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User`s Manual (December 2014)

1. 21 4 1 igi or seat 21 4 2 Install the hologram processing software 21 4 3 Process holograms using HOLO Batch and HOLO Detail 22 4 4 HOLO Batch automated batch processing of multiple holograms 23 TIFF files output DY HOLO Batch EEEEE EE 32 CSV files output DY HOLO BaiCh iii i 32 IMAT e eg DY HOLO BUC E 33 oT ies ee e Ee 34 Summary of files created by HOLO_ Patch 35 4 5 HOLO Detail processing of individual holograms 36 EE MR 36 Advanced SENO m P 36 Set ROI Regen Kernel and Reconstruct Buttons esses isse senses nane nnns a nas 37 Glean Slack SHO E 37 IMOS Ee 39 Zoom and Reset ButtonS iii 39 Cz METRE 39 Save Image I E I 40 Measure BUON sscsspsiriesr iit renisde rror RELI E EERE ESPERES TREINA EErEE IES EER EEEO EREEREER EEEE CRISES 40 4 6 LISST HOLO User s Community 40 5 EISST Holo Field Deployment ian 41 5 1 MOUE ON E 41 5 2 reiege le e Pe MEET 41 Selecting the start stop program using the PC iii 43 5 3 Preparing for Deplovment ii 43 with the EMM mstailed 43 without the EMM mstailed iii 43 5 4 Wake up power up LISST HOLO i 44 5 5 Stant Data CONC CHOI RR O RR A 44 5 6 Stop RER s MR P 44 5 7
2. l MATLAB Packaging x Filename Filesize Filetype Last modified Note that the destination directory window is empty COTTO III I III Empty directory Wa 21660150 Seite v VN Tr Focus on the directory listing in the bottom right reat aoe ee es Quocerrect window 4 WM Queve empty gg LISST HOLO User s Guide 45 Filename images Filename 011 0216 pgm 011 0217 pgm 011 0218 pgm 011 0219 pgm 011 0220 pgm e 011 0221 pgm 011 0222 pgm Filename 011 0216 pgm 011 0217 pgm Filesize 1 922 065 1 922 065 Filesize File folder Filesize Filetype PGM File PGM File PGM File PGM File PGM File PGM File PGM File 1 922 065 1 922 065 1 922 065 1 922 065 1 922 065 1 922 065 1 922 065 Filetype PGM File PGM File Last modified 10 26 2011 10 49 00 PM Last modified 10 21 2011 1 36 00 PM 10 21 2011 1 36 00 PM 10 21 2011 1 36 00 PM 10 21 2011 1 37 00 PM 10 21 2011 1 37 00 PM 10 26 2011 3 26 00 PM 10 26 2011 3 26 00 PM Last modified 10 21 2011 1 36 00 PM 10 21 2011 1 36 00 PM Permissions Permissions Permissions IW TW TW rW TW rw Owner Gro Owner Gro 00 00 00 00 00 00 00 Owner Gro Double click the folder called images The holograms on the internal drive are now displayed Select the holograms you wish to offload or delete Use the SHIFT key to select a range of holograms Us
3. 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 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 LISST HOLO User s Guide 71 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 at
4. Address C C Documents and Settingsiole mikkelseniDesktop LISST HOLO data Name Type kj 7osetransmission csv Microsoft Office Exc 70 transmission mat MATLAB Data PGM Fie IPG File PG File File and Folder Tasks A QJ Make a new folder 70 transmission pgm Publish this folder to the Web i 70 transmission dep ipg I 70 transmission mon ipg Eg s0 transmission csv A 80 transmission mat a 20 transmission pgm leor ansmission dep jpg Gh s0 transmission mon ipg KN Share this folder Microsoft Office Exc MATLAB Data PGM Fie PG File IPG File Microsoft Office Exc MATLAB Data PGM File 3G File IPG File PGM Pie ig 90 transmission csy 90 transmission mat 90 transmission pgm Ki sosttransmission dep jpg la 90 transmission mon ipg la Coffee pom Date Modified 10 28 2010 10 26 AM 10 28 2010 10 26 AM 7 9 2010 1 51 PM 10 28 2010 10 26 AM 10 28 2010 10 26 AM 10 28 2010 10 26 AM 10 28 2010 10 26 AM 7 9 2010 1 51 PM 10 28 2010 10 26 AM 10 28 2010 10 26 AM 10 28 2010 10 25 AM 10 28 2010 10 25 AM 7 9 2010 1 51 PM 10 28 2010 10 25 AM 10 28 2010 10 25 AM 7 9 2010 9 56 AM v Ed Go Processing updates will be printed to the text box in the processing window Processing times per hologram vary greatly The time depends on the size and number of ROls the reconstruction step size selected outputs performance option selection number of particles and computer ha
5. In this example 2 overlapping ROPs with a size of 1024x1024 pixels are chosen Particle counts will then be obtained from both ROls and adjusted so that particles in the overlapping parts are only counted once If you click the Add button a 3 ROI will be added which you can then drag to the desired location If you click the Delete button the last added ROI will be deleted The Image Size parameter should not be adjusted unless the images have been cropped from their original size Reconstruction of holograms is memory demanding so on PC s with smaller memory 4GB or slower processors lt 2GHz the 512x512 pixels ROI should be selected Note that you can delete and add ROPs using the Delete and Add buttons In this example to the left one of the 1024x1024 pixel ROI s have been deleted Subsequently the Delete button has been grayed out HOLO Batch Processing ROI Editing 1600 ROI Size 512x512 1024x1024 Image Size E HOLO Batch advanced HOLO Batch Advanced Parameters Offset mm 28 Pixel Size um 44 Wavelength nm 658 Index of Refraction Minimum Threshold Clean Stack Ge Scale Length um Minimum Particle Area pix DK Cancel In this example another 1024x1024 ROI has been added Note that the ROls do not have to be aligned with each other Click the OK button when the ROI size and location is satisfying Note that the processing time doubles every time yo
6. 1 36 00 PM 1021 2011 1 37 00 PM r 21 2011 1 37 00 PM IW rW rw 26 2011 3 26 00 PM rw nw rw 26 2011 3 26 00 PM 26 2011 3 40 00 PM Create directory 012 0001 pgm Refresh 26 2011 3 40 00 PM 4012 0002pgm 26 2011 3 40 00 PM 012 0003 pgm E 3 40 00 PM 1012 0004 pgm Renare 6 2011 3 40 00 PM 012 0005 pgm 26 2011 3 41 00 PM 012 0006 pgm 26 2011 3 41 00 PM 1 922 065 1 922 065 1 922 065 1072 NES FPW IW rW rw rw rw e d e d A e DO 00 00 VW DA DA 0 00 00 00 00 00 00 00 IW TW TW TW TW rw TW TW rW TW TW rW TW TW rw TW TW rw Copy URL s to clipboard File permissions IW TW rW rW TW rw Confirmation needed You will be asked to confirm the deletion gg o Really delete 5 files The holograms are then deleted from the internal drive on the LISST HOLO WHEN THE HOLOGRAMS HAVE BEEN DELETED THEY CANNOT BE RECOVERED 46 LISST HOLO User s Guide 5 8 Viewing raw holograms in OpenSeelt To quickly view the raw holograms use the Browser mode of the OpenSeelt software If you have set OpenSeelt to be used for all PGM files you can simply double click on one of the holograms in order to see it in OpenSeeit If you press lt Enter gt within OpenSeelt when a hologram is displaying the View mode changes to Browser mode Otherwise follow the instructions below fa OpenSeelt v0 47 164 File Edit Options Slideshow Filte
7. 16 12 0 14 1 13 0 22 8 26 9 24 8 17 14 1 16 7 15 4 26 9 31 8 29 2 18 16 7 19 7 18 1 31 8 37 5 34 5 19 19 7 232 21 4 37 5 44 2 40 7 20 23 2 27 4 25 2 44 2 52 2 48 0 21 27 4 32 4 29 8 52 2 61 6 56 7 22 32 4 38 2 35 2 61 6 72 7 66 9 23 38 2 45 1 41 5 72 7 85 7 78 9 24 45 1 53 2 49 0 85 7 101 93 1 29 53 2 62 8 57 8 101 119 110 26 62 8 74 4 68 2 119 141 130 21 74 1 87 4 80 5 141 166 153 28 87 4 103 94 9 166 196 181 29 103 122 112 196 232 213 30 122 144 132 232 273 252 31 144 169 156 273 322 297 32 169 200 184 322 381 350 33 200 236 217 381 449 413 34 236 279 256 449 530 488 35 279 329 303 530 625 576 36 329 388 357 625 738 679 37 388 458 421 738 871 802 38 458 541 497 871 1028 946 LISST HOLO User s Guide 67 68 39 40 41 42 43 44 45 46 47 48 49 50 541 637 1952 888 1047 1236 1458 1721 2031 2397 2828 3338 LISST HOLO User s Guide 637 752 888 1047 1236 1458 1721 2031 2397 2828 3338 3939 587 692 817 964 1138 1343 1584 1870 2206 2604 3073 3626 1028 1213 1431 1689 1993 2352 2775 3275 3865 4561 0382 6351 1213 1431 1689 1993 2352 2775 3275 3865 4561 0382 6351 7495 1116 1317 1555 1835 2165 25995 3014 3558 4198 4954 5846 6899 12 Hologram PGM File Format Structure The holograms stored on the flash drive are saved in PGM format and are composed of two parts The first block of bytes in a hologram is the standard PGM format as follows P5 If 1600 1
8. C Lower Upper Median Lower Upper Median 125 1 48 1 36 2 50 2 95 2 72 1 48 1 74 1 60 2 95 3 48 3 20 1 74 2 05 1 89 3 48 4 11 3 78 2 05 2 42 2 23 4 11 4 85 4 46 2 42 2 86 2 63 4 85 572 5 27 2 86 3 38 3 11 5 72 6 75 6 21 3 38 3 98 3 67 6 75 7 97 7 30 3 98 4 70 4 33 7 97 9 40 8 65 4 70 5 09 5 11 9 40 11 1 10 2 5 55 6 55 6 03 11 1 13 1 12 1 6 55 7 72 7 11 13 1 15 4 14 2 7 72 9 12 8 39 15 4 18 2 16 8 9 12 10 8 9 90 18 2 21 5 19 8 10 8 12 7 11 7 21 5 25 4 23 4 12 7 15 0 13 8 25 4 30 0 27 6 15 0 17 7 16 3 30 0 35 4 32 5 Rei 20 9 19 2 35 4 41 7 38 4 20 9 24 6 22 7 41 7 49 2 45 3 24 6 29 1 26 7 49 2 58 1 23 0 29 1 34 3 31 6 58 1 68 6 63 1 34 3 40 5 37 2 68 6 80 9 74 5 40 5 47 7 43 9 80 9 95 5 87 9 47 7 56 3 51 9 95 5 113 104 56 3 66 5 61 2 113 133 122 66 5 78 4 72 2 133 157 144 78 4 92 6 85 2 157 185 170 92 6 109 101 185 218 201 109 129 119 218 258 237 129 152 140 258 304 280 152 180 165 304 359 331 180 212 195 359 424 390 212 250 230 424 500 460 250 295 272 500 590 543 295 348 320 590 696 641 348 411 378 696 822 756 411 485 446 822 970 893 485 572 527 970 1144 1053 LISST HOLO User s Guide 65 66 38 39 40 41 42 43 44 45 46 47 48 49 50 572 675 197 940 1109 1309 1545 1823 2151 2539 2996 3536 4172 LISST HOLO User s Guide 675 197 940 1109 1309 1545 1823 2151 2539 2996 3536 4172 4923 621 133 865 1021 1205 1422 1678 1980 2337 2151 3255 3841 4533 1144 1350 1593 1880 22
9. C Save particle statistics CSV Save generated background 7 Show data visualization Paths gt LISST 100X type B LISST 100X type C 5 LISST 100X RANDOM type B 5 LISST 100X RANDOM type C Performance Options Speed Memory Speed Memory Files 30 Select Holograms to Process Select Background File s DI HOLO_Batch Processing SEQUOIA Equivakot Spherical Diameter wm HOLO_Bati MOLO Batch Press GO to bagin MOLO Sarca recti Frate 22 7 beg Temperature C Partides Per Image z gt gt Depth nm LISST HOLO User s Guide If you have a hologram obtained in clean water or air that you would like to subtract from the holograms select it here Selecting a background hologram can reduce the noise in the composite output image You can select multiple background 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 none will be subtracted All selections are now complete 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 HOLO
10. Take another 1 2 holograms with other types of material in the laser beam e g a screw or blow some dust through the laser beam when the hologram is captured The LISST HOLO comes with a 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 small gap Center the openings of the chamber on the windows and insert the U shaped spacer so that the O rings seal on the area around the window To put the LISST HOLO to sleep click the Home button then click the Sleep button If the Sleep button is not present at 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 You can now safely disconnect the power to the LISST HOLO To continue Getting Started with the LISST HOLO please read Section 4 Hologram Processing with Holo Batch and Holo Detail or skip to Section 5 LISST HOLO Field Deployment LISST HOLO User s Guide 19 20 LISST HOLO User s Guide 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 IBE I DIC p DEI en DN A HIEN Detal d DI wor te venei met Ls Extracti
11. The instrument should be disconnected from power when not in use 56 LISST HOLO User s Guide LISST HOLO User s Guide 57 8 Ethernet Communicati 8 1 Router Use A static IP address is required for acc ons ess to the LISST HOLO via a network If you are able to simply plug in your LISST HOLO to your local network all you have to do is enter the IP address of the LISST HOLO http 192 168 0 150 However the LISST HOLO may conflict with the user s or user s administrator security settings thereby preventing direct connection to the LISST HOLO via the local network In that case a router is required to communicate with the LISST HOLO Connecting to the router via your network Connecting to the router wirelessly Updating LISST HOLO software via the Internet The LISST HOLO comes with a Linksys E1000 router that has been programmed to communicate with the LISST HOLO Plug your computer s Ethernet port and the LISST HOLO into any of the numbered ports on the E1000 router Turn on the router then power up the LISST HOLO and open up a web browser Then initiate communication with the LISST HOLO as described in section 3 2 You may also use a wireless connection to communicate with the router You must 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 password whic
12. as a particle Clean Stack is used to remove pixels that are less than a certain percentage of the maximum gray scale value Enter the percentage you would like to be remove here usually between 0 and 5 This can be useful for removing background noise The Scale Length is the length of the scale bar in um being added to the composite images created during processing The Minimum Particle Area is a measure used to exclude particles that could appear simply due to noise in the image The default minimum area is 9 meaning that unless a particle has a minimum area of at least 9 coherent pixels Equivalent Spherical Diameter of 15um it is being excluded from further consideration when computing size distribution etc Click OK when you are satisfied with your selections LISST HOLO User s Guide 25 Reconstruction Parameters If you wish you can change the Reconstruction Parameters Min Depth mm Min Depth indicates where to start reconstructing images A value of 0 Max Depth m mm will start reconstruction at the receiving window of the LISST HOLO a Max Depth indicates where to stop reconstruction A value of 50mm will Step Size 0 5 mm stop the reconstruction at the opposite window transmit window of the LISST HOLO Step Size determines how many millimeters apart the reconstructed images will be In the example to the left the entire sampling volume will be reconstructed 0 50mm at an
13. cable to 8 pin bulkhead connector 2 just above the serial number Note that the External Memory Module and the Ethernet cable share the 8 pin bulkhead connector The cables are now correctly connected to the LISST HOLO It is necessary to have BOTH cables connected in order to power 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 left Connect the router power cable to the router Plug the router power supply into a 110 220VAC power source When the router completes its booting procedure it can be located as LISST Holo ona wireless network The password for connecting to the router is manyholograms this information is also located on the bottom of the router Establish a Wi Fi connection between the router and your PC before you proceed If you do not have a Wi Fi enabled PC use the black Ethernet cable for connecting the router to the Ethernet port on your PC When you are connected to the router plug in the power to the DB 9 connector It is not necessary to have the DB 9 connector attached to the PC IMPORTANT MAKE SURE THAT THE POWER CABLE IS FIRMLY SEATED IN THE CONNECTOR EVEN MORE IMPORTANT NEVER UNPLUG THE POWER TO THE LISST HOLO WHILE IT IS RUNNING ALWAYS PUT THE INSTRUMENT TO SLEEP BEFORE UNPLUGGING POWER Make sure that the magnetic switch on the connect
14. for the Start Condition to occur before capturing holograms It will continue to capture holograms at the programmed rate until the stop condition is reached The holograms are stored either on an External Memory Module EMM if it is installed on the 8 pin connector on the endcap If the EMM is not installed holograms will be stored on the internal drive 82 GB of the LISST HOLO The EMM is pressure rated to the same depth as the LISST HOLO 300m Up to four different set of Start Stop and Sampling conditions can be pre programmed into the LISST HOLO The sections below describe in detail how to configure start and stop 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 Ethernet connection as described in Sections 3 2 and 3 3 indi ena Veboo Mal X IISST Holo Home x 4 0 1921680139 3 1 Pratt Q Clicking on the Home tab will show a summary of the four sets of sampling conditions Each of the four sets can be configured differently To set up a sENUOIA aS wal i sampling program click on the Program hyperlink h is in the 0 position and has been toggled 0 tines Sampling is paused Digital 1 0 Digital signal 27 0 Aux 5 0 Aux 6 0 Salacr program ar click om the program to adit Start condition 1 Selected The Start Condition Sampling
15. ib 54 Vd Lei ale alo SNO O WIN amen teers art ne ee Em 54 Momne ncadog a PT E 54 6 7 ADOUL PAGS iii 54 Handling Cleaning Maintenance and Storage eecceeeeeeeeeeees 56 7 1 will e DEE 56 7 2 CFLS las Merc Ec 56 7 9 Maintenance eee METTE 56 7 4 SOlI GE DRE 56 EthernetCommunications alla 58 8 1 misa ccm lai 58 Connecting to the router via your pehwork enne nnns nna annes sna nnns ssa a ananas nna 58 Connecting to the router wirelessly iii 58 Updating LISST HOLO software via the lnuternet esses esee 58 8 2 Changing the IP address of the Linksys E1000 routier 58 8 3 Changing the LISST HOLO IP address iii 59 FAOSGR RL telai 61 Enacap LED Status LightIndicators a ia 63 LISST HOLO Size e TEE 65 Size Ranges based on LISST 100X SPHERICAL particleS 65 Size Ranges based on LISST 100X RANDOMLY shaped particles 67 Hologram PGM File Format Structure 11 eee rei 69 rige M ES T1 1 Introduction Thank you for purchasing the LISST HOLO Submersible Digital Holographic Camera The intent with this introduction is to get you started using the LISST HOLO as quickly as possible Sequoia s goal with the LISST HOLO is to make the user interface so friendly that no manual would be required for normal operation except as a first time introduc
16. 19 2618 3090 3646 4303 5078 5992 7071 8344 1350 1593 1880 2219 2618 3090 3646 4303 5078 5992 7071 8344 9847 1243 1467 1731 2043 2410 2844 3357 3961 4674 5516 6509 7681 9065 11 2 Size Ranges The LISST HOLO outputs the size distribution in 50 size ranges logarithmically placed from 1 00 based on LISST 3939 microns in diameter type B or 1 90 7495 microns type C In both cases the upper size in 100X RANDOMLY each bin is 1 180 times the lower These size ranges are chosen so that they are similar to the two shaped particles different size ranges for the LISST 100X submersible particle size analyzer from Sequoia Scientific Inc in order to facilitate merging of data from the two instruments 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 bin for type B and C instruments Type B Type C Size bin Lower Upper Median Lower Upper Median 1 1 00 1 18 1 09 1 90 2 25 2 07 2 1 18 1 39 1 28 2 25 2 65 2 44 3 1 39 1 64 1 51 2 65 3 13 2 88 4 1 64 1 94 1 79 3 13 3 69 3 40 5 1 94 2 29 211 3 69 4 35 4 01 6 2 29 2 70 2 49 4 35 5 14 4 73 ie 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 TU 10 4 44 5 24 4 82 8 44 9 96 9 17 11 5 24 6 18 5 69 9 96 11 8 10 8 12 6 18 7 29 6 71 11 8 13 9 12 8 13 7 29 8 61 7 92 13 9 16 4 15 1 14 8 61 10 2 9 35 16 4 19 3 17 8 15 10 2 12 0 11 0 19 3 228 21 0
17. 200 255 lt lf gt plus 1600 x1200 bytes containing the hologram data The second block of has a size of 1024 bytes and follows immediately after the hologram data This block holds binary data as follows Bytes 0 7 8 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 115 116 119 120 123 124 127 128 131 132 135 136 139 140 143 144 147 148 151 152 155 156 159 160 163 164 167 168 171 172 173 174 181 182 1023 Description Seconds since epoch Time stamp indicating when image was obtained Unsigned long integer Pressure in counts Unsigned long integer Temperature in counts Battery power supply voltage in counts Exposure time in 600ns increments Laser power in counts Laser photo diode reading in counts Camera brightness Camera brightness minimum value Camera brightness maximum value Camera shutter Camera shutter minimum value Camera shutter maximum value Camera gain Camera gain minimum value Camera gain maximum value Not used Depth coefficient DepthA Floating point number Depth coefficient DepthB Floating point number Depth coefficient DepthC Floating point number Temperature coefficient TemperatureA Floating point number Temperature coefficient TemperatureB Floating point number Temperature coefficient TemperatureC Floating point number Temperature coefficient TemperatureSlope Floating point number Temperature co
18. Downloading Raw Holograms sccccccseeeceeceeeeeecaeeeeecaeeeeeaeeceeseeeeeesseeeesseeeesssageeesseneessnaeeees 44 Downibaaing TOM EMM P 44 Downloading and deleting from LISST HOLO internal drive EMM not installed 44 5 8 Viewing raw holograms in OpenSeelt i 47 5 9 Next Deployment or Powering Down 48 6 Reviewing Instrument Info and Other Settings eee cessere 49 6 1 Intro to Gier ent E 49 6 2 PROMO Oe e M 49 10 11 12 13 14 VICE RIE EEN 49 Eeer 49 FOGA AGRO IRON ii orli 49 6 3 E ESE RR A 49 6 4 LOO ster 50 6 5 OFAN US e Le 51 6 6 TOOS ACS P I T I LT tacit 51 COTTE COMO OS E N A AATA A E A tp 51 ELISE mp 51 IMAGE THE TAC mrt 51 SAINI conobbi lia 51 Stelle CS INAINCNANGCE DELE 52 LEE EE 52 POWO OTOIO o e LE 52 EE ee 52 Seme ZONE PE 52 EE 52 Change external trigger polarity EE 52 Hestore der l valo 2c ee E alle dii ALIM E 52 SUDIMIIOO ee UE 53 Generale OO TC lo OS es ai de eee naa 53 GHECK TOF UDO ACS acts varias alia ae 53 NetWork parare 53 Ee T M 53 PDS OV eis Se H 54 Camera brightness gain shutter and power 54 Manual CX DOS UNC e EE 54 Commando SUOS V ON ee desinit tas Donau ss pois Se Ase sae avn leo MEM ila
19. E Save reconstructed slices 7 Save Dep Mon Images 7 Save particle statistics MAT F Save particle statistics CSV Save generated background Show data visualization Paths LISST 100X type B 9 LISST 100X type C 5 LISST 100X RANDOM type B 5 LISST 100X RANDOM type C Performance Options Speed Memory Speed Memory Files Select Holograms to Process Select Background File s Process Bg HOLO_Batch File Options Help HOLO Batch Processing Initialisation Reconstruction Parameters Save reconstructed slices E Save Dep Mon Images Save particle statistics MAT 7 Save particle statistics CSV Save generated background E Show data visualization Paths Min Depth 0 mm Change ROIs Max Depth 50 mm Advanced Step Size 0 5 mm Output Options Bin Sizes 5 LISST 100X type B LISST 100X type C 5 LISST 100X RANDOM type B D LISST 100X RANDOM type C Speed Memory Performance Options i D Speed Memory Fi a Select Background File s Select Holograms to Process Process Finally click the Size Distributions button to select the folder where you want the particle size distributions to be stored If you have selected to output CSV or MAT files this is where they will be stored If you wo
20. E the Mac OS X version is only available from Sequoia s website You must select the software that matches your machine Inside the software 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 is included in the software package and has 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 LISST HOLO User s Guide 21 Confirmation a tion folder CAProgram Files MATLAB MATLAB Compiler Runtime v 3 Insta Bation Size 1 716 MR Products MATLAB Compiler Runtime 8 3 MathWorks f TENE is complete MATLAB R20 4a coa A MathWorks 4 3 Process holograms using HOLO Batch and HOLO Detail 22 LISST HOLO User s Guide An overview of installation will be displayed click next to start the installation The installation ma
21. FTP utility like Filezilla http filezilla project org as described in section 5 7 The LISST Holo 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 LISST HOLO User s Guide 50 6 5 Configure page 6 6 Tools page Current conditions Take test image Image file name Sampling control Selecting Configure on the home page main menu will bring up a window listing many parameters and allows their values to be changed Values on this page should not be changed without detailed knowledge of the parameter s use or without detailed instructions By default this page has restricted access and the user should NOT change any of these values w o being asked to do so by Sequoia Selecting Tools on the main menu brings up a window that allows the user to take a test image and to change additional parameters such as IP address send Log file for analysis check for firmware updates synchronize time with standard time and other settings These options are described in detail in the following Input voltage 12 50 volts 2 254 Temperature 20 79 C 2 240 Depth 0 8 m 2 139 357 Current conditions Refresh The current voltage temperature and depth are displayed Also displayed are the digital counts Click the Re
22. G THE MAGNETIC SWITCH TO THE 1 POSITION The sampling rates and modes also need to be selected There are two modes e Fixed Rate Mode and e Burst Mode The Fixed rate mode will take one hologram at the specified interval Holograms can be taken 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 second interval If more than 20 holograms are captured within a burst there will be a slight gap in the data every for every 20 holograms as the file system cannot write the holograms to the memory as fast as they are taken The Burst Interval will automatically be recomputed to take this delay into account if more than 20 holograms are captured within a burst The Stop Conditions also have multiple options Date Time Fixed Duration Greater than or less than Depth External Signal 1 or 2 Magnetic switch or fixed number of Samples The Date Time Stop is used to stop collection at a particular time and date The date and time can be GMT or a local time if a time offset has been entered on the Tools page see section 6 6 The Stop after setting will stop the sampling after the specified amount of time from the start of data collection The gt Depth value will stop when the depth is deeper than the specified depth The lt Depth value will stop when the depth is shallower than the speci
23. LISS T HOLO User s Guide Version 3 0 December 2014 SEQUOIA Sequoia Scientific Inc 2 00 Richards Road Suite 107 Bellevue WA 98005 USA Tel 1 425 641 0944 Fax 1 425 643 0595 info SequoiaSci com www SequoiaSci com Technical assistance To obtain technical assistance related to your LISST HOLO 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 Sequoia Scientific Inc Contact Information Telephone 1 425 641 0944 Email info sequoiasci com Waste Electrical and Electronic Equipment Smaltimento di apparecchiature elettriche ed elettroniche da rottamare Table of Contents 1 MOOC ON oa 9 2 Contents and Technical Specifications 11 rire 11 2 1 General E 11 2 2 Parameters Measured and Derived ccccseeccccceceeeseeeeceeeeeeeesseeeeceeeesaeeeeeeessaeaseeeeessaaeeeeessaaees 11 2 3 Particle Size and Concentration iii 11 2 4 TO NOOY RR 11 2 5 Mechanical and Electrical TTE Tm 11 BE OA RE TOT 12 BUlIkNEAG EE spe VIERTEL 13 3 Geno Started RR iaia 15 3 1 Ier geen E 15 3 2 Connect cables and power up 15 3 9 AKC Baier Ol AM RR m 17 4 Hologram Processing with HOLO Batch and HOLO Detail
24. OLO must be connected to the internet and it must be rebooted after the Send Log button has been clicked for the log to transfer Creates a text file in the FTP directory for analysis Generate log file Generate Log The Generate Log file button creates a text file of the instrument log in the images folder of the LISST HOLO which can be offloaded using FTP It is useful for troubleshooting Check for code updates Updates will be installed at the next reboot Internet connection required Check for updates Clicking the Update button will prompt the LISST HOLO to check for software updates and automatically install them It is necessary for the LISST HOLO to be connected to the internet and the unit must be rebooted before the changes will take effect IP Address 192 168 0150 Changes will occur Netmask 2552552550 immediately Change the Network parameters Gateway 192 168 0 1 IP address in your Apply DNS 12041302553 browser DNS 2 192 168 0 1 Use Network parameters to change the IP address of the LISST HOLO Click Apply 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 HOLO This will delete allimages This will not delete the Delete all images that are stored internally images on the External Memory Module EMM Click the Delete button to delete all files on th
25. QUOIA 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 Customer base
26. SEQUOIA gt ipconfig renew Windows IP Configuration Ethernet adapter Local Area Connection 2 Connection specific DNS Suffix IP dr gt 192 168 0 1 Subnet Mask gt 255 255 255 0 Default Gateway 192 168 0 1 C Documents and Settings gtuai SEQUOIA gt 8 3 Changing the LISST HOLO IP address IP Address Changes will occur 192 168 0 150 immediately Change the Netmask 2552552550 IP address in your Network parameters Gateway 192 168 0 1 browser Apply DNS 1 192 168 0 1 DNS 2 192 168 0 1 5 Change the Local IP Address from 192 168 0 1 to your new desired IP address 6 Make a note in this manual of the new local IP address in case you need to change it in the future New router IP address Date New router IP address Date New router IP address Date New router IP address Date 7 Nowclick the Windows Start Button on your PC 8 Typecmdin the search 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 192 168 0 1 to the IP address you selected To change the IP address of the LISST HOLO use the web interface Connect as described in section 3 2 and go to the Tools page of the LISST HOLO web interface Scroll down until you get to Network Parameters Change the IP address to the desired address and click the Apply bu
27. Start sampling button to simulate the magnetic switch This can be useful for example in a laboratory environment where the LISST HOLO may be in a tank or similar and you want to control the start and stop of the sampling manually LISST HOLO User s Guide 51 Storage maintenance Sleep or reboot Power profile Set time Set time zone Set time manually Change external trigger polarity Restore default values Run storage maintenace Storage maintenance atthe next reboot Schedule Maintenance Periodically it is necessary to perform storage maintenance on the internal drive of the LISST HOLO The LISST HOLO will notify you about this need by displaying a warning message saying xxx on the Home page When you see this message click the Schedule Maintenance button and then the Reboot button immediately below Reboot Sleep Sleep or reboot Click the Sleep button to put the LISST HOLO to sleep Click the Reboot button to reboot the LISST HOLO If you reboot you must re enter the LISST HOLO IP address in your browser window to re establish communication 4 Check here if the instrument is powered externally and should This will allow continuous Apply web access but Power profile consumes power remain on between samples If the Power 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
28. _Batch Processing Locating particles About 927 particles found Done Writing particle statistics Done Calculating size distributions Done Hologram processing time 0 34 Estimated time remaining 0 34 3 3 Processing 90 transmission pgm Loading image Recorded 09 Jul 2010 20 30 53 Depth m NaN Temperature C 7 62 Done Reconstructing slices Done Locating particles About 302 particles found Done Writing particle statistics Done Calculating size distributions Done Hologram processing time 0 29 Estimated time remaining 0 00 End m HOLO Batch DataVis HOLO Batch Processing 70 m EM 0 ai z 3 E eegen GE BN A SI 4 S 8 1 E TR TE 4 0000 A E 2 2 30 Si 600 9 E E 2 20 5 400 2 gt 5 z 10 Ki 200 S 0 1 10 100 1000 10000 Pi Equivalent Spherical Diameter um ie About 256 particles found in mage e 58 182 particles extracted H 56 Recorded 05 Mar 2012 22 44 36 2 Depth my 13 90 E 54 Temperature C 5 22 a Caiculaeng sce distributons 52 Done 5 5 Reconstrecting 003 9600 Started 18 Nov 2014 14 29 59 Fa i Recons itractng sices 03 04 Done Locating particles Calculstng Pardcie Statstics About 217 particles found in mage 148 particles extracted 1 Recorded 0 Mar 2012 23 46 25 Depth m pr De C Documents and Settingslole mikkeisen Desktop LISST HOLO data gt 5 P Search E Folders i
29. an exposure while manually controlling the Manual exposure laser Objects in motion may be blurred Do not use without first consulting Sequoia support Command to subsystem Do not use without first consulting Sequoia support Watchdog shutdown 10 minutes Set to 0 to disable watchdog Do not adjust without first consulting Sequoia support Motherboard log Do not use without first consulting Sequoia support sEMUOIA Research and Products for Environmental Science Home Images Log Configure Tools About 425 641 0944 Handler code version Sep 13 2011 12 21 44 Imager code version Sep 13 2011 14 12 21 Motherboard code version 110616 Laser controller code version 110720 External memory module not installed Camera serial number cannot be determined Check camera power Unit serial number 1415 54 LISST HOLO User s Guide 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 OpenSeelt and Filezilla software LISST HOLO User s Guide 55 7 Handling Cleaning Maintenance and Storage 7 1 Handling 7 2 Cleaning 7 3 Maintenance 7 4 Storage When handling the instrument at all times please remember that the LISST HOLO is a high precision optical instrument Avoid mechanical shocks and impact to the housing as this may cause misal
30. arameters Min Depth 0 mm Max Depth 50 mm Step Size 0 5 mm Output Options Bin Sizes D LISST 100X type B Q9 LISST 100X type C LISST 100X RANDOM type B LISST 100X RANDOM type C Save reconstructed slices 7 Save Dep Mon Images 7 Save particle statistics MAT 7 Save particle statistics CSV Im Performance Options Save generated background Speed Memory Show data visualization Speed Memory Paths Files Process Il LISST HOLO User s Guide Reconstruction Parameters and these should normally not be changed 23 A B HOLO_Batch_roiedit HOLO_Batch Processing ROI Editing 1 1600 ROI Size 512x512 a 1024x1024 Image Size HOLO Batch Processing ROI Editing HOLO Batch Processing ROI Editing 1600 24 LISST HOLO User s Guide The Change ROls button opens up a window for selecting the ROI Region Of Interest to be processed The ROI is the part s of the hologram that will be reconstructed Particle counts will only be computed from the reconstructed part of a hologram ROI s must be defined as a square region to allow for correct hologram reconstruction Therefore the rectangular image 1600 x 1200 cannot be treated as a single ROI Once selected the ROI will be the same for all holograms
31. article images and volume distribution Automated firmware updates possible when instrument is connected to the Internet 2 2 Parameters Measured and Derived Particle images for observation and classification Particle volume distribution Temperature Depth 2 3 Particle Size and Concentration e Size range 25 2500um equivalent spherical diameter e Concentration range Beam attenuation coefficient of 0 4 m see also FAQ in section 9 e Resolution 50 log spaced size classes 18 bin widths 2 4 Technology e Solid state diode laser 658 nm e 4 4 um pixel size digital camera 1600 x 1200 pixels 2 5 Mechanical and Electrical Dimensions 13 3 cm 5 25 x 77 cm 30 27 L Weight 9 5 3 6 kg 21 8 Ibs in air water 300 m depth rating 32 GB internal solid state drive 32 GB External Memory Module included Battery life for the Optional External Battery Pack 10 000 holograms for standard 15V 42Ah battery LISST HOLO User s Guide 11 External power input 15VDC nominal 1 A 12 to 16V Sampling frequency up to 0 2 Hz one hologram every 5 seconds Current consumption sleeping 0 020 A max at 12 VDC input Current consumption idling not sampling laser off camera off 0 500 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 reach 1 200 A when all systems are turnin
32. 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 HOLO User s Guide 37 Boo vsu File Options pal eund SITA Dore rte tf Tentbraegent Boo pews File Options EATE E Sequel SST a Dinev atf Tenciraegenn J tateuergeate pn D 1 n m sg na 24 az et D D A e os ae as ase or na na ain Vin en ep 0 af EE D l Set ROC 768 Mx ege Cem Reconstruct T n imag Prote Save mage Measure Ord Zoom Reset a24 Stee Sam em o ___ HOLO Qeha v5 Sepa Scertife Cun ace 100 IL Boo pets File Options Seeciput C Saequaatd SST 4OC Defter akfTextitraeac levet Se Deph 0 000 sat 00 1500 atot 4 2500 3008 4 a a sto 100 sp 230 250 in sn Vin Doph rn 0 j D Set ROL A 768 Jace eget rere 50 ecenstruct I P O Lmrege preti za zap Measure on zem Ree ye om emn H mp HOLO Dusad 3 Sacuces Scientific Cur sack 0 0 C Sugal SST MOL DUI rte ctf Tentbrmegunt 2 in Degen em H J J senn Jee ise eg gem 50 1024 Stee Sum ren 05 NOLO Dat v3 Succes Scasedibo 38 LISST HOLO User s Guide When the ROI is in the desired location DOUBLE CLICK it so that the ROI turns red Note that the Reconstruct button then becomes activ
33. bject 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 72 LISST HOLO User s Guide 14 Index PDO DADC s odit etes tet edet e iati 19 54 Battery CASS eekleg 12 je a 11 Cables CONMCCHING illa 16 ethernelt i 15 Pella 15 Camera settings i 54 CIS AIAG reina 56 Concentration 62 Nata 11 ele nl A PRO RR EE ON ET 47 62 GContigure page lilla 51 Connectors maintenance eeneg Ee 56 PIO 13 Current CONSUMPHONiialc i 12 Delete holograms 46 53 DIMENSIONS
34. ced section of HOLO_ Batch Note that only the part of the hologram covered by the ROI is displayed on the mon image The rest of the hologram was not analyzed and therefore cannot be displayed The dep suffix image is a color coded image where the particles within the ROI have been colored according to their depth of focus As with the mon image only the part of the hologram covered by the ROI is displayed on the dep image The scale bar is all blue and displayed in the bottom left corner The color bar in the bottom right corner shows the location of the particles relative to the transmit window Red particles are very close to the transmit 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 particles A composite file with the name firsthologram_lasthologram_All csv where firsthologram and lasthologram are the filenames of the first and last holograms that were selected for processing This file is always generated for each run of Holo Batch This composite file has all the information about sample date and time water depth temperature and the size distribution given as the volume concentration in ul I per size bin Finally the composite file has in its first row the lower limit of the size bin for the size distributions in columns 26 75 In the 209 row is the mid poi
35. d pause repeat 0 5 second green flash once every five seconds 0 5 second flash every 2 seconds 0 5 Hz green flashing 1 Hz green flashing Steady yellow 2 green flashes 2 second pause What the LISST Holo is doing LISST Holo is sleeping Flashes are initiated by the motherboard when the power is removed from the Linux system Linux system is booting External trigger caused motherboard to wake up Linux system If this continues beyond approximately 60 seconds the internal flash drive has failed Motherboard initiates this display when it applies power to the Linux system If it does not occur the motherboard has not been booted If this display lasts more 40 seconds the Linux system is not responding or the internal flash drive has been corrupted This display ends when the Linux system sends the first command to the motherboard Could also be that the Linux system could not initiate the serial communications between the Linux system and motherboard Fatal error Record number of red flashes and contact Sequoia for troubleshooting and or possible repair of the instrument Indicates Linux system is operational and idling It may be sampling or waiting for input No external flash drive detected Linux system commands the motherboard to show this display If it does not occur the Linux system has not booted Camera is being set up If this condition persists more than a few seconds there is a camera or Fi
36. d become familiar with the instrument and its operation Section 4 describes how to install and use the software for processing the raw holograms Section 5 discusses how to configure and deploy the instrument in the field In order to program and offload 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 up Inside you will find a number of cables and power supplies described below The yellow cable is an Ethernet cable used for communication with the LISST HOLO This is not a waterproof cable The black cable is a 5 pin cable used to power the LISST HOLO when working in the laboratory The 5 pin cable is being used to provide power to the LISST HOLO using the included 110 220VAC power supply it is NOT being used for communication The yellow Ethernet cable must be used for communication NOTE If you have an external LISST HOLO battery pack you should use the 5 pin cable that shipped with the external battery pack if you wish to power the LISST HOLO from the external battery pack LISST HOLO User s Guide 15 16 LISST HOLO User s Guide Look at the LISST HOLO connector endcap Disconnect the External Memory Module if it is connected Undo the dummies and connect the 5 pin cable to the 5 pin bulkhead connector 1 just below the serial number and the yellow Ethernet
37. d on this noncompliance provided that Customer gives SEQUOIA 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 and settlement of the claim in which event SEQUOIA will reimburse the reasonable out of pocket costs incurred by Customer to provide such assistance Customer does not settle the claim without the prior written consent of SEQUOIA and upon SEQUOIA s request Customer returns the Non Complying Product to SEQUOIA for modification replacement or a refund of the purchase price paid by Customer to SEQUOIA for the Non Complying Product less a reasonable allowance for Customer s use prior to return 4 Exclusive Warranties THE WARRANTIES SET FORTH IN PARAGRAPH 1 ABOVE ARE EXCLUSIVE AND IN LIEU OF ALL OTHER WARRANTIES EXPRESS OR IMPLIED SEQUOIA DISCLAIMS ANY AND ALL WARRANTIES EXPRESS OR IMPLIED INCLUDING BUT NOT LIMITED TO ANY IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE AND ANY IMPLIED WARRANTY ARISING FROM COURSE OF PERFORMANCE COURSE OF DEALING OR USAGE OF TRADE OTHER THAN THOSE SPECIFICALLY SET FORTH IN PARAGRAPH 1 5 Exclusive Remedies CUSTOMER S RIGHTS AND REMEDIES SET FORTH IN PARAGRAPHS 2 AND 3 ABOVE ARE EXCLUSIVE AND IN LIEU OF ANY AND ALL OTHER RIGHTS AND REMEDIES FOR ANY BREACH OF OR OTHER FAILURE TO COMPLY WITH ANY WARRANTY WITH REGARD TO ANY PRODUCT
38. der located on the ship disk Browse For Folder Select Directory to Open 4 Computer Os C e DVD RW Drive D a Removable Disk E a Removable Disk F a Removable Disk G ew Removable Disk H FRI Folder Make New Folder From the drop down menu select a hologram to display The selected hologram will then show in the left part of the window Only one hologram at the time can be selected displayed and processed in HOLO Detail 36 LISST HOLO User s Guide Advanced Settings Restore Detours C UUsersiTLeeuwiOee eo piL SST IOLOU oKeroc 20 14 compled Io Save Settings on Dit HOLO Detail Advanced Parameters Offset mm 28 Pixel Size um 44 658 Index of Refraction 1 333 i IC Calculate reconstruction kernel first Set ROI and Reconstruct Buttons Additional reconstruction options are available under Options gt Advanced Settings The only parameter that should be adjusted is the index of refraction An average value of 1 333 for water is set as the default This should be changed if the hologram was taken in air or in any other substance with a different index of refraction The Offset Pixel Size and Wavelength should not be adjusted Select the size of the ROI using the radio buttons in the lower left corner After selecting the ROI size press the Set ROI button The ROI box will appear
39. e Now set the minimum and maximum depth for the hologram reconstruction as well as the step size in mm Click the Reconstruct 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 reconstructed image are in calibrated units um The Z axis the focus depth is displayed above the reconstructed image 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 Setect path neng SST AC OU mere athl anthra 9C klranemi tb pon 1500 3000 n A sta mp 140 3101 op sto ta i n f 230 250 EU 512 Vin ep inm 0 J f seen 768 Mace eget Zeen st Reconstruct a la T image prote zg mage Measue Gu E 1024 Stee Sum een 05 HOLO Deui v3 Sacucia Sci Hnc fi The Image Profile button can be used to get an idea of the intensity variation along a line transect To use click the Image Profile button and a will appear Move it to the location on the slice you want to examine in more detail and click once Now drag the cursor to draw a line Click once to set a point double click to mark the end of the transect In the image to the left a transect composed of 3 lines at right ang
40. e showing the particles in B amp W Useful for more detailed information about the shape and structure of the particles filename dep jpg filename mon jpg Comma separated ASCII file firstfilename lastfile with size distribution and name_All csv other output as described in the section above Reconstructed slices of the filename znnn jpg hologram nnn indicates the slice number MATLAB MAT file with N x 17 structure with particle statistics as described in the section above N is the number of particles in the hologram Rows 1 3 of the pstat file contain the size bins filename pstat mat Comma separated ASCII file with N x 17 matrix with particle statistics as described in the section above N is the number of particles in the hologram Rows 1 3 of the pstat file contain the size bins filename pstat csv Saves the selected background hologram or the average of multiple selected background holograms background pgm LISST HOLO User s Guide 35 4 5 HOLO Detail processing of individual holograms B oo Detail Open the program by clicking the HOLO_ Detail executable Seti path C UjeereiTLeeu wee copiL 35T 1OLOV oicProc 20 MComplled 641100 Select Path Click the Select Path button to select a folder for browsing your holograms Select the folder where your holograms are stored then click OK If you are just getting stated navigate to the Example Holograms fol
41. e internal hard drive of the LISST HOLO You will be asked to confirm When you have confirmed the Tools page will refresh and another 5 seconds after this the LISST HOLO will begin to delete the holograms During the time the LISST HOLO is deleting holograms it WILL NOT RESPOND Clicking any of the links will result in a time out and a blank browser page Deleting 1000 s of holograms can take 5 10 minutes Upon completion the LISST HOLO will become responsive again There will be no indication from the LISST HOLO that it is responsive but clicking on the Images page will show that no images are available The parameters described below should NOT be changed without first consulting Sequoia They are to be used for troubleshooting and problem resolution only LISST HOLO User s Guide 53 Laser Camera brightness gain shutter and power Manual exposure Command to subsystem Watchdog shutdown Motherboard log 6 7 About page Laser power 200 max 200 Laser On Laser Off Laser Controller Off Do not adjust without first consulting Sequoia support Camera brightness Brighiness 8 Min 0 max 255 Apply Camera power must be cycled Camera gain Gain 56 Min 56 max 739 Camera power must be cycled asc EEG Shutter 30 Min 0 max 1164 Typ 30 Apply Camera power must be cycled Camera power Control power to camera Camera is on Do not adjust without first consulting Sequoia support Take
42. e of 0 5 mm or more If this option is selected a warning message will remind you of the requirements of running the higher memory setting NOTE The Speed Memory is only available in the 64 bit version of Holo Batch LISST HOLO User s Guide 27 x Bg HOLO Batch File Options Help HOLO Batch Processing Initialisation Reconstruction Parameters Min Depth 0 mm Change ROIs Max Depth 50 mm Advanced Step Size 0 5 mm Output Options Bin Sizes 7 Save reconstructed slices Save Dep Mon Images C Save particle statistics MAT F Save particle statistics CSV 7 Save generated background T Show data visualization Paths gt LISST 100X type B LISST 100X type C 5 LISST 100X RANDOM type B 5 LISST 100X RANDOM type C Performance Options Speed Memory D Speed Memory Files Process wy Ga Libraries Da xa Organize v Fe Favorites zB ENTRE BE Desktop gt Library E Downloads amp Dropbox lt Pictures d OneDrive LU Library Recent Places E A Libraries d Music i Pictures E Ez Videos S Comnuter Documents T Folder Libraries Music aS Library Videos Library Sec ae 8 Bg HOLO Batch File Options Help HOLO Batch Processing Initialisation Reconstr
43. e the CTRL key to select several individual holograms Here 5 holograms have been selected 10 21 2011 1 36 00 PM 10 21 2011 1 37 00 PM FW TW TW 10 21 2011 1 37 00 PM 10 26 2011 3 26 00 PM 10 26 2011 3 26 00 PM 10 26 2011 3 40 00 PM 1922065 PGM File 1 922 065 1 922 065 1 922 065 TFW TW TW oti 0218 pgm 1011 0219 pgm 011 0220 pgm 011 0221 pqm 011 0222 pgm 012 0000 pgm PGM File PGM File PGM File PGM File PGM File 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 Filesize Last modified Filename Filetype d 011 0216 pgm 011 0218 pgm 011 0219 pgm had 011 0221 pgm 011 0222 pgm PGM File PGM File PGM File PGM File PGM File 10 26 2011 5 24 12 10 26 2011 5 24 12 10 26 2011 5 24 14 10 26 2011 5 24 14 10 26 2011 5 24 15 1 922 065 1 922 065 1 922 065 1 922 065 1 922 065 To DELETE the holograms right click on the selected holograms on the images drive on the LISST HOLO and select Delete Filename Filesize Last modified Permissions Owner Gro WW 1011 0216 pgm 011 0217 pgm 1011 0218 pgm 11011 0219 pgm e 011 0220 pgm 4 Download GERE Ae Add files to queue 011 0222 pgm View Edit 012 0000 pgm Filetype 00 00 00 PGM File PGM File PGM File DONA Cila 10 21 2011 1 36 00 PM 10 21 2011 1 36 00 PM 10 21 2011
44. efficient TemperatureOffset Floating point number Auxiliary input A D channel 2 8 bits 0 to 255 Auxiliary input A D channel 3 8 bits 0 to 255 Auxiliary input A D channel 4 8 bits 0 to 255 Auxiliary input A D channel 5 12 bits 0 to 4095 Auxiliary input A D channel 6 12 bits 0 to 4095 Not used Inter frame delay in milliseconds Millisecond time stamp Use to determine time between previous or following hologram Unassigned set to 0 LISST HOLO User s Guide 69 70 LISST HOLO User s Guide 13 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 above SE
45. es 1922065 bytes 1922065 bytes 1922065 bytes 1922065 bytes 1922065 bytes 1922065 bytes 1922065 bytes 1922065 bytes Details Details Details Details i Details Details Details Details Details Details Details Details Details Image details for 011 6698 pgm Taken Monday January 31 2011 day 031 at 19 59 47 GMT Depth 0 3 meters Temperature 25 0 degrees C Input voltage 12 48 volts Image size 1600 x 1200 Exposure units of 600ns 10 Laser power 80 Laser photo diode 22 Camera brightness 0 0 to 255 Camera shutter 30 0 to 1164 Camera gain 56 56 to 739 Imager code version Jan 28 2011 14 47 08 The hologram file name is a hyperlink to the file on the internal drive of the LISST HOLO Click on the file name to download the file to a temporary folder and open the file in OpenSeelt To copy the file to a specific folder right click on the file name and choose Save Target as or Save Link as and then enter a folder to store the file to To see specific information about the hologram such as date and time depth and temperature click on the Details button The Details Button then opens up a 2 window showing the details Click the Delete button to delete a hologram You can only delete one hologram at the time using the Delete button To download or delete multiple holograms from the internal drive you will need to use an
46. es Maximum Concentration um phi mg l 1 95 9 00 Clay 8 3 9 8 00 Very Fine Silt 15 7 8 7 00 Fine Silt 31 15 6 6 00 Medium Silt 62 31 25 5 00 Coarse Silt 123 62 5 4 00 Very Fine Sand 247 125 3 00 Fine Sand 494 250 2 00 Medium Sand 987 If you cannot see any interference patterns in the hologram lots of concentric rings the concentration is too high and you most likely won t get any sensible data out of the hologram when processing it For Sequoia s LISST 100X and LISST STX instruments the user has the option to process the data assuming two different types of particle types Spherical particles and Randomly shaped particles sediment grains The size ranges differs between these two processing options In order to make it easier for LISST HOLO users to merge their data with LISST 100X data this option has been transferred to the HOLO_Batch processing software as well It has no influence on the processing of the holograms only on the size bins used for the final size distributions Adjust the laser power and exposure fields either on the tools page if capturing images from the tool menu or in the sampling program page if running a sampling program 62 LISST HOLO User s Guide 10 Endcap LED Status Light Indicators This table describes the LED signals visible from the end cap LED sequence 0 5 second green flash once every 30 seconds Yellow flashing twice a second for 40 to 60 seconds x red flashes 2 secon
47. fied depth The External 1 signal and External 2 signal setting will stop collection when the selected signal is less than 0 8 volts The Magnetic Switch option will cause sampling to stop when the switch is in the 0 position Selecting the start stop program using the PC Select Program 9 Program 1 Program 2 Program 3 Program 4 Apply 5 3 Preparing for Deployment with the EMM installed Sleep or reboot Leg ato without the EMM installed The Samples setting will stop data collection when the specified number of samples has been collected After making changes to the settings press on the Apply button to save the settings and refresh the page All four sets of start and stop conditions can be programmed When the four start and stop conditions have been programmed you can select which program you want to use by selecting the appropriate radio button and clicking apply Now that the sampling parameters are configured we can prepare the instrument for deployment and start the sampling The procedure is slightly different depending on whether the LISST HOLO is deployed with or without the External Memory Module EMM These two scenarios are described below The first 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 applied OR while the instrument is in
48. fresh button to update Duration 255 max 10 Images 20 Power 200 max 200 Comment Test Take images In order to take a manual hologram click 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 duration and power settings control the output power of the laser and the duration that it is on Changing these may cause the hologram to become completely white or black If this happens go to the FAQ page on the About page section 6 7 If you change the laser power and duration here it ONLY affects the laser power and duration for the test holograms Laser power and duration during regular sampling initiated by one of the four programs section 5 is NOT affected The deployment number Deployment number and image number are Max is 999 11 combined to create the Image number file name ddd iiii pgm lf Maxis 9999 0 the image number Comment Test Apply exceeds 9999 the deployment number is incremented and the image number is reset to 0 Image file name You can force the LISST HOLO to start at a certain deployment number or image hologram number You can also enter a comment that can be used later to identify the holograms e g the location Remember to click the Apply button Sampling control Emulates magnetic switch control Start sampling Use the
49. g log files to Sequoia It is not necessary to have the instrument connected to a network or the Internet but it can be useful when needed The LISST HOLO comes configured with a pre selected IP address netmask gateway DNS 1 and DNS 2 These settings will work with the provided wireless router but they will probably not work with your existing local area network Because the LISST HOLO requires a static IP address an IP address must be selected so as not to interfere with other computers on your network It is highly recommended that users work with their network administrators to determine the proper settings for their network The new value can be entered on the Tools page see section 8 3 Be sure to double check the values before pressing the Apply button on the Tools page Once the Apply button is clicked the IP address will change immediately and you will need to log into the new IP address before LISST HOLO communication can be re established If incorrect values are entered it is possible to change them manually through serial port communication Contact Sequoia for details of this procedure Processing or reconstruction of a hologram is a mathematically intensive task Therefore a LISST HOLO hologram is split up into ROls Regions Of Interest which are each processed separately This is in order to avoid memory problems during processing Once the ROls have been processed they are merged into one image with particles and processed for s
50. g on This maximum draw will be lower than 1 200 A if the operating temperature is warmer than 0 C Drawings 00 DIAMETER 25 DIAMETER 127 133 LISST HOLO dimensions in inches mm LISST HOLO External Battery Case OPTIONAL ACCESSORY Dimensions in inches 12 LISST HOLO User s Guide Bulkhead connector Pin outs Five pin connector Teledyne Impulse part MCBH WB 5 MP SS Pin Function 1 Power Ground 2 12 to 15 V 1 A power supply or battery 3 Communications Ground 4 RS232 EIA level 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 Digital Input 1 6 Digital Input 2 Eight pin Communications Connector Teledyne Impulse part MCBH WB 8 MP SS Pin Function 1 Ethernet ATX 2 Ethernet ATX 3 Ethernet ARX 4 Ethernet ARX 5 USB Vcc 6 USB Data 7 USB Data 8 USB Ground LISST HOLO User s Guide 13 14 LISST HOLO User s Guide 3 Getting Started 3 1 Introduction 3 2 Connect cables and power Up This section is designed to enable the first time user to unpack the LISST HOLO and capture a hologram within a few minutes after opening the case for the first time The experienced user may find this section useful for a quick review of the various procedures It is not necessary to install any software to go through this section an
51. gvortes Took Heb WR Space setup LINKSYS by Cisco Femware Version 1 0 03 Wireless G Broadband Router WRTS4G2 Applica tions Setup Wireless Security eeng 5 amp Gaming Administration Basic Setup MAC Address Clone Advanced Routing internet Connection Type Automatic Configuration DHCP This setting is most commonly used by Cable operators Automatic Configuraton DHCP v Optional Settings 2 outer Name WRT54G2 required by some ISPs gen Host Name Enter the host Host Name name provided by your ISP Ooman Name um Domain Name Enter the domain name provided by your Sce Loca P Address 192 16 Local IP Address Ths is the Router IP address of the router Subnet Mast 255 255 255 0 v Subnet Mask This i De subnet mask of the router Network Address DHCP Server Os A Server Settings DHCP sini Vv Enable Disable DHCP Server Allows the of router to manage your P 50 addresses Starting P Address 492 168 0 100 Maximum Number DHCP Users Client Lease Time 0 minutes 0 means one day Starting IP Address The ei Ze E ia p Q intenet Rio en C WINDOWS system32 cmd exe Microsoft Windows XP Version 5 1 2666 CC Copyright 1985 2661 Microsoft Corp C Documents and Settings gtuai SEQUOIA gt ipconfig release Windows IP Configuration Ethernet adapter Local Area Connection 2 Connection specific DNS Suffix Subnet Mask Default Gateway C Documents and Settings gtuai
52. h is manyholograms Then power up the LISST HOLO and initiate communication as described in section 3 2 The Internet port on the E1000 router can be connected to your network to give the LISST HOLO access to the Internet for software updates To log on leave user name blank and enter admin for the password 8 2 Changing the IP address of the Linksys E1000 router Connect to 192 168 0 1 E The server 192 168 0 1 at WR T5452 requires a username and password Warning This server is requesting that your username and password be sent in an insecure manner basic authentication without a secure connection User name Remember my password It may be necessary for you to change the IP address of the E1000 router You do NOT have to change the IP address of the router if you are only changing the last element of the LISST HOLO s IP address 150 If you are changing any of the first 3 elements of the LISST HOLO s IP address 192 168 0 you MUST change the IP address of the router to match 1 Apply powerto the Linksys E1000 router 2 Connect the Ethernet jack in a computer to Ethernet port 1 of the router Light 1 should come on 3 Open Internet Explorer and navigate to 192 168 0 1 58 LISST HOLO User s Guide 4 Leave the user name blank Enter admin as password This will open up the setup page below Basic Setup Windows Internet Explorer e E hitp 192 168 0 1 basic htm Fle Edt Yew F
53. ignment of the optical parts The instrument pressure housing should not be opened The glass windows of the instrument can be scratched Do not use abrasive cleaners on glass or anodized surfaces When cleaning windows be careful not to drag and hard particles such as sand across the windows Use glass cleaner or liquid dish soap to clean windows Make sure that the windows are as clean as possible The windows can be cleaned with Windex but often a mild lukewarm soap solution is the best for cleaning optical 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 equivalent on a frequent basis DIOR NOM MUS Ne i e BUER MEOR Grease may prevent the dummies or cables from mating with the connectors and allow water to penetrate and cause corrosion or short circuit the connector To preserve the file structure integrity on the internal drive regular maintenance of the file system is needed Use the button Schedule Maintenance on the Tools page to perform maintenance You should always perform this maintenance before deploying the instrument for a longer duration The LISST HOLO should be thoroughly cleaned with fresh water and dried out before storage Store in a clean dry place or inside the provided ship case Make sure the dummy plugs for the connectors are in place before storage
54. interval of 0 5mm This will result in 101 reconstructed images Note that the processing time increases linearly with the number of Steps Upon processing all particles in all intervals slices will be combined into one focused image B HOLO Batch The next step is to select output options nate Options Help A csv file containing the size distribution for each hologram is written by default even if none of the check boxes or the right are selected HOLO Batch Processing Initialisation Reconstruction Parameters Min Depth 0 mm Change ROIs Max Depth 50 mm Advanced Step Size 0 5 mm Bin Sizes LISST 100X type B LISST 100X type C LISST 100X RANDOM type B LISST 100X RANDOM type C During 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 Dutput Options Save reconstructed slices Save Dep Mon Images Save particle statistics MAT Save Dep Mon Images saves depth and montage images of particles These are composite images that show all the detected particles in one 2D plane Examples are show on page 32 Save particle statistics CSV Performance Options Save generated background Speed Memory Show data visualization Speed Memory The Save particle statistics MAT option creates a par
55. ize area shape etc The 2 minute processing time per hologram is the maximum expected time on a standard 2 2GHz windows PC with 4GB of memory However since the processing is fully automated it is possible to process holograms overnight or during weekends No It typically takes 2 minutes to reconstruct a hologram into an image that can be analyzed for particle size shape area etc No The LISST HOLO does not support DHCP Dynamic Host Configuration Protocol The maximum sample rate for the LISST HOLO is 0 2 Hz one hologram every 5 seconds No You must always connect via the supplied router or a local network With the router you can connect wirelessly to your PC If your PC does not have wireless capability you can plug the router into your PC However in both circumstances the LISST HOLO must be plugged into the router and LISST HOLO User s Guide 61 my PC What is the maximum concentration that the LISST HOLO can be used with How do I tell if the suspended sediment concentration is too high Why can I choose between spherical and random size ranges in HOLO Batch Why are my holograms completely black NOT the PC The concentration limits for a LISST HOLO are roughly as tabulated in the table below See also this article on Sequoia s website http www sequoiasci com article what are the concentration limits for the lisst holo for a more thorough explanation Mean Particle Diameter Wentworth Grad
56. leale 11 Reiles tee e 44 External Battery Case n nnoannnnnneannnennennenenne 12 External Memory Module 11 installalo nali laid 43 zio EE Em 61 SE 11 Files created by HOLO Batch 35 created by HOLO Detail 40 download from EMM saannnnaannnnannnnannannann 44 download via FTP aaannnnannnnnnnnnnannnoennnnnnn 44 POA PR ETT T 35 69 PGM file structure 69 SIE 44 55 Tira 44 h st address coss st ata a 44 DASSWOld Me NEP 44 Getting started Pm 15 Saal Te emt NEP 56 FOEO Balen isse poches d bx M etum 23 advanced parameters 25 background hologram 30 ISI ZO ENS 27 factory default settings 23 output options 26 performance options 27 reconstruction parameters 23 ROI Region Of Interest 24 HOLEO D6eltallsdesisusxcicedisuliess E 36 Hoogfamspi ica 61 detesta 50 download from EMM 44 download from internal drive 44 50 enter Comment o1 file NAME iii 51 PGM file structure 69 DIOCESES SING ertet D 22 processing time enennenennnesennensennenrnnnnne 61 view in OpenSeelt 47 mi
57. les to each other has been selected When you 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 Clicking the zoom button enables you to zoom in on a part of the slice Click and drag the cursor to draw a rectangle on the slice and release to zoom to the rectangle Note that if you use the arrows to move back and forth between the slices after you have zoomed the zoom area is retained on the other slices Click the Reset button to zoom out again 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 HOLO User s Guide 39 Save Image Button Measure Button Bg o ons File Options mr gen C 9sens ATL esu Denti ESST HOLOSPscific Teste 6 nino wThrcuginieial 214 0025 pom 1260 SESS aea E FE UE ET EH m rn 207 400 60 mp mp 1207 140 1600 1600 2000 2207 5 2 Ate Dust ime 9 EI D Sah wa Max Dest nis E eccottruct nage Prose Sava imagi Gm zom s JI 24 S ep Size imm os E i s CkanShek 00 MOTT tad v Seguon Scusa 4 6 LISST HOLO User s Community TERMS amp CONDITIONS SOFTWARE GALLERY USERS Home Welcome to the holoproc site a community resource for holographic image processing If you have not a
58. longer wish to keep on the EMM See section 5 8 for instructions on how to view the raw unprocessed holograms using OpenSeelt See section 4 for instructions on how to process the holograms Downloading and deleting from LISST HOLO To download holograms from the internal drive you will need an FTP utility like internal drive EMM not installed Filezilla http filezilla project org When you have started the FTP application you will need to specify a host username and password The host is the IP address of the LISST HOLO typically 192 168 0 150 unless Host 192 168 0 150 you have changed it to another IP address see section 8 3 Username The password is anonymous Password eeeeeeee 44 LISST HOLO User s Guide Click the Quickconnect button to start the FTP transfer EET eT tra Filezilla will connect to the LISST HOLO and display Pest 192 268 0250 Users MUT Mods Paese sessersereeeei pot ama the images folder in the bottom right window To the left is the destination folder selection Navigate to the desired destination folder Free Filetype Last modes Permissions OmmeriGro File foiser 19 26 2011 1040460 Pas dir atx an 4 WM Queue empty ss lnthis example we will offload to a folder on the C bel A Documents and Settings drive called HOLO Offload G A Drivers 3 a Freemake_do_not_remove_this_folder E e HOLO Offload o A Infor Global Solutions G A Intel
59. lready done so please read the Terms amp Combipons and then register to obtain access to the rest of the site 40 LISST HOLO User s Guide The Save Image button enables you to save the current view of your slice as an image on your computer The image is saved with a PNG Portable Network Graphics extension The measure button will allow you to measure objects in the reconstructed slices After selected the measure button a will appear when you mouse over the image Click and hold to drag a line across an object in the image When you release the mouse button the length of the line will be displayed in microns Dr Alex Nimmo Smith of University of Plymouth hosts a user s community website for holographic image processing holoproc http holoproc marinephysics org On the holoproc website you will find additional MATLAB files that can be used for processing LISST HOLO data developed by other LISST HOLO users and shared via the holoproc user community SEQUOIA SCIENTIFIC INC DOES NOT PROVIDE ANY SUPPORT OR ASSISTANCE RELATED TO HOLOGRAM PROCESSING WITH FILES DOWNLOADED FROM THE HOLOPROC WEBSITE QUESTIONS SHOULD BE ADDRESSED DIRECTLY TO THE USER WHO CREATED THE FILE 5 LISST Holo Field Deployment 5 1 Introduction The LISST HOLO has many features that make it easy to deploy in the field Start and Stop conditions can be programmed into the instrument in advance Once the instrument is turned on it will wait
60. m green to red indicating that sampling has begun lt will blink slowly until the start condition is reached and it will be on continuously during the acquisition of a hologram It will return to green when the stop condition has been reached 5 6 Stop Data Collection Data collection will continue until the selected Stop Condition is reached To Stop the data collection at any time move the switch to the 0 position Within a few seconds the LED on the endcap should change from Red to Green If the data collection has already stopped the LED will be blinking green regardless of the switch position However the switch should be always be placed in 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 drive of the LISST HOLO The offload procedure is different for those two scenarios and will be described in the following Downloading from EMM Raw holograms stored on the EMM can be downloaded using the provided USB cable Remove the EMM from the instrument Leave the locking ring attached to the connector on the instrument Plug the mating underwater connector of the USB cable onto the EMM and then plug the USB end into your PC The USB flash drive inside the EMM should now appear on your PC You can now transfer files as you would from any USB flash drive and subsequently delete the holograms you no
61. m top left of hologram Unit um um um um Dimensionless Dimensionless um um um um Pixels 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 HOLO User s Guide 33 12 Focus Depth from emit window mm 13 Bounding Box Pixels 14 Orientation Degrees 15 Euler Number Dimensionless 16 Extent Dimensionless 17 Perimeter um TIFF files of individual slices If the check box Save Individual Slices was checked HOLO Batch will save a TIFF image for each reconstructed slice showing the in focus 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 222 500 TIFF meaning it was reconstructed from hologram 016 0270 pgm at a distance of 22 5 mm from the transmit window 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 34 LISST HOLO User s Guide Summary of files created by HOLO Batch o Check Box Checked Save Save Dep Mon Background Images Always Filename and type Content Gead Color coded DEPth image showing the location of the particles in the depth dimension Black and White MONtage imag
62. mode and rate and the Stop Condition will need Nov v 1 2014 07 y 0 00 GMT to be set Start on Saturday November 01 2014 at 07 00 00 GMT SMart after a delay of 1 Je gt To set the Start condition choose between a Date Time start delayed start n a depth start External Signal 1 External Signal 2 or the Magnetic Switch External signal 1 goes high CR I To set the sample mode choose between Fixed rate and burst sampling 9 Magnetic switch is in the 1 position Must be in 1 position to sample regardless of start condition 9 Fixed Rate Mode Sample interval i i i i 5 seconds Burst Mode e L3 Sample interval D pu HI M 0 seconds burst ME HE HU N i Images per burst Hi 3 images Burst interval M M 20 Minutes Oct v 12 2011 Date Time start will wait until the selected GMT time is reached before sampling 00 15 v 00 iocs is started and the magnetic switch is in the 1 position If it is past the specified eso wea OM 5 ITI UM T Se 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 HOLO has the correct GMT time Date Time LISST HOLO User s Guide 41 Start after a delay of 1 Minutes e gt Depth 100 meters External signal 1 goes high External signal 2 goes high Magnetic switch is in the 1 position Must be in 1 regardiess of start condition Fixed Rate Mode Sample interval ES i i E Bu
63. n If you do not wish to re install the External Memory Module you should install the 8 pin dummy on the connector There is no need to connect the Ethernet cable 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 the instrument is not sampling or writing files the power can simply be disconnected However power should only be disconnected when the instrument is in its low power sleep mode The instrument will automatically go into lower power sleep mode after 10 minutes of no activity if the power profile is checked on the Tools page The green LED will blink every 30 seconds when in sleep mode When the instrument is awake but idle the LED will blink every 5 seconds 48 LISST HOLO User s Guide 6 Reviewing Instrument Info and Other Settings 6 1 Intro to Other Settings 6 2 Home page System Status Select program Select Program gt 2 Program 1 m O Program 2 Program 2 EN KA Program 4 Programming Information 6 3 Images page In addition to the Start and Stop Conditions there are other parameters that can be changed using the Ethernet connection This section will discuss some of the additional parameters that can be accessed from the home page The Home page shows the System Status Selected Program and Programming Information In addition it also shows Star
64. ng MATLAB Compiler Runtime R2014a for qa installation Installation will start once all files are extracted Uralppire com udis mind 139295554 anc MATLAB Compiler Runtime Installer To install MATLAB Compiler Runtime 8 3 on your computer click Next MATLAB R20i4e MATLAB and Senulink are regetered trackernarks ot The MathWorks Inc Please see www matiraorks ccm trademarks for list of additional trademarks Other product or brand names may be trademarks or registered trademarks of ther respective holders WARNING This program s protected by copyright law and erlemabonal teatis Copynght 1984 2014 The Math Works Inc Protected by U S and other patents See Math iceks com patents The MathWorks inc MATLAB COMPILER RUNTIME MCR LIBRARIES LICENSE IMPORTANT NOTICE BY CLICKING THE YES BUTTON BELOW YOU ACCEPT THE TERMS OF THES LICENSE IF YOU ARE NOT WILLING TO DO SO SELECT THE NO BUTTON AND THE INSTALLATION WILL BE ABORTED e A Folder Selection Enter the Full path to the installation folder ume MATLAB Restore Defsuk Folder re R20 4e To install the software plug in the disk that was shipped with your instrument and locate the LISST HOLO software folder Or visit www sequoiasci com and download the software package from the LISST Holo page Our software supports 32 bit Windows 64 bit Windows and Mac OS X operating systems NOT
65. nt of the size bin for the size distributions in columns 26 75 and in the 3 row is the upper limit of the size bin for the size distributions The table below shows the parameters in columns 1 75 of the CSV file Column Value 1 Year YYYY 2 Month MM 3 Dav DD 4 Hour HH 5 Minute MM 6 Second SS 7 1 100s of a second hhh 8 Depth 32 LISST HOLO User s Guide Unit N A N A N A N A N A N A NOTE Currentlv not available NaN Not a Number displaved instead m 20 24 25 26 75 Temperature Input Voltage Exposure Laser Power Laser Photo Diode Briahtness Shutter Gain Deplovment ID Image Number Number of Particles Reserved for Future Use Total Volume Size Distribution MAT file output by HOLO_ Batch C N A N A N A N A N A N A N A N A N A N A ul ul If the Save particle statistics MAT checkbox was selected a MATLAB MAT file will be created The MAT file can only be opened up in MATLAB It contains a structure called PartStats It has dimensions Nx17 where N is the number of particles detected in the ROI The 10 columns have the following information about each particle Column 1 2 10 11 Particle Property Particle Area based on pixel count Particle Equivalent Diameter based on pixel count Major Axis Length Minor Axis Length Solidity Eccentricity Filled Area Convex Area Equivalent Convex Area Diameter Particle Volume Centroid X Y fro
66. o ejojorezm e M PN 40 HOMEPAGE eae a 18 49 Images page 18 49 IP address change LISST HOLO 59 change router s sneennnsennensnnnenrnneernrnnnne 58 Belo RR RR RR 50 Magnetic switch EEN 51 Ewe ue 56 Manual sampling DEE 51 ODEN ceel eea rc cei 47 55 Password changing router Pierri 58 connecting to router 16 connecting via FTP 44 PNG Mage e E 40 arg 12 GISCOMMECL ricalca 19 lee EE 11 Power Prole 48 Process holograms using HOLO Batch 23 using HOLO Detail 36 Programming Start ele tele vira a 41 ele feele e E 42 Rief EE 58 CONNECING Meer 16 SEICE PrO A WEE 49 USING THe PG cli ease 43 Set time automatically srir 52 Maldini ii 52 elE e ue ladino 65 67 Seen 52 Software stalli area 21 SPEcificalions cine 11 Start data collection n 44 Stop data collection n 44 SIOF QOO naan e 56 System eli UM 49 Test chamber It E te EE 19 TIME ZONES dela 52 TOOLS PAJE Er T 18 51 Dee ee ere te eee eae eee 17 User community 40 VELE PROTEST REO EET 71 VVC LOIN ERR TREE 11 LISST HOLO User s Guide 73
67. or endcap is in 0 position off The magnetic switch does not need to be in the 1 position to communicate with the LISST HOLO Plug in the LISST HOLO power supply in order to apply power to the LISST HOLO 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 colors and status light indicators NOTE The LISST HOLO has no internal power Whenever power is applied to the instrument the internal processor is powered on and initiates its boot up procedure The LISST HOLO cannot boot up any faster than 30 seconds 3 3 Take a hologram If you have followed the instructions in section 3 2 the LISST HOLO is now powered up and connected to your PC It is time to take a hologram mou Open up a web browser on your computer e g Firefox Google Chrome or Internet 6 De le 192 168 0 150 Explorer To connect to the LISST HOLO use URL hittp 192 168 0 150 Note The IP address of the instrument can be changed and in most cases it must be LISST HOLO User s Guide 17 18 pgm format LISST HOLO User s Guide changed see your local system administrator for more information on how to get a static IP address See the FAQ in section 9 for more information on how to change the IP address of the LISST HOLO The LISST HOLO home page will then show To take a hologram click
68. program does not instal bke most Windows programs Here s how to metaf it 1 Download the OpenSeet pooed file Create a foilor x Program Fikes OperSeet tick on the OpenSoet tip Sie and ortract to OpenSouit exe file o x P rogans Fi penSeett a me Corel Pare Dorbe cock on Foder Opsons r on the Fio Types tan 6 Chch on the New tutton in tw Create New geng wndow tpe in pgr en chok fa OK burton 8 Under eat for POM extension cick the Change button Select Select me program hom a ia 10 in the Open Witt wrdow ckck on the Browse button 11 Navigate to Re OpenSeut fokfer you created in step 2 and Goutte click onthe OparSaeti exe Be 12 Cosa afl wndows How do download or delete multiple images Use a FTP program such as pc You wil need the P of te unt fw user rame and password Drit down to metfiasn to finche images The images are named with sequential numbers The largest number most recort image Ploase be very careful abost what pou delete or modry o e wor cag 894 24 3 Bee DU 0 T e ve dom IL sevo The About page shows the FAQ where you can find more information about how to download install and use OpenSeelt to view the unprocessed holograms If you took a hologram without anything in the laser beam your hologram will typically look something like this Try taking another hologram but hold a hair or thin piece of string into the laser beam You should then see something like the image to the left
69. rdware Processing is complete when End is displayed in the text box and the Cancel button changes to an Exit button Processing can be aborted at any time by pressing the Cancel button It may take a minute or so for the processing to 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 showing the progress of the batch processing After processing 100 holograms the plots will begin to scroll with the data this avoids using an excess amount of memory for visualization i e the plots only show the last 100 holograms worth of data Go to the folder s you specified as output paths for your processed data You will notice that a number of files have been created for each hologram The exact number of files created depends on what you have selected for output options In the following sections these files are briefly described LISST HOLO User s Guide 31 TIFF files output by HOLO Batch CSV files output by HOLO_Batch If you selected to output dep mon images two TIFF files will be created for every hologram process They will be placed in the reconstructed images folder The mon suffix image is a montage of all the in focus particles that were found in all the planes within an ROI The scale bar length can be adjusted prior to processing in the Advan
70. rewire board problem The laser will come on during this time for warm up Sampling enabled but the sampling conditions have not been met Either the magnetic switch is in the 1 position of the sampling was enabled on the Tools page Start condition met sampling Taking sample File maintenance taking place If the internal flash drive is error free this will take about 5 minutes If errors are found this can anywhere from 15 to 60 minutes depending on the severity of the problem LISST HOLO User s Guide 63 64 LISST HOLO User s Guide 11 LISST HOLO Size Ranges 11 1 Size Ranges based on LISST 100X SPHERICAL particles Size bin CO ND OFF fF DUNN EN o NE ONU OR OR Vie ONE Vibe Vie Tv 9 9 EM B A BE N Oo OF W N Ht SO DOAN OA Go Mk O ADA AN OO gt Go NMP o The LISST HOLO outputs the size distribution in 50 size ranges logarithmically placed from 1 25 4923 microns in diameter type B or 2 5 9847 microns type C In both cases the upper size in each bin is 1 180 times the lower These size ranges are chosen so that they are similar to the two different size ranges for the LISST 100X submersible particle size analyzer from Sequoia Scientific Inc in order to facilitate merging of data from the two instruments 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 bin for type B and C instruments Type B Type
71. rs Help Zoom Keep zoom factor Enlarge to fit Shrink to fit Keep aspect ratio Browser mode Enter Fullscreen mode Ctrl F File Edit Options View Slideshow Filters Help CA Science Test holograms 30 transmission pam 40 transmission pam 60Xtransmission pgm 7O transmission pgm 80 transmission pgm 90 transmission pgm Open up OpenSeelt and select Browser Mode from the View Menu Navigate to the folder where your holograms are stored They will all be displayed in the bottom left of the OpenSeelt window Use up down arrow keys to scroll through the holograms You can use this functionality to quickly determine which holograms will be suitable for processing and which will not 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 HOLO User s Guide 47 sod OpenSeelt v0 47 1 File Edit Options View Slideshow Filters Help E c os E C k Science 30 transmission pgm 40 transmission pgm EDXtransmission pgm 7O0 transmission pgm 80 transmission pam 90 transmission pam 5 9 Next Deployment or Powering Down This hologram will process well because the interference patterns are clearly visible and distinct The External Memory Module can now be re installed on the LISST Holo and sampling can be started again by moving the switch to the 1 positio
72. rst Mode Sample interval iu m us 10 Images per bunt MA MA IM M 3 Burst interval m mm H 10 Minutes Stop Condition Nov wl 15 well 2010 sl 23 00 ne 00 jv curt Date Time O Stop after 110 Minutes O gt Depth 5 meters O lt Depth 10 meters O External signal 1 goes low O External signal 2 goes low O Magnetic switch is in the 0 position Placing the switch in the 0 position will always pause sampling Samples 10 42 LISST HOLO User s Guide NOTE It is possible to set the LISST HOLO time to local time if a Time Offset is entered on the Tools page See section 6 6 for details The Delay Start will start after the specified delay The delay must be an integer number and can be specified as Minutes or Hours In this example the LISST HOLO will start sampling 1 minute after the magnetic switch has been turned to 1 On position The Depth Start will wait until the depth is greater than the specified value before starting In this example the LISST HOLO will start sampling once the depth exceeds 100 m and the magnetic switch is in the 1 position The External 1 and External 2 will wait for the voltage on the selected External input located in the Auxiliary 6 pin connector to be greater than 2 4V and the magnetic switch is in the 1 position The Magnetic switch option will start sampling when the switch is in turned to the 1 position NOTE ALL PROGRAMS MUST BE STARTED BY TURNIN
73. sleep mode Navigate to the Tools page and click the Sleep button at the Sleep or reboot line This will shut down the primary data logger and the green LED on the endcap should be blinking every 30 seconds instead of every few seconds Disconnect the Ethernet cable and plug in the External Memory Module using the special threaded locking part to hold it in place Proceed with section 5 4 It is NOT necessary to install the EMM in order to sample with the LISST HOLO In this case the holograms will be stored to the internal drive of the LISST HOLO If the EMM is not used the 8 pin dummy MUST be installed onto the 8 pin connector Failure to do so may short circuit the instrument and damages the electronics Unplug the yellow Ethernet cable and install the 8 pin connector Proceed with section 5 4 LISST HOLO User s Guide 43 5 4 Wake up power up LISST HOLO __ lf the system is still powered up but asleep move the switch to the 1 position and then quickly back to the 0 position This will wake up the instrument If the system is disconnected from power make sure the switch is at the 0 position then power it back on The LISST HOLO will boot up and be ready in approximately 30 seconds When the green LED is flashing every few seconds the instrument is awake and ready to start sampling 5 5 Start Data Collection To start the data collection program move the Switch to the 1 position The LED on the endcap will change fro
74. t and Stop conditions for the four different sampling programs The System Status shows the available memory on the internal flash drive input voltage current temperature and depth endcap switch position and the state of the two digital inputs The Select Program buttons lets the user select which program should control the LISST HOLO sampling Up to 4 programs can be loaded in the LISST HOLO In the example to the left Program 1 is selected If another program is to be selected click the appropriate radio button and then click the Apply button The details on the start stop conditions for the four different programs are reviewed in section 5 2 and will not be repeated here In addition to the External Memory Module the LISST Holo has an internal flash drive When the External Memory Module is not attached the holograms will be stored on the internal drive The Images page shows a listing of the holograms saved on the internal drive LISST HOLO User s Guide 49 KA Internet Protected Mode On fa v 6 4 Log page SE UOIA Research and Products for Environmental Science Home Images Log Configure Tools About Click on the image name to download 011 6698 pgm 011 6697 pgm 011 6696 pgm 011 6695 pgm 011 6694 pgm 011 6693 pgm 011 6692 pgm 011 6691 pgm 011 6690 pgm 011 6689 pgm 011 6688 pgm 011 6687 pqm 011 6686 pgm 1922065 bytes 1922065 bytes 1922065 bytes 1922065 bytes 1922065 byt
75. tch Open the program by clicking the HOLO_Batch executable File Options Help There are 5 main procedures to be performed before processing can begin HOLO_Batch Processing Initialisation Reconstruction Parameters Min Depth 0 mm e Select Reconstruction Parameters Max Depth 50 mm e Select Output Options on stoe m e Select Particle Bin Size Output Options Bin Sizes e Select Paths Folders 7 Save reconstructed slices B LISST 100X type B e Select Files LISST 100X type C 5 LISST 100X RANDOM type B 5 LISST 100X RANDOM type C E Save Dep Mon Images Save particle statistics MAT 7 Save particle statistics CSV 7 Save generated background Performance Options E Q9 Speed Memory Show data visualization Speed Memory Paths Files The HOLO Batch is shipped with factory default settings for the Unlock Reconstruction Parameters However if necessary they can be changed by selecting Unlock Restore Factory Defaults Reconstruction Parameters in the Options Menu v Save Settings on Exit B HOLO Batch The Change ROls and Advanced buttons then become active File Options Help Also the three input boxes for selection of the minimum and maximum focal length as well as the step size become active WO Batch Processing Initial Change ROIs Advanced Reconstruction P
76. the Original image that created the hologram Thus the LISST HOLO does NOT capture and store an image of the suspended particles It is the hologram of the particles that is stored During data processing the image of the suspended particles is reconstructed from the hologram Subsequently standard image processing methods can then be applied to get information about particle shape size area etc It takes a few micro seconds to capture the hologram using the digital camera The image captured by any digital camera is made up by a large number of pixels If the particles in the water move more than half a pixel during the time it takes to capture and store the hologram it is impossible to process the hologram and get reliable results For the pixel size used in the LISST HOLO a flow speed of more than 0 5 m s will begin to blur the hologram Consequently if the LISST HOLO is used on a profiling platform e g a CTD the profiling soeed must be 0 5 m s or less Likewise if the LISST HOLO is deployed on a mooring or tripod the current velocity around the instrument must be less than 0 5 m s Connecting the LISST HOLO to a local area network that is connected to the Internet has benefits The first benefit is that the instrument is accessible from different locations across the network Connecting the instrument to the Internet has other advantages such as checking for firmware updates syncing the time with international standards and transmittin
77. the Tools option On the tools page click the Take Images button to take a hologram Note that the laser turns on then off It takes a few seconds to capture a hologram in this manner because the laser has to warm up first The actual hologram is taken a few milliseconds before the laser turns off Then click the Images menu item to go to the 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 you can process the hologram If you want to process a hologram you always need to save it to a folder on your PC Holograms are stored in pgm format which is a lossless compression format In order to see the holograms on your PC you may need to download and install OpenSeelt http openseeit sourceforge net which is a FREE viewer for pgm files See the FAQ on the About page of the web interface for more information about OpenSeelt You can of course also use OpenSeelt to view holograms you have already downloaded and stored on your computer See section 12 for more information about the hologram pgm file structure d code version 200013 Lager costole code varmon 10051 1 nw nrbe 1454 Cic herz for Sequaa Soemhcs powacy policy regarding software updates FAQs ese Windows aed cannot view the ima The Windows viewer does not recogrize rhe POM image Ses Use Ceenseet The Open Get
78. ticle statistics file in MATLAB mat format for every image processed It will contain information about each particle detected in the image See page 33 for details Files The Save particle statistics CSV option creates a particle statistics file in Comma separated values ASCII format for every image processed It will contain the bulk properties of the image See page 32 for details The Save generated background option saves the background image used for processing if background files are selected background removal is discussed later in this section Show data visualization will show continually updated plots of total volume concentration number of particles per hologram temperature and depth This option is the fastest way to visualize data after it has been collected 26 LISST HOLO User s Guide S Bg HOLO Batch File Options Help Reconstruction Parameters HOLO_Batch Processing Initialisation Min Depth 0 mm Change ROIs Max Depth 50 mm Advanced Step Size 0 5 mm Output Options Bin Sizes Save reconstructed slices Save Dep Mon Images C Save particle statistics MAT C Save particle statistics CSV Save generated background 7 Show data visualization Paths LISST 100X type B 9 LISST 100X type C LISST 100X RANDOM type B 5 LISST 100X RANDOM type C Speed Memor
79. tion to the instrument The LISST 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 Router Serial Cable with Power Supply and a spare 5 pin cable for connecting the LISST HOLO to alternate power source such as a CTD Sequoia Scientific Inc is pleased that you have chosen one of our products Thank you We strive to make our instruments rugged reliable and simple to operate If you should have any difficulties or questions regarding this product please feel free to contact us at info sequoiasci com LISST HOLO User s Guide 9 10 LISST HOLO User s Guide 2 Contents and Technical Specifications 1 LISST HOLO with External Memory Module EMM installed 2 Instrument stands 3 Clear box with power supplies and communication cables 4 Clamps 5 Chamber for testing 6 Box with Manual CD with software wireless router 2 1 General Features e In situ digital in line holographic technology e Self contained with internal data logger Ethernet connection to PC for programmable data collection no software is needed for programming or offloading data Power via external battery pack Optional not included or 12 15V external power source cable provided Programmable data collection Optical path length 50 mm standard Sample volume 1 86 cm3 Data processing yields in focus p
80. to shore power or to the external power supply You should UNCHECK this checkbox if the LISST HOLO is powered with an external battery This preserves battery life The Sleep button on the Home page will disappear if the checkbox is checked synchronize time to a time server An Internet Set time E connection is required Settime Time zone 8 Set time zone Set to 0 for GMT Apply Set time manually Apply Click the Set time to synchronize the LISST HOLO to a time server If you want your local time to be displayed on the home page enter the Time zone and click Apply If you do not have internet access you can set the time manually Change level at which Change external sampling starts and trigger polarity stops Currently starts when signal is 1 Change Polarity Set duration laser power brightness gain and Set Defaults Restore default values shutter to known good values Clicking the Set Defaults button will restore the brightness gain and shutter to factory defaults 52 LISST HOLO User s Guide Submit log for analysis Generate log file Check for updates Network parameters Delete all images sends log and configuration files to Sequoia for troubleshooting at the SendLog next reboot Internet connection required Submit log for analysis Clicking the Send Log button will send the deployment log to Sequoia for troubleshooting The LISST H
81. torney 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 by the government is su
82. tton The changes will take effect LISST HOLO User s Guide 59 60 LISST HOLO User s Guide immediately 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 New LISST HOLO IP address Date 9 FAQs What is a hologram Why can t the LISST HOLO be used when the flow speed is more than 0 5 m s Why should connect the LISST HOLO to the Internet How do connect the LISST HOLO to the Internet Why does it take 2 minutes to process one hologram Is it possible to get data in real time from the LISST HOLO Does the LISST HOLO support DHCP What is the maximum sample rate for the LISST HOLO Can I connect the LISST HOLO directly to the Ethernet port on Fundamentally holograms are 3 D images that have first been projected and then stored on a 2 D surface In the type of holograms captured by the LISST HOLO so called in line holograms a laser beam is emitted and a small part of it is being scattered by the particles in the water The part of the laser beam that is not being scattered by particles interferes with the scattered light This creates an interference pattern a hologram The interference pattern is captured by a small digital camera Upon processing of the captured interference pattern i e the hologram it is possible to recover
83. u add a new ROI The advanced button opens up the settings menu for the advanced parameters The values listed in the window to the left are the factory default settings With the exception of Minimum Threshold Scale Length Clean Stack and possibly the Index of Refraction none of these values should ever be changed unless instructed by Sequoia support personnel to do so The Offset is the distance in mm from the receive window to the CCD array The reconstruction software needs this distance in order to properly reconstruct the holograms For the LISST HOLO this value is 28 mm DO NOT CHANGE THIS VALUE The Pixel Size is the size of each pixel in micro meters um For the LISST HOLO the pixel size is 4 4 um DO NOT CHANGE THIS VALUE The wavelength is the wavelength of the laser in nm For the LISST HOLO the wavelength is 658 nm The reconstruction software needs this value 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 LISST HOLO is used in air e g for measuring pollen or snowflakes the refractive index should be changed to that for air 1 0003 The Minimum Threshold is used for creating a composite image of all the particles in the hologram Decreasing this value will cause more pixels to be identified as being a particle increasing it will cause less pixels to be identified
84. uction Parameters Min Depth 0 mm Change ROIs Max Depth 50 mm Advanced Step Size 0 5 mm Output Options Bin Sizes 7 Save reconstructed slices Save Dep Mon Images C Save particle statistics MAT F Save particle statistics CSV 7 Save generated background T Show data visualization Paths gt LISST 100X type B LISST 100X type C 5 LISST 100X RANDOM type B 5 LISST 100X RANDOM type C Performance Options Speed Memory Speed Memory Files Select Holograms to Process Select Background File s Process 28 LISST HOLO User s Guide 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 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 options are not selected in the output options nothing will be written to the folder you select As above a browser window will open up prompting you to select a folder S Bg HOLO_Batch File Options Help HOLO_Batch Processing Initialisation Reconstruction Parameters Min Depth 0 mm Change ROIs Max Depth 50 mm Advanced Step Size 0 5 mm Output Options Bin Sizes
85. uld like to process a subset of holograms in the directory you can press Select Holograms to Process The directory you have selected for Raw Holograms will open in a browser window you can now select which holograms you would like to processs If you would like to process all of the holograms in the directory you can ignore this button LISST HOLO User s Guide 29 B HOLO Batch File Options Help HOLO_Batch Processing Initialisation Reconstruction Parameters Min Depth 0 mm Change ROIs Max Depth 50 mm Advanced Step Size 0 5 mm Output Options Bin Sizes 7 Save reconstructed slices Save Dep Mon Images F Save particle statistics MAT Save particle statistics CSV 7 Save generated background T Show data visualization gt LISST 100X type B LISST 100X type C 5 LISST 100X RANDOM type B 5 LISST 100X RANDOM type C Performance Options Speed Memory Speed Memory Files Select Background File s Select Holograms to Process i Bg HOLO Batch File Options Help HOLO_Batch Processing Initialisation Reconstruction Parameters Min Depth 0 mm Change ROIs Max Depth 50 mm Advanced Step Size 0 5 mm Output Options Bin Sizes Save reconstructed slices E Save Dep Mon Images C Save particle statistics MAT
86. y Speed Memory Files Bg HOLO Batch File Options Help Reconstruction Parameters HOLO Batch Processing Initialisation Min Depth 0 mm Change ROIs Max Depth 50 mm Advanced Step Size 0 5 mm Output Options Bin Sizes Save reconstructed slices Save Dep Mon Images Save particle statistics MAT 3 Save particle statistics CSV T Save generated background Show data visualization Paths D LISST 100X type B Q9 LISST 100X type C 5 LISST 100X RANDOM type B D LISST 100X RANDOM type C Performance Options Speed Memory Speed Memory The next step is to select the bin sizes for your particle size distributions The size bins for the LISST HOLO are based on the LISST 100X so that data from the two instruments can be easily merged While the LISST 100X has an upper size bin of 250um type B or 500um type C the LISST HOLO simply expands the upper limit of the size bins to 8000 um 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 Memory The Speed Memory option should not be used unless you are running a computer with at least 6 GB of RAM and are using a reconstruction step siz
87. y take a significant amount of time depending on your machine A new window will appear once the installation is complete Select the finish button to complete the installation process The Holo Batch and Holo Detail applications do not need to be installed on your computer The exe file contained in each folder can be run as a stand alone application You can move the Holo Batch and Holo Detail folders to a location of your choosing for example into the Programs folder It may also be helpful to create 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 Pin to Taskbar or Pin to Start Menu Two different programs are supplied for processing holograms HOLO Batch and HOLO Detail HOLO Batch will do batch processing of a selection of holograms and automatically output the size distribution as well as composite images showing the in focus particles HOLO_ Detail only processes one hologram at the time but allows the user to zoom and analyze a hologram in great detail in case more detailed image analysis is needed than what is provided with HOLO Batch In the following sections the use of these two programs will be explained 4 4 HOLO Batch automated This section describes how to use the automated batch processing program batch processing of multiple HOLO_ Batch holograms B HOLO Ba

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