo Detail - Sorting Holograms Based On Depth Or Content

    Holo Batch. Sequoia Scientific has develped a method to quickly estimate the particle density in a hologram. We call this metric, the Hologram Content Rating (HCR).
  • Page 30 ‘Save Selected Holograms’ button. This will copy the selected holograms from the current directory, to a new specified folder. This can usual to further subdivide a group of holograms based on timestamp, depth, or content ration. LISST-Holo2 User’s Guide...

  • Page 31: Lisst-Holo2 Field Deployment

    LISST-Holo2 endcap. Use only the battery charger supplied by Sequoia Scientific. The endcap of the LISST-Holo2 has a vent that must be open for the batteries to charge. The vent is the white plastic tab on the LISST-Holo2 endcap. Unscrew the vent until the red O-ring is clearly visible, as shown on the left.
  • Page 32 After connecting the Battery Charger to the LISST-Holo2 and connecting to AC power the charger will initialize and evaluate the battery before charging will being. This takes about 5 to 10 seconds. During this time, the LED will be a mix of red and green before turning to either solid red or green.

  • Page 33: Programming

    1 position. If it is past the specified time the sampling will start immediately if the magnetic switch is in the 1 position. Be sure to check the homepage to make sure your LISST-HOLO2 has the correct GMT time.
  • Page 34 All four sets of start and stop conditions can be individually programmed. Selecting the start/stop program using the When the four Start and Stop conditions have been programmed, you must select which program you want to use by selecting the appropriate radio button and clicking apply. LISST-Holo2 User’s Guide...

  • Page 35: Wake Up / Power Up Lisst-Holo2

    1 position and then quickly back to the 0 position. This will wake up the HOLO2 instrument. The LISST-HOLO2 will boot up and be ready in 40 to 60 seconds. When the green LED is flashing every few seconds the instrument is awake and ready to start sampling.
  • Page 36 Filezilla will connect to the LISST-HOLO2 and display the images folder in the bottom right window. To the left is the destination folder selection. Navigate to the desired destination folder. In this example, we will offload to a folder on the C drive called HOLO-Offload.

  • Page 37: Viewing Raw Holograms In Openseeit

    To DELETE the holograms, right click on the selected holograms on the images drive on the LISST-HOLO2 and select Delete. You will be asked to confirm the deletion. The holograms are then deleted from the internal drive on the LISST-HOLO2.
  • Page 38 The hologram on the left will not process well, because there are no visible interference patterns (concentric rings). This is due to the particle concentration being too high. LISST-Holo2 User’s Guide...

  • Page 39: Next Deployment Or Powering Down

    Moving the Switch Lever to the ‘1’ position will start the current sampling program. For short term or long term storage of the LISST-Holo2 it should be put into Sleep mode. The instrument will automatically go into lower power sleep mode after 10 minutes of inactivity if the automatic sleep has not been disabled on the Tools page.

  • Page 40: Reviewing Instrument Info And Other Settings

    Select program The Select Program buttons lets the user select which program should control the LISST-HOLO2 sampling. Up to 4 programs can be loaded in the LISST-HOLO2.

  • Page 41: Log Page

    5.7. 6.4 Log page The LISST-Holo2 writes information to a file as it is operating. This file contains information that can be helpful in troubleshooting problems and it can be sent to Sequoia for evaluation. The Log option of the main menu allows the user view the contents of the log file.
  • Page 42 Remember to click the Apply button. Sleep or reboot Click the Sleep button to put the LISST-HOLO2 to sleep. When the LISST-Holo2 goes to sleep you will lose connection with the instrument. Click the Reboot button to reboot the LISST-HOLO2. If you reboot you must re-enter the LISST- HOLO2 IP address in your browser window to re-establish communication.
  • Page 43 IP address in your browser to continue working with the LISST-HOLO2. Delete all images Click the Delete button to delete all files on the internal hard drive of the LISST-HOLO2. You will be asked to confirm. If you confirm, deletion will begin immediately, and takes only a few seconds.

  • Page 44: About Page

    The top of the About page contains information about the hardware and firmware loaded in the instrument, as well as the serial number of the instrument. Below this section are a few FAQ’s, as well as links to the free OpenSeeIt and Filezilla software. LISST-Holo2 User’s Guide...

  • Page 45: Handling, Cleaning, Maintenance And Storage

    Handling, Cleaning, Maintenance and Storage 7.1 Handling When handling the instrument, please remember that the LISST-HOLO2 is a high-precision optical instrument. Avoid mechanical shocks and impact to the housing, as this may cause misalignment of the optical parts. The instrument pressure housing should not be opened.

  • Page 46: Ethernet Communications

    A static IP address is required for access to the LISST-HOLO2 via a network. If you are able to simply plug in your LISST-HOLO2 to your local network, all you have to do is enter the IP address of the LISST-HOLO2 (http://192.168.0.150/).

  • Page 47: Changing The Lisst-Holo2 Ip Address

    IP address in the Router Information box is set to the desired value 8.3 Changing the LISST-HOLO2 IP address To change the IP address of the LISST-HOLO2 use the web interface. Connect as described in section 3.2 and go to the Tools page of the LISST-HOLO2 web interface.
  • Page 48 Once connected and the LISST-Holo2 is fully booted, press the enter key several times. You should see a response similar to the one on the left. The ‘error’ messages displayed in the terminal are normal and should be ignored. The IP address will be listed before the login prompt.

  • Page 49: Faqs

    Toggling the switch When the internal batteries are very low on charge, too low even to boot up, the LISST-Holo2 will go didn’t work. Why not? into deep sleep. To wake from deep sleep, you must apply external power, either from the battery What now? charger (through the 6-pin connector) or the separate power supply (through the 5-pin).
  • Page 50 LISST-Holo2. Instructions for that are beyond the scope of this manual. What is the maximum The concentration limits for a LISST-Holo2 are roughly as tabulated in the table below. See also this article on Sequoia’s website: concentration that the http://www.sequoiasci.com/article/what-are-the-concentration-limits-for-...

  • Page 51: Endcap Led Status Light Indicators

    10 Endcap LED Status Light Indicators The LISST-Holo2 connector end cap has a red-green-blue LED that indicates its state and activity. LED state What the LISST-Holo2 is doing Dark System is asleep YELLOW (green and red mixed) System is booting up. This typically takes 40 to 60 seconds.

  • Page 52: Technical Specifications

    11 Technical Specifications LISST-Holo2 with internal NiMH battery Instrument stands Large Clear box with battery charger, power supplies and power/communication cable Small Clear Box with Test chamber, cleaning supplies and Clamps Box with Manual, USB memory card with software, wireless router and Ethernet cables 11.1 General Features...

  • Page 53: Dimension Drawing

    RS232 output, 115.2 kbaud, 8 bit, no parity* MALE FACE VIEW RS232 input* * The communications cable supplied with the LISST-Holo2 converts the RS232 signals to USB. The USB/RS232 port is used only for troubleshooting, not for routine operation. LISST-Holo2 User’s Guide...

  • Page 54: 6-Pin Bulkhead Connector Pin Assignments

    11.8 6-Pin Bulkhead Connector Pin Assignments Function Teledyne Impulse part MBCH(WB)-6-MP SS Power Ground Battery Charge Input Digital Output, active low Digital Input, active high Digital Common MALE FACE VIEW No Connection LISST-Holo2 User’s Guide...

  • Page 55: Warranty

    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.
  • Page 56 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 limited 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.

  • Page 57: Index

    ROI (Region Of Interest) ......15 installation ..........12 HOLO_Detail ............ 25 Tools page ..........11, 41 Hologram ............49 URL ..............10 details ............41 Warranty............55 download from internal drive ... 35, 41 Weight .............. 52 LISST-Holo2 User’s Guide...

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