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LISST-100X User’s Guide

Appendix G: BioBlock Use

The BioBlock Anti-Biofouling Shutter system is a bolt-on optional accessory that is available for the
LISST-25X and LISST-100X. Copper disks are placed very near the optical widows. The copper
discourages any biology from growing on the optical windows. The BioBlock is self-contained with
its own battery pack. It uses a 5V logic signal from the dedicated BioBlock connector on the
LISST-100X connector endcap.

This appendix is separated into three parts. The first section covers the installation of the BioBlock
onto the LISST-100X in 6 steps.

The second section discusses configuring the firmware in the instrument to recognize the BioBlock
and use it during data collection.

The third section discusses general maintenance such as cleaning and battery replacement.

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Summary of Contents for LISST-100X

Page 1: ...User s Manual Version 5 0 2700 Richards Road Suite 107 Bellevue WA 98005 4200 Tel 425 641 0944 Fax 425 643 0595 LISST 100X Particle Size Analyzer...

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Page 3: ...This document is copyrighted by SEQUOIA SCIENTFIC INC...

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Page 6: ...ce For technical assistance please contact your local Distributor or Sequoia Please be sure to include the instrument serial number with any correspondence IMPORTANT Please read APPENDIX H TECHNICAL A...

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Page 8: ...Waste Electrical and Electronic Equipment Smaltimento di apparecchiature elettriche ed elettroniche da rottamare...

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Page 11: ...ed Real time data processing 64 Step by Step Procedure Configuring data collection 69 INSTRUMENT COMMUNICATION 75 LISST 100X COMMAND SUMMARY 79 LISST 100X COMMAND DETAILS 81 PERFORMANCE OPTIMIZATION 9...

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Page 13: ...of laser light is observed at multiple small forward angles At these small angles light scattering is determined almost entirely by light diffracted by the particle The light transmitted through the p...

Page 14: ...o size distribution involves a mathematical inversion In this step a size distribution is found that would produce multi angle scattering that fits the observation There exists a vast literature on th...

Page 15: ...we have provided software that obtains the inverted volume distribution NV 1 Agrawal Y C I N McCave and J B Riley 1991 Laser diffraction size analysis in Principles methods and applications of particl...

Page 16: ...ded in the Windows software For MATLAB users inversion scripts are available for download from Sequoia s website www SequoiaSci com The principal measurement angular scattering distribution is obtaine...

Page 17: ...large such as typically happens during profiling applications External I O Ports The LISST 100X is also equipped with an external ANALOG IN port for recording the output of one other analog instrument...

Page 18: ...to 24 VDC external power Cables up to 50 meters can be provided to supply external power and communication with the instrument This can allow real time observation of the size distributions When not u...

Page 19: ...LISST 100X User s Guide 7...

Page 20: ...8 LISST 100X User s Guide...

Page 21: ...nstrument please handle it gently as you would handle a very expensive camera Critical alignments may be disturbed if the instrument is subjected to shock or rough handling Evidence of shock rough han...

Page 22: ...ower cable and Allen wrench set Step 1 Remove Instrument from shipping case Start by removing the white plastic instrument stands and set them on a flat working surface Remove the LISST 100X from the...

Page 23: ...k Use 5 pin connector Used for serial communication and external power See Appendix C Connector Pinouts for LISST 100X 6 pin connector Used for analog in and digital in out signals See Appendix C Conn...

Page 24: ...ons Cable Remove the Communications cable from the shipping crate It is the 2 meter cable with the 9 pin DB 9 connector on one end and the 5 pin underwater connector on the other Remove the underwater...

Page 25: ...rogram Data Sequoia LISST100 This is the default folder for saving your data but you can change it in the software There are 2 very important files in this folder InstrumentData txt and LISST ini Thes...

Page 26: ...ment status will be displayed If the cable connections are not correct or if the battery is not installed a warning message will appear after the time expires The serial port settings can be checked b...

Page 27: ...ill print ZZZ to the screen every 30 seconds To wake the instrument from the Terminal window press the Stop button immediately after the ZZZ is displayed The instrument will only respond to the Stop b...

Page 28: ...strument The image below shows an example of this display It is opened by either selecting Collect Background Scatter Data from the LISST menu or by pressing the button on the toolbar After selecting...

Page 29: ...Laser power value can also be an indication of optical misalignment Step 11 Configuring Instrument for Deployment The Operating Modes window is used to set all of the deployment parameters To open the...

Page 30: ...ution displays This mode sends the raw data to the LISST SOP software for conversion to Size Distribution and displaying on the screen No data is saved on board the instrument when this mode is used B...

Page 31: ...ed Choose the Start Condition tab at the top of the window There are five options Depth Time External Mechanical Switch External Digital Input and Time Delay Select the mode by clicking on the button...

Page 32: ...en an LOP extension which will identify it as a LISST Operating Procedure File Comments can be entered before saving in the box below the summary Previously saved LOP files can be opened using the Bro...

Page 33: ...inning the data collection Step 17 Background file warning If the background file you selected is more than 6 hours old a File Warning dialogue box will appear alerting you that final data quality cou...

Page 34: ...being flicked to the 1 position Only then will actual sampling begin If you select the No button the warning below appears informing you how you can start the instrument When the instrument has been s...

Page 35: ...h Start and Depth Stop For all other Start Conditions the program will terminate and return to the L100X prompt To stop a running program use the Stop button on the Terminal window or the button on th...

Page 36: ...a Transfer Status window will appear The data is offloaded at 115K baud If you click the cancel button in the upper right corner of the transfer window the current file transfer and any remaining file...

Page 37: ...select the background scatter file to use when processing the data The LISST SOP will do a check of the laser power value in the selected background scatter file If the laser power is 0 zero a warning...

Page 38: ...created depends on the selections in the Settings selection in the File menu The software will automatically determine the Instrument Type B or C using the Serial Number and the InstrumentData Txt fi...

Page 39: ...II files and as binary files with a PSD extension The PSD files can be opened and viewed on the screen To open a processed Particle Size Distribution file choose Open Particle Distribution File or pre...

Page 40: ...Guide To view the value of the auxiliary parameters such as time and depth select the View Auxiliary Parameter Frame from the DataFrames menu A display similar to the one below will appear showing th...

Page 41: ...he display will be reduced The Start and Stop conditions will not be used and therefore their settings are not relevant NOTE For extended Real Time sessions it is recommended to use external power The...

Page 42: ...s not being used Pressing the next button will command the LISST to make a measurement and transmit the data to the SOP for display The Spherical Random Shape radio buttons can be selected in order to...

Page 43: ...ment back to sleep After finishing with the instrument it should be put back into its low power sleep mode In this mode with the communication cable disconnected the drain on the battery is only about...

Page 44: ...32 LISST 100X User s Guide of these steps are covered in detailed Step by Step instructions in the following sections...

Page 45: ...g deployment follow these processing steps that includes optional displays and procedures Page 40 Batch Processing Multiple raw data files Data that has been downloaded from the datalogger is in a raw...

Page 46: ...0 Advanced Real time data processing The advanced real time data processing allows for using all data collection modes and start stop options e g burst mode delayed start pressure start with the real...

Page 47: ...ions program started L100X prompt showing 3 Open the Collect Background Scatter Data from the LISST menu or by pressing the button on the toolbar After selecting the factory background scatter file to...

Page 48: ...some of the inner 6 rings are high 6 Note down the 33rd and the 36th value they should be around 1000 1500 for most LISST 100X s Element 33 factory Element 36 factory Elements 33 and 36 from the fact...

Page 49: ...the file name on the list Multiple files can be selected by hold down the CTRL key while clicking on files Use the SHIFT key to select a range of files Files selected and path set Press the OK button...

Page 50: ...se errors during offloading If an offload error occurs you can change the offload baud rate as follows 6 Go to Settings in the File Menu and click the Serial Port tab In the File Offload Baud Rate dro...

Page 51: ...ISST menu A list of files on the datalogger will appear 3 Select the files to be deleted then click the OK button Use the CTRL key to select multiple files or the SHIFT key to select a range of files...

Page 52: ...and calibrated data This is useful for loading into spreadsheets such as Excel etc The LOG file is a space delimited ASCII file containing the raw data from the LISST 100X data logger This is useful f...

Page 53: ...e the Spherical particle model The reason for this is that no other laser manufacturer provides a randomly shaped particle model for inversion so there will be nothing to compare to Generally it is re...

Page 54: ...d Instrument serial number selected Only the serial numbers of the instruments loaded into the InstrumentData Txt file and have the calibration values loaded into the LISST INI file in the Windows dir...

Page 55: ...same base name but with different extensions Note file types other than the default PSD file must have been selected before starting the Open Raw Data file command See step 2 Output data file name se...

Page 56: ...yed at a time Use the Next and Previous buttons to move through the complete datafile The triangles on the lower edge of the upper display will indicate where in the complete datafile the currently di...

Page 57: ...creen will show the current sample or frame Pressing the Select First button will set the current cursor position as the starting point for processing Similarly selecting Select Last will set the end...

Page 58: ...SCII file containing all the processed data The LOG file is a space delimited ASCII file containing the raw data from the LISST 100X data logger Select file types to be created 3 You must also select...

Page 59: ...manufacturer provides a randomly shaped particle model for inversion so there will be nothing to compare to Generally it is recommended that you keep both boxes checked this is also the default optio...

Page 60: ...d have the calibration values loaded into the LISST INI file in the Windows directory can be used 6 Select the background scatter file zscat file to be used for processing your data Click the select b...

Page 61: ...LISST 100X User s Guide 49...

Page 62: ...another directory The Raw Files List box now shows all the raw data files DAT or LOG extension that are in your Raw Files Directory while the Output Files Box shows ASC PSD and LOG files that may alr...

Page 63: ...6 processed files for each raw data file An ASC PSD and LOG file for both spherical and random shape inversions Note that the files processed using the randomly shaped inversion method have an _rs su...

Page 64: ...the command line The paths and file names are stored in the LISST INI file which resides in the C Program Data Sequoia LISST100 directory You can examine the LISST INI file before and after batch pro...

Page 65: ...LISST 100X User s Guide 53 Notes...

Page 66: ...tafile selected 4 After selecting the processed file a window similar to the one shown below will appear The left hand display is the volume distribution in units of micro liters liter in each size cl...

Page 67: ...this window is shown below 7 The scale of the Volume Distribution plot can be changed by using the Scale button After selecting the button a display similar to the one shown below will prompt you for...

Page 68: ...urrent display can be sent to the printer by choosing Print from the File menu Print Preview and Print Setup are also available Display printed 9 When finished viewing the processed data close the win...

Page 69: ...ument becomes older and to some extent with temperature Values around 0 5 2 mW are the most common values Laser Reference should never be 0 or very close to 0 e g 0 02 mW If this is the case the laser...

Page 70: ...ues generally are in the 0 98 0 995 range your measurements are taken in very clear water This means that the signal to noise ratio will be low and the data may have a lot of noise in them but can mos...

Page 71: ...LISST 100X User s Guide 59 Notes...

Page 72: ...binary PSD file must be selected before any other file type will be stored This is used to display the processed data to the screen The ASC type is a spaced delimited file containing all the processed...

Page 73: ...ons The slide button next to the Timer button controls the sample speed If it is set too fast it will automatically reset to the maximum allowed rate Timer button pressed and samples updating automati...

Page 74: ...by selecting the View Rings command from the File menu An example of this display is shown below Value of rings for current frame displayed 11 A single sample may be saved to a separate file by pressi...

Page 75: ...the window is closed However if the window is left open the power will remain on potentially draining substantial life from the battery To turn off the power without exiting the Real Time session pre...

Page 76: ...g Open Real Time Session Select Output from the Options menu The window below will appear Select output settings A binary PSD file must be selected before any other file type will be stored This is us...

Page 77: ...file Background and Output file selected 5 Open up the operating mode windows and select the desired operating mode In this case burst mode is being selected Instrument configured with the desired ope...

Page 78: ...de can always be stopped by selecting the Stop button in the SOP window Stop condition selected 8 Now click Apply and then OK You will be asked if you wish to start the instrument It is very important...

Page 79: ...ing the realtime data and select an output file name Then click OK and the realtime window will open up Check the Listen Mode check box Prepare real time window for listen mode 11 Next open the termin...

Page 80: ...s being saved as default but it is very strongly recommended that the user also always selects a LOG file output option in File Settings Output tab before starting the real time processing Please note...

Page 81: ...LISST menu or by pressing the button on the toolbar When first opening the Operating Modes window the LISST SOP program will send a Ctrl C to the LISST 100X If a program is running it will be stopped...

Page 82: ...set the type of sampling RealTime Burst or Continuous You can also select the samples per average and sample rates on this screen The RealTime mode is used for real time size distribution displays Thi...

Page 83: ...to configure when the instrument will begin sampling There are five options Depth Time External Mechanical Switch External Digital Input and Time Delay Select the mode by clicking on the button next t...

Page 84: ...the Base Program on the instrument will return to waiting for the Start condition For example if the start and stop conditions were set to External Mechanical Switch then multiple sampling sessions ca...

Page 85: ...6 hours old a warning is issued and the user is being given a choice between selecting a different file collecting a new background or accepting the risk and continue For best results the zscat file s...

Page 86: ...al window The Run button is equivalent to typing RUN and pressing Enter from any terminal program 11 The Base Program will display text to the screen as it is running to confirm that it is running and...

Page 87: ...screen and then return to sleep The instrument firmware is retained in on board flash memory and will start executing when power is applied After a power up pressing the ENTER key will cause an echo o...

Page 88: ...is switch once a second If the switch is in the on or 1 positions the program will go directly to the data collection routine It will continue checking the switch status until the switch is moved to t...

Page 89: ...s the instrument is moving up and down If the Start Condition is Depth Start the Base program will return to checking for the Start Conditions For all other Start Conditions the when the current depth...

Page 90: ...aved has been reached the program will stop and return to the L100X prompt Maximum Memory or Low Battery The Maximum Memory or Low Battery Stop condition will continue to sample until the memory capac...

Page 91: ...o x BI x Set Burst Interval SB x Set Samples per Burst SC mm dd yy hh mm ss Set Clock with time and date where mm month dd day yy year hh hour 24 format mm minute ss seconds Example ST 01 05 2005 21 0...

Page 92: ...80 LISST 100X User s Guide consumption...

Page 93: ...is 778B 155F Directory of C L040305_ BIN 4 136 03 05 04 6 30p L183705 BIN 1 672 03 05 04 6 37p 2 file s 5 808 bytes 0 dir s 15 933 440 bytes free L100x DS Display current status information Syntax DS...

Page 94: ...f text Setup Commands OM Set Operating Mode Syntax OM x or om x Description Sets the Operating Mode to one of the following types 1 Real Time Mode 2 Burst Mode 3 Fixed Rate Mode OM command only withou...

Page 95: ...hen the GO command is issued The start condition data is used with the Start Condition setting as follows If the Start Condition is Depth Start option 1 the input will be start depth in meters If the...

Page 96: ...he input for TD will be the stop date and time If the Stop Condition is Fixed Number Stop option 5 the input will be the number of samples to collect before stopping The TD setting is ignored for Mech...

Page 97: ...nute ss seconds If no values follow the SC or sc command prompts for entering the time and date will be displayed Example input SC 01 05 2001 21 05 03 output Command Data in SC is 01 05 01 21 05 03 Cu...

Page 98: ...nd to verify the current settings Then confirm 1 yes 0 no that these settings should be burned into the EEPROM to be used with the AutoStart setting Example input SD output LISST 100X Current Status a...

Page 99: ...ll be displayed as part of the DS status if the store mode is disabled WARNING Data storage disabled Data will not be saved ZD Reset Depth Sensor Offset Syntax ZD or zd Description The ZD or zd comman...

Page 100: ...tax GX or gx Description Acquires single averaged sample and displays the result to the screen Example Input GX Output 32 ring values 8 Aux parameters Notes The GX command does not store the sample to...

Page 101: ...hen acquiring a background Example Input ZS Output 32 ring values 8 Aux parameters repeat 20 times Notes The ZS command does not store the sample to a datafile ZZ Go into deep sleep mode minimum power...

Page 102: ...les It is very important that clean and bubble free water is used The water can be fresh or salt water For most applications it has been found that steam distilled water is sufficient Steam distilled...

Page 103: ...is very important that a good background file be obtained with very clean water As particle concentrations increase the relative signal to background noise ratio also increases thus reducing the impo...

Page 104: ...ner rings are shown on the left side of the background display The most important rings for misalignment indication are rings 1 4 in the background scatter file As the focused laser starts to move awa...

Page 105: ...aller diameter section is the suggest mounting area The U shaped mounting block provided with the instrument fit this diameter and can be used for mounting the instrument The clamps supplied with the...

Page 106: ...is a sensitive instrument When not in use the instrument should be stored in its shipping case For longer storage year or so the communication cable should be disconnected and the battery pack should...

Page 107: ...pressure and temperature sensors can be re calibrated if desired The performance of the instrument can be checked with the use of a sample of particles of a known size distribution Such samples ship a...

Page 108: ...t remove the end cap by gently threading the long bolts in evenly They will bottom out against the edge of the pressure housing and slowly force out the connector endcap When the O ring becomes visibl...

Page 109: ...t the position of the connectors to minimize the diameter of the assembly If the connectors are not arranged properly it will be difficult to insert the battery into the pressure case Battery wrapped...

Page 110: ...98 LISST 100X User s Guide...

Page 111: ...micron Resolution 32 size classes log spaced Data storage memory 1GB 12 million measurements standard Maximum sample speed 1 size distributions per second standard Temperature sensor range 10 to 45o C...

Page 112: ...e in a text editor Auxiliary Parameter Display Label Multiplier Offset Units Parameter 1 Laser Power mW Parameter 2 Battery 0 01 0 volts Parameter 3 External Instrument volts Parameter 4 Laser Referen...

Page 113: ...2 5 27 6 27 2 86 3 38 3 11 5 72 6 75 6 21 7 26 3 38 3 98 3 67 6 75 7 97 7 33 8 25 3 98 4 70 4 33 7 97 9 40 8 65 9 24 4 70 5 55 5 11 9 40 11 1 10 2 10 23 5 55 6 55 6 03 11 1 13 1 12 1 11 22 6 55 7 72 7...

Page 114: ...5 14 4 73 7 26 2 70 3 19 2 93 5 14 6 06 5 58 8 25 3 19 3 76 3 46 6 06 7 15 6 59 9 24 3 76 4 44 4 09 7 15 8 44 7 77 10 23 4 44 5 24 4 82 8 44 9 96 9 17 11 22 5 24 6 18 5 69 9 96 11 8 10 8 12 21 6 18 7...

Page 115: ...rst size range for type C randomly shaped particles bins 1 x rho 0 31 lower limit bins 2 x rho 1 32 upper limit bins 3 sqrt bins 1 bins 2 mid point B_all logspace 0 log10 200 33 0 1 create 33 logspace...

Page 116: ...24 0 482 0 222 0 262 0 241 11 22 0 524 0 618 0 569 0 262 0 309 0 284 12 21 0 618 0 729 0 671 0 309 0 365 0 336 13 20 0 729 0 861 0 792 0 365 0 430 0 396 14 19 0 861 1 02 0 935 0 430 0 508 0 467 15 18...

Page 117: ...0 465 0 428 0 197 0 232 0 214 12 21 0 465 0 548 0 505 0 232 0 274 0 252 13 20 0 548 0 647 0 596 0 274 0 324 0 298 14 19 0 647 0 764 0 703 0 324 0 382 0 351 15 18 0 764 0 901 0 829 0 382 0 451 0 415 16...

Page 118: ...Elements Parameter 1 32 Light intensity on detectors 1 through 32 33 Laser transmission Sensor 34 Battery voltage in raw counts 35 External Auxiliary input 1 0 to 5V 0 to 4096 36 Laser Reference senso...

Page 119: ...calibrated units mW 36 Laser Reference sensor in calibrated units mW 37 Pressure in calibrated units m 38 Temperature in calibrated units C 39 Day 100 Hour at which data taken 40 Minutes 100 Seconds a...

Page 120: ...nnector Pinouts for LISST 100X The LISST 100X has 3 separate underwater connectors A 5 pin a 6 pin and a 3 pin connector The photograph shows the placement of each connector The following text describ...

Page 121: ...an Diego CA USA Connector Part Number Bulkhead MCBH WB 5 MP Stainless Steel Mating Cable Part Number MCIL 5 FS Connector Pin Use 1 Power Serial Ground 2 External Power In 9V nom 6 15V 8 3 Power Serial...

Page 122: ...rt Number MCIL 6 FS Connector Pin Use 1 Digital Ground 2 Digital In 1 3 Digital In 2 4 No Connection 5 Analog In 0 to 2 50V max 6 Analog Ground BioBlock Connector 3 pin connector Connector Manufacture...

Page 123: ...t Clock Sets the internal instrument clock to match the currently connected computer clock Operating Modes Opens the Instrument Sampling Configuration window where operating mode and sampling schemes...

Page 124: ...the Print button will be activated Pressing the button will send the current display to the printer Put LISST to sleep Attempts to wake up instrument from low power sleep mode This may take up to 40 s...

Page 125: ...ip and replace files Unzip the file to a temporary folder on your hard drive and then REPLACE the following 4 four files with the files you already have on your PC Factory_zsc_2002 asc replace with th...

Page 126: ...amber first clean the windows of the LISST 100X NOTE On older versions of the LISST 100X it may also be necessary to remove the endcap ring and standoffs on the optics endcap Remove the three screws o...

Page 127: ...l of the chamber It may be necessary to press on the top bottom and sides of the Slider to get it to slide out without binding Step 5 Once the slider is positioned such that the O ring is engaging the...

Page 128: ...BioBlock is self contained with its own battery pack It uses a 5V logic signal from the dedicated BioBlock connector on the LISST 100X connector endcap This appendix is separated into three parts The...

Page 129: ...st for correctly positioning the unit during installation The BioBlock should be removed from the LISST 100X in the Closed position to facilitate re installing it at a later date The BioBlock may be c...

Page 130: ...to hold the BioBlock in place Step 4 Slowly slide the BioBlock shutter assembly straight down between the Crossbar Standoffs and the windows the LISST 100X sample volume taking care not to drag the c...

Page 131: ...to the LISST 100X and configure the instrument using the instructions on the following pages Then verify normal operation by cycling the system using the LISST EXE software The BioBlock shutter shoul...

Page 132: ...xample issuing a BB 10 command will enable the connection and send the command to close the BioBlock A BB 11 command will also enable the connection and send an open command During normal sampling the...

Page 133: ...LISST 100X User s Guide 121 command the BioBlock to remain open By monitoring the battery the BioBlock can be left in the open position before the battery voltage is too low...

Page 134: ...a battery mount attached to the connector endcap Remove the batteries and replace with fresh alkaline batteries If desired wrap each battery with electrical tape to keep it in place during installatio...

Page 135: ...annot use the psd or asc files produced by the LISST SOP for troubleshooting do not include these in your email We can only help you if you supply the information listed in 1 3 above Q When I try to q...

Page 136: ...inside the cable The voltage should read 12 V If it does not the cable may be defect Short the female pins 4 and 5 on the communication cable using one or both paperclips Type some characters into MO...

Page 137: ...re save the edited LISST INI file in C ProgramData Sequoia LISST100 Q When I try to offload the data I get an error and the offload stops I can talk to the instrument and program it but it will not of...

Page 138: ...s The standard underwater connectors for communications and power are molded to the cable Full Path Mixing Chamber Allows the submersible LISST 100 100X to also be used as a laboratory particle size a...

Page 139: ...measured without the need for permanent optical pathreductions PRMs are available to reduce the optical path by 50 80 and 90 Large Volume Test Chamber Horizontal acrylic chamber with O ring and drain...

Page 140: ...128 LISST 100X User s Guide Replacement Zscat Chamber Used for doing background scatter measurement zscat before deployment One chamber ships as standard with the LISST 100X...

Page 141: ...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 specifica...

Page 142: ...o 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 su...

Page 143: ...Digital Inputs 5 E Error Messages could not find Instrumentxxxx 125 no valid query response 123 External I O Ports analog 5 digital 5 76 77 External Power Supply 6 99 F File type asc 27 40 107 dat 10...

Page 144: ...ndard Particles 95 Start Conditions 71 depth start 76 external digital input 76 external mechanical switch 76 time delay 76 time start 76 Stop Conditions 72 depth stop 77 external digital input 77 ext...

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