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LISST-

HOLO User’s Guide

21

4

Hologram Processing with HOLO_Batch and HOLO_Detail

4.1 Intro

The holograms are processed using two MATLAB-based programs called HOLO_Detail and
HOLO_Batch.

You do not need to be connected to the LISST-HOLO in this chapter.

4.2 Install the hologram
processing software

To install the software, insert the CD into your computer, and locate the
LISST-HOLO software folder. Or visit

www.sequoiasci.com

and download the

software package from the LISST-Holo page. Inside the software package (or
listed on the website) there are 3 folders; one with software for 32-bit
Windows, one for 64-bit Windows, and one for Mac OS X. You must select the
software that matches your machine.

Inside the folder you will see two folders and one application. The folders
contain the Holo Batch and Holo Detail applications. However, before these
programs can be run, Matlab Compiler Runtime (MCR) must be installed. The
installer for the MCR should be included in the software package and have a
name such as ‘MCR_R2014a_win64_installer.exe’.

Double click the MCR installer. It will start by extracting files, which may take
several minutes. (Note that the installation may appear slightly different on
Mac OS X)

Once files are done extracting, the installer will open, click next to proceed.

Accept the License agreement and click next.

The installer will chose a default location to install the MCR. Either accept the
default location or enter the location where you would like the program to be
installed.

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Содержание LISST-HOLO

Страница 1: ...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 LISST HOLO User s Guide Version 3 0 December 2014...

Страница 2: ......

Страница 3: ...ocal 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 correspo...

Страница 4: ......

Страница 5: ...Waste Electrical and Electronic Equipment Smaltimento di apparecchiature elettriche ed elettroniche da rottamare...

Страница 6: ......

Страница 7: ...Summary of files created by HOLO_Batch 34 4 5 HOLO_Detail processing of individual holograms 36 Select Button 36 Advanced Settings 36 Set ROI Regen Kernel and Reconstruct Buttons 37 Clean Stack Slider...

Страница 8: ...xposure 54 Command to subsystem 54 Watchdog shutdown 54 Motherboard log 54 6 7 About page 54 7 Handling Cleaning Maintenance and Storage 56 7 1 Handling 56 7 2 Cleaning 56 7 3 Maintenance 56 7 4 Stora...

Страница 9: ...ISST HOLO was shipped to you in a Pelican case with custom foam padding Included in the shipping box are the LISST HOLO clamps stands External Memory Module with USB cable Ethernet cable Wireless Rout...

Страница 10: ...10 LISST HOLO User s Guide...

Страница 11: ...processing yields in focus particle images and volume distribution Automated firmware updates possible when instrument is connected to the Internet 2 2 Parameters Measured and Derived Particle images...

Страница 12: ...500 A max at 12 VDC input Current consumption laser on 0 6 00 A max at 12VDC input Current consumption laser and camera on 0 880 A max at 12 VDC input NOTE Upon power up the current draw may briefly...

Страница 13: ...l out 19 2K 8 bit no parity 5 RS232 EIA level in Six pin Auxiliary Connector Teledyne Impulse part MCBH WB 6 MP SS Pin Function 1 Ground 2 Digital Output 1 3 Digital Output 2 4 Digital Output 3 5 Digi...

Страница 14: ...14 LISST HOLO User s Guide...

Страница 15: ...data from the LISST HOLO you need a PC with a web browser and access to a power source Take out the instrument stands and place the LISST HOLO on the stands Take out the clear plastic box and open it...

Страница 16: ...r and communicate with the LISST HOLO No power is supplied through the yellow Ethernet cable only communication Connect the yellow Ethernet cable to the wireless router DO NOT use the port to the far...

Страница 17: ...The LISST HOLO will boot up The endcap LED will flash yellow for approximately 30 seconds When it is ready the LED will blink green every 5 seconds See section 10 for more information about the LED c...

Страница 18: ...Images page where all holograms on board the memory card are listed Click the hologram you wish to view You will be asked if you want to save it to disk or to view it Select the Save option so that y...

Страница 19: ...test chamber that can be installed between the windows and be filled with water for testing To install the chamber remove the U shaped spacer and press the sliding part into the chamber leaving a sma...

Страница 20: ...20 LISST HOLO User s Guide...

Страница 21: ...st select the software that matches your machine Inside the folder you will see two folders and one application The folders contain the Holo Batch and Holo Detail applications However before these pro...

Страница 22: ...reate a shortcut of the batch and detail applications and place them on the desktop Should you like to add the program to the taskbar or start menu you can right click on the program icon and select P...

Страница 23: ...truction Parameters Select Output Options Select Particle Bin Size Select Paths Folders Select Files The HOLO_Batch is shipped with factory default settings for the Reconstruction Parameters and these...

Страница 24: ...osen Particle counts will then be obtained from both ROIs and adjusted so that particles in the overlapping parts are only counted once If you click the Add button a 3 rd ROI will be added which you c...

Страница 25: ...ue in order to properly reconstruct the holograms DO NOT CHANGE THIS VALUE The Index of Refraction is for the medium in which the LISST HOLO is being used An average value for water is 1 333 If the LI...

Страница 26: ...hologram reconstruction an image containing both in focus and out of focus particles is created at every step Check Save reconstructed slices if all slices are to be saved Save Dep Mon Images saves d...

Страница 27: ...bins to 8000 m see section 11 for details Select the LISST 100X equivalent size bins desired for your output size distributions Next select Performance Options The default selection is for Speed Memor...

Страница 28: ...your raw holograms are stored and click OK Now click to select the folder where you want the reconstructed images to be stored This is where reconstructed and Dep Mon images will be stored If these op...

Страница 29: ...MAT files this is where they will be stored If you would like to process a subset of holograms in the directory you can press Select Holograms to Process The directory you have selected for Raw Hologr...

Страница 30: ...nd files which will be averaged into one background file before subtracting It is not necessary to supply a background hologram in order to process your holograms if you do not select a background non...

Страница 31: ...o exit If the data visualization option is selected the plots shown at the left will be updated after each hologram is processed A status bar will be also be displayed at the bottom of the screen show...

Страница 32: ...it window blue particles very close to the receive window Using a pair of 3 D glasses will display the particles in a 3 D effect where the red particles will appear closer to the viewer than the blue...

Страница 33: ...ructure called PartStats It has dimensions N 17 where N is the number of particles detected in the ROI The 10 columns have the following information about each particle Column Particle Property Unit 1...

Страница 34: ...cus and out of focus particles that appear on that particular slice The distance from the transmit window of each slice is given in the image filename For example the image on the left is 016 0270 z22...

Страница 35: ...ribution and other output as described in the section above filename znnn jpg Reconstructed slices of the hologram nnn indicates the slice number filename pstat mat MATLAB MAT file with N x 17 structu...

Страница 36: ...Click the Select Path button to select a folder for browsing your holograms Select the folder where your holograms are stored then click OK From the drop down menu select a hologram to display The sel...

Страница 37: ...or in any other substance with a different index of refraction The Offset Pixel Size and Wavelength should not be adjusted Set ROI and Reconstruct Buttons Select the size of the ROI using the radio b...

Страница 38: ...construct button to initiate the reconstruction process Upon reconstruction the individual slices can be viewed on the right by clicking on the left and right arrows The X Y and Z axes of the reconstr...

Страница 39: ...double click to mark the end of the transect a figure similar to the one on the left will pop up showing the pixel intensities along the selected transect Zoom and Reset Buttons Clicking the zoom but...

Страница 40: ...e the mouse button the length of the line will be displayed in microns 4 6 LISST HOLO User s Community Dr Alex Nimmo Smith of University of Plymouth hosts a user s community website for holographic im...

Страница 41: ...op the data collection as well as how to offload hologram from the EMM and the internal drive 5 2 Programming To configure the Start and Stop conditions you must connect to the instrument using the Et...

Страница 42: ...at a frequency of up to 0 2 Hz 5 second interval The Burst Mode can be used to take a burst of holograms at a fixed time interval between the start of each burst The maximum sample rate is 0 2 Hz 5 se...

Страница 43: ...step is to put the instrument into low power sleep mode so that we can disconnect the Ethernet cable and install the EMM In order for the EMM to be recognized it must be in place before power is appli...

Страница 44: ...n the 0 position when sampling is complete 5 7 Downloading Raw Holograms The raw holograms are saved to the External Memory Module if it is installed Otherwise the holograms are stored on the internal...

Страница 45: ...splay 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...

Страница 46: ...ave been selected Now drag the selected holograms straight across to the destination folder window on the left side of the screen The selected holograms will then transfer to the destination folder To...

Страница 47: ...ser mode Otherwise follow the instructions below Open up OpenSeeIt and select Browser Mode from the View Menu Navigate to the folder where your holograms are stored They will all be displayed in the b...

Страница 48: ...able and establish communication with the instrument unless the setting for the Start and Stop conditions needs to be changed If the instrument is not going to be redeployed it can be powered down If...

Страница 49: ...ature and depth endcap switch position and the state of the two digital inputs Select program The Select Program buttons lets the user select which program should control the LISST HOLO sampling Up to...

Страница 50: ...lick on the Details button The Details Button then opens up a 2 nd window showing the details Click the Delete button to delete a hologram You can only delete one hologram at the time using the Delete...

Страница 51: ...lick the Take images button You can take up to 20 holograms by selecting the number using the drop down menu If you enter a comment it will display when reviewing the image details see section 6 3 The...

Страница 52: ...er profile check box is checked as in the example above the instrument will not go to sleep between samples Use this setting if the instrument is connected to shore power or to the external power supp...

Страница 53: ...pply when you have changed it but make sure that it is correct The changes will take effect immediately so you will need to enter the new IP address in your browser to continue working with the LISST...

Страница 54: ...st without first consulting Sequoia support Manual exposure Do not use without first consulting Sequoia support Command to subsystem Do not use without first consulting Sequoia support Watchdog shutdo...

Страница 55: ...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...

Страница 56: ...tical windows Dip a finger in the soapy solution and gently rub the windows Rinse several times with clean particle free water The connectors and cables should be lubricated with 3M Silicone Spray or...

Страница 57: ...LISST HOLO User s Guide 57...

Страница 58: ...st still connect the LISST HOLO to the router Then turn the router on and have your computer search for the SSID which is LISST Holo When you have connected to the router you need to enter the WAP PSK...

Страница 59: ...h command line and press Enter You should see the black DOS prompt window 9 Type ipconfig release and press Enter 10 Type ipconfig renew and press Enter 11 The IP address has now been updated from 192...

Страница 60: ...iately so you will need to enter the new IP address in your browser to continue working with the LISST HOLO New LISST HOLO IP address Date New LISST HOLO IP address Date New LISST HOLO IP address Date...

Страница 61: ...etwork or the Internet but it can be useful when needed How do I connect the LISST HOLO to the Internet The LISST HOLO comes configured with a pre selected IP address netmask gateway DNS 1 and DNS 2 T...

Страница 62: ...oncentric rings the concentration is too high and you most likely won t get any sensible data out of the hologram when processing it Why can I choose between spherical and random size ranges in HOLO_B...

Страница 63: ...the Linux system and motherboard x red flashes 2 second pause repeat Fatal error Record number of red flashes and contact Sequoia for troubleshooting and or possible repair of the instrument 0 5 seco...

Страница 64: ...64 LISST HOLO User s Guide...

Страница 65: ...05 1 89 3 48 4 11 3 78 4 2 05 2 42 2 23 4 11 4 85 4 46 5 2 42 2 86 2 63 4 85 5 72 5 27 6 2 86 3 38 3 11 5 72 6 75 6 21 7 3 38 3 98 3 67 6 75 7 97 7 33 8 3 98 4 70 4 33 7 97 9 40 8 65 9 4 70 5 55 5 11...

Страница 66: ...1109 1021 1880 2219 2043 42 1109 1309 1205 2219 2618 2410 43 1309 1545 1422 2618 3090 2844 44 1545 1823 1678 3090 3646 3357 45 1823 2151 1980 3646 4303 3961 46 2151 2539 2337 4303 5078 4674 47 2539 2...

Страница 67: ...1 64 1 94 1 79 3 13 3 69 3 40 5 1 94 2 29 2 11 3 69 4 35 4 01 6 2 29 2 70 2 49 4 35 5 14 4 73 7 2 70 3 19 2 93 5 14 6 06 5 58 8 3 19 3 76 3 46 6 06 7 15 6 59 9 3 76 4 44 4 09 7 15 8 44 7 77 10 4 44 5...

Страница 68: ...1689 1555 42 888 1047 964 1689 1993 1835 43 1047 1236 1138 1993 2352 2165 44 1236 1458 1343 2352 2775 2555 45 1458 1721 1584 2775 3275 3014 46 1721 2031 1870 3275 3865 3558 47 2031 2397 2206 3865 456...

Страница 69: ...hutter minimum value 36 37 Camera shutter maximum value 38 39 Camera gain 40 41 Camera gain minimum value 42 43 Camera gain maximum value 44 115 Not used 116 119 Depth coefficient DepthA Floating poin...

Страница 70: ...70 LISST HOLO User s Guide...

Страница 71: ...prompt written notice of the claim SEQUOIA has exclusive control over the defense and settlement of the claim Customer provides such assistance as SEQUOIA may request in connection with the defense an...

Страница 72: ...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 intellec...

Страница 73: ...gion Of Interest 24 HOLO_Detail 36 Hologram 61 details 50 download from EMM 44 download from internal drive 44 50 enter comment 51 file name 51 PGM file structure 69 processing 22 processing time 61 v...

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