SenSorTrace Pro 3.0 uSer manual
Contents
1. KEPEEG tin fs is possible to have a motor for all three axes Z X and Y The motor should be automatically detected However occasionally this does not happen and you must press SCAN to detect the ET ES motor Clicking MOTOR VELOCITY allows you to select the velocity of the motor s connected The speed is set to 1000 um sec as default Unisense recommends that you not increase this speed If the sensor is driven too fast there will be little time to intervene if the sensor is heading for a collision Also a slower speed NOTE may be recommendable if you are measuring in very hard or Settings for the coarse grained sediment allowing the sensor to adjust around sensors and obstacles Press OK channels can not When all settings are OK press START The settings are stored in be changed after the output file When START is pressed the sensor and hardware pressing Start settings are saved and five more tabs appear Comments Calibration Profile X Y Visualize and Activity You are taken automatically to the Calibration Tab please see below for details 10 COMMENTS TAB In the Comments tab you can make notes about the experiment Experimental motes can be entered here this is a test run of sediment profiling IV 1 Sensor 1 220 70 mv File shows the path and the filename selected previously in the START window Experiment notes allows you to enter text directly2. box below and this is not peer reviewed Unisense thus recommends that this feature of SensorTrace PRO is used as an easy instrument 27 for getting acquainted with the concept of activity calculation and for fast feedback For publication we recommend that PROFILE which is the program written by Peter Berg et al to implement their method is used to prepare data since this method is peer reviewed The PROFILE program can be obtained from Peter Berg by e mail pb8n virginia edu The Activity tab has a button Write input file for PROFILE Pressing this button creates an input file for the program PROFILE ver 1 0 How TO USE THE ACTIVITY CALCULATION NOTE 1 Start by choosing the sensor and profile The analysis that should be analyzed in the Active can only be sensor and Profile No fields This will performed when display the chosen profile in the graph the concentration window Note The analysis can only be performed when the concentration is measured in umol l and if the sensor has been calibrated before measuring the profile SensorTrace PRO 2 0 Testing for PRO2 manual xis IV 1 Sensor 1 221 90 mv 2 Enter depth and zone settings in the Interval and zones Choose the start and end points of the profile where the 28 is measured in umol calculation should be performed This will typically be the top of the sediment and the end of the profile Then choos
3. Comments Here you can add comments to your experiment by pressing COMMENT or use the keyboard shortcut Ctrl K This will result in a dialog with a timestamp and a text field You can then enter text in the text field and either leave the time stamp unchanged or update it Thus this feature allows the user to either 1 press the button just when observing an unforeseen event and then write the appropriate text later or 2 write the text 11 first wait for an expected event and press UPDATE TIME when the event occurs The events will be shown in the table to the right and mark is displayed in the graph in the Strip chart window Hovering the cursor over the mark displays the event text All notes and comments are stored in the final output excel file CALIBRATION TAB To convert sensor signals mV into a corresponding concentration or pH value a calibration must be performed Calibrations are performed on the Calibration tab SensorTrace PRO 2 0 Testing for PRO2 manual xis Time Slope _ Intercept r2 Comment 1 14 08 0 7647 1 6188 1 0000 The buttons in the top left corner show whether the sensors are calibrated or not Uncalibrated Calibrated Choose the sensor you would like to calibrate The sensor name type and calibration unit is shown under Active calibration Signal Shows the current raw sensor signal for the chosen sensor The sensor signal can also be followed
4. g Calculated bottom flux nmol cm s h Integrated production in nmol cm s When all calculations are done the solution with the highest number of zones that is significantly better than the previous solution p lt 0 05 is TECHNICAL DETAILS The Berg et al 1998 optimization method is based on the Downhill Simplex Method using two steps 1 Estimates the production in an increasing number of equally spaced zones 2 Finds the statistically best fit and then decreases the number of zones by joining zones with similar production The method of SensorTrace PRO is based on a Powel optimization method In addition the method does not use equally spaced zones but also estimates the zone width The method uses the steps 1 Estimates production and zone width in a profile with N zones starting with 1 zone Splits each zone of the above profile in two and uses this as an initial guess of zones in a profile with N 1 zones Find the best solution among these N different solutions with different starting conditions Further reading on optimization http en wikipedia org wiki Optimization_ mathematics boundary conditions http en wikipedia org wiki Boundary_condition 32 highlighted in the table However it is advisable to visually check the other estimated solutions by clicking and thus highlighting these in the table Furthermore the effect of changing boundary conditions and or minimum zone widt
5. continuously in the strip chart window in the bottom of the tab 13 CALIBRATION PROCEDURE 1 Prepare the calibration standards 2 Choose the sensor you would like to calibrate 3 Inthe Concentration box enter the appropriate value When using oxygen sensors you can also click the button O2 The dialog that appears allows you to enter temperature and salinity and SensorTrace PRO will automatically calculate the corresponding concentration of oxygen at atmospheric saturation 4 Insert the sensor into the calibration sample 5 Add the calibration point by pressing ADD POINT when the sensor signal has stabilized Several calibration points can be added at each concentration by pressing the ADD POINT button repeatedly 6 Change to a new solute concentration and repeat steps 3 5 7 When satisfied with your calibration press APPLY CALIBRATION When a calibration is applied the calibration parameters can be seen in the calibration table see below 8 Repeat steps 2 7 for other sensors All calibration points can be removed by pressing CLEAR ALL POINTS A single point can be cleared by right clicking the point and choosing Remove Three point or multi point calibrations can be applied by making calibration points at for example a range of concentrations Calibration curves are calculated from a linear regression The calibration table shows the calibrations for the chosen sensor Each calibr
6. in New um For example if you want to define the surface of the study sample as the zero position move the sensor tip to the sample surface using the up and down arrow keys OR by manually moving the sensor When the sensor approaches the surface or if the sensor is hard to see it is a good idea to use small increments Verify the position e g with a microscope Enter 0 in the New um field and press SET ACTUAL Subsequently the values in Actual and Depth um will reflect the re defined depth scale Sometimes if it is not possible to see the sensor it will be necessary to do the first profile find the sample surface from there and redefine the depth scale using the above procedure If subsequently you want to move the sensor to a specified position e g 300 um above the sediment type 300 under Depth um and click Move Profile Start um End um and Step size um In the left part of the profile box you can set the primary parameters of the desired profile start position end position and step size All distances 17 are given in um Negative values are above a surface and thus normally the start position should be negative Safe position The safe position is the position where the motor will rest between cycles The safe position is to ensure that the sensor is resting outside the tissue or sediment be
7. not show up in the Motor table in the Settings tab when you press Scan The Motor unit and or connector cables are not installed properly Close down the program Search for the connected devices on the computer and choose to install automatically The computer should ask for both the USB RS232 adapter driver and the driver for the motor controller If the computer is unable to find the appropriate driver for the adapter install it from the CD that came with the motor controller and cables If you encounter other problems and need scientific technical assistance please contact sales unisense com for online support we will answer you within one workday 40 Ry UNISENSE UNISENSE DENMARK www unisense com info unisense com
8. up at the bottom of the profile This implies that there is a zero concentration and also a zero concentration gradient at the bottom of the profile and the boundary concentration Bottom conc bottom flux is appropriate with zero as the parameters entered in the boxes below This is also the most common boundary condition for nitrate profiles For sulfide profiles on the other hand the concentration is typically zero over an interval at the top of the profile and consequently also the flux is zero so in this case Top conc top flux is appropriate 5 Press the Analyze button to start the activity analysis The progress will be shown on the screen while the method is running The calculation starts first with one zone and then makes the calculation for increasingly high zone numbers until the specified maximum zone number For each zone number a row in the table is created with the following parameters a Zones The number of zones in the calculation b SSE Sum of Squared Errors is the difference between the simulated and observed profile The smaller this number the better c P Value the probability of the hypothesis that including an extra zone 31 significantly improves the prediction The hypothesis is calculated based on the F value see Berg et al 1998 d Calculated top concentration in mol l e Calculated bottom concentration in umol I f Calculated top flux in nmol cm s
9. 9850159 331 0270691 4 17 2009 13 24 00 450 438 9098206 334 0285034 skResRsRebesResRsRsEE 4 17 2009 13 24 07 500 436 8208618 332 4309998 4 gt Comments Sensors Calibration data Calibration Profiles z m Ready 34 graphics which are not saved in the output Excel file To export a graph right click on the graph This returns a small menu with two options Export and Print Choosing Export makes a dialog box appear with three tabs Picture Native and Data and the buttons Copy SAVE SEND and CLOSE The chosen tab determines the type of data e Picture the data is a graphic either a bitmap or a Windows metafile Native this tab is redundant and can be disregarded Data the data are data values in a format chosen by the user It is possible to choose only one sensor in the series drop down box Each sensor is mentioned two times The first time a sensor is mentioned data represents uncalibrated measurements the second time data represents calibrated measurements ce Export Dialog Picture Format as Metafile Colors Default E Monochrome Preview The buttons have the following functions Copy copies data to the Windows Clipboard to be pasted directly into Excel or other program by pressing CTRL V or Edit Paste SAVE prompts for a filename and path where the data is saved SEND sends data as an attachment to an email CLOSE closes the di
10. LECTING SEVERAL CYCLES The program will make one Z profile then move in the X direction make another profile and so on When all profiles are performed in the X direction it will move one step in the Y direction and repeat When all profiles are made in the X Y grid it will return to the safe position and wait for a period of time given by the Delay between s For all three axes you must select whether the profiles will be perfomed manually or using motor control If a motor is not connected or found by the software you will not be able to select Motor control here and both the Movement boxes and the Motor control boxes will appear shaded 20 CONTROLLING THE HORIZONTAL MOVEMENT X Movement and Y Movement Start um End um and Step size um Set the start position end position and step size in the X or Y direction All distances are given in um X Motor control and Y Motor control The options in the X Motor control and Y Motor control correspond to the motor control from the Z axis depth Please see section above for explanations VISUALIZE TAB This tab is for advanced visualization of your measured profiles You can plot your measurements as normal profiles or as contour plots For the examples described below You have made 3 measurement cycles in 3 dimensions Start End Step size Z 0 5000 100 0 500 250 Y 0 500 250 22
11. Profile plot of a time series of oxygen profiles in a photosynthesizing biofilm after the light has been turned off CONTOUR PLOT Contour plots allow you to view concentration contours of a plane of your choice You must select to view all measurements in exactly two parameters Z X or Y and then press CONTOUR PLOT Example 1 Plot a horizontal section in the depth 700 um of sensor 1 in cycle number 1 Choose Sensor 1 Cycle 1 Z depth 700 X position all Y position all There are two options for contour plots normal and filled shown below To switch between them check the check box Filled 2D Contour plot filled 2D of the oxygen distribution ina transect througha photosynthesizing biofilm PROFILE PLOT Profile plots allow you to view concentration changes with depth in relation to different horizontal positions of your choice Choose the sensor and the variables your would like to view X Y and cycle number Press PROFILE PLOT 23 Example 1 Plot how a profile changes over time Profile with sensor 1 in position X 250 and Y 500 Choose Sensor 1 Z depth all Cycle all X position 250 Y position 500 Cycle 1 Example 2 Plot a vertical section of sensor 1 in X 0 and Y 0 500 in cycle number 2 Choose Sensor 1 Z depth all Cycle 2 X posi tion 0 Y position all Adjust zero depth It is possible to drag the zero line directly on the profile graph and then cl
12. Time Depth um Concentration umol Signal mV 3 14 17 2009 13 20 34 1000 287 3865662 218 1541901 4 4 17 2009 13 20 41 950 287 0737 217 9149323 4 17 2009 13 20 48 900 286 1364746 217 1982117 6 4 17 2009 13 20 55 850 286 2156372 217 2587433 17 2009 13 21 02 800 286 0479126 217 1304779 g 4 17 2009 13 21 09 750 286 0636292 217 1425018 9 4 17 2009 13 21 17 0 285 9248657 217 0363922 40 4 17 2009 13 21 24 650 285 8215027 216 9573364 44 14 17 2009 13 21 31 600 285 8191223 216 9555206 42 4 17 2009 13 21 38 550 285 6255798 216 8075104 4 17 2009 13 21 45 500 285 6341553 216 8140717 4 17 2009 13 21 52 450 285 8023987 216 9427338 4 17 2009 13 21 59 400 285 772583 216 9199219 4 17 2009 13 22 06 3 285 6999512 216 8643951 4 17 2009 13 22 13 300 285 4558716 216 6777344 4 17 2009 13 22 20 250 285 5209961 216 7275391 CL 4 17 2009 13 22 27 200 285 4934387 216 7064667 7 4 17 2009 13 22 35 150 286 2733154 217 3028412 4 17 2009 13 22 42 100 285 745697 216 8993683 4 17 2009 13 22 49 50 287 8505859 218 5090485 4 17 2009 13 22 56 294 598175 223 6691132 4 17 2009 13 23 03 50 314 837738 239 1469116 4 17 2009 13 23 10 100 344 9969177 262 2105408 4 17 2009 13 23 17 150 373 4891357 283 9993591 4 17 2009 13 23 24 200 394 0458538 299 7181702 4 17 2009 13 23 31 250 415 9232788 316 4500122 4 17 2009 13 23 38 300 423 197052 322 0124817 4 17 2009 13 23 46 350 423 7573547 322 4409485 4 17 2009 13 23 53 400 434
13. UNISENSE SENSORTRACE PRO 3 0 USER MANUAL AN SENSORTRACE PRO 3 0 User Manuat SENSORTRACE PRO 3 0 USER MANUAL Copyright 2010 Unisense A S Version October 2010 UNISENSE A S TABLE OF CONTENTS SENSORTRACE PRO 3 0 USER MANUAL CONGRATULATIONS WITH YOUR NEW PRODUCT SUPPORT ORDERING AND CONTACT INFORMATION OVERVIEW a kur ken INSTALLING SOFTWARE GETTING STARTED et SENSORTRACE PRO INTERFACE THES TRIPCHAR Te kaye cok n sanan acted boas SETTINGS TAND 252 does da aid accus COMMENTS TAB 2 sue cures onu CALIBRATION TAB CALIBRATION PROCEDURE PROFILE TAB int ee mien PAU tal ans VISUALIZE TAB s eue ACIIVILY TAGs tease acne idee ous OUP FIN scat s h Here cut nakin b n 4 WARRANTY AND LIABILITY REPAIR OR ADJUSTMENT TROUBLESHOOTING nu n sen CONGRATULATIONS WITH YOUR NEW PRODUCT SUPPORT ORDERING AND CONTACT INFORMATION If you wish to order additional products or if you encounter any problems and need scientific technical assistance please do not hesitate to contact our sales and support team We will respond to your inquiry within one working day E mail sales unisense com Unisense A S Tueager 1 DK 8200 Aarhus N Denmark Tel 45 8944 9500 Fax 45 8944 9549 Fur
14. age to the tip of the sensor is not covered by the warranty Liability In no event will Unisense be liable for any direct indirect consequential or incidental damages including lost profits or for any claim by any third party arising out of the use the results of use or the inability to use this product REPAIR OR ADJUSTMENT Sensors and electrodes cannot be repaired Other equipment that is not covered by the warranty will if possible be repaired by Unisense with appropriate charges paid by the customer In case of return of equipment please contact us for a return authorization For further information please see the documents Conditions for Sale and Delivery for Unisense and Warranty and Shipping Information 38 TROUBLESHOOTING Problem Possible cause 1 Solution Possible cause 2 Possible cause 3 Solution Problem Possible cause 1 Solution Possible cause 2 Possible cause 3 The following error message appears RS x 4 D converter is not recognised Board S N IF problem persist please contact Unisense Do you want to start configuration utility Yes No __w You have not connected your meter or A D converter Connect the meter The program does not recognize the analog to digital converter An A D converter with different bit resolution have just been connected Choose yes to open the configuration utility InstaCal InstaCal will remove any old A D converte
15. alog 36 REFERENCES Berg Risgaard Petersen N and Rysgaard 5 1998 Interpretation of measured concentration profiles in sediment pore water Limnology and Oceanography 43 7 1500 1510 Ullman W J and Aller R C 1982 Diffusion Coefficients in Nearshore Marine Sediments Limnology and Oceanography 27 3 552 556 Iversen N and Jorgensen B B 1993 Diffusion Coefficients of Sulfate and Methane in Marine Sediments Influence of Porosity Geochimica et Cosmochimica Acta 57 3 571 578 Revsbech N P Nielsen L P and Ramsing N B 1998 A Novel Microsensor for Determination of Apparent Diffusivity in Sediments Limnology and Oceanography 43 5 986 992 37 WARRANTY AND LIABILITY Microsensors are consumable items The sensors are tested thoroughly before packaging and shipment Warranty for sensors sensors 60 days from shipment Standard Oxygen sensors 180 days from shipment All other sensors excluding special sensors 90 days from shipment If within the above specified period the sensor s fail to perform according to the specifications Unisense will replace the sensor s free of charge Unisense will only replace dysfunctional sensors if they have been tested according with the instructions in the manual upon receipt of the sensor s The warranty does not include repair or replacement necessitated by accident neglect misuse unauthorized repair or modification of the product Physical dam
16. ange V Select the voltage range for the A D converter Select this range as small as possible to increase the resolution of the A D converter However if the signal gets beyond the selected range the A D converter will be saturated Normally Unisense microsensors have a pA signal below 1000 pA corresponding The Chart format dialog to 1000 mV Choosing 1 V allows the best resolution of the A D converter in this case Name Write a name describing your sensor optional Comment Write a comment about your sensor optional BACKGROUND FREQUENCY To the right of the table SensorTrace PRO allows you to select the frequency of the background data acquisition This determines the frequency with which the A D converter reads the signals from the instrument s Note the background frequency is not the logging frequency and thus does not denote the number of data points in a profile If you are using a computer which may be slow or less powerful than specified in the computer requirements for the program you can set this to slow This will cause the program to acquire data with a speed of 100Hz 100 times per second instead of 1000 Hz This will put less strain on the computer but result in more noisy measurements In most instances especially if your computer meets the standards in the specifications you should leave the background data acquisition on Normal vs ku Motors The table below shows the Motor settings It
17. ation will appear here with information on calibration number time of calibration regression data slope intercept and r2 as well as additional comments A mark for each calibration will also be displayed in the Strip chart window All calibration data are stored in the output Excel file For information on calibration of different sensors consult the sensor manuals RECALIBRATION PROCEDURE If the sensor response changes during an experiment e g due to tempearture changes sensors can be recalibrated The new calibration will apply from the time of calibration onwards 1 Press Clear all points 2 Follow step 1 7 in the Calibration procedure RETRIEVING A CALIBRATION Pressing RETRIEVE CALIBRATION will retrieve the calibration of the selected sensor channel made the last time the program was running The user should make sure that this calibration actually applies to the sensor that is currently connected Remember to press APPLY CALIBRATION after retrieving a calibration IMPORTANT When retrieving a calibration you will load the last calibration made the previous time the program was running Make sure that the retrieved calibration matches your current sensor in terms of signal size and units 15 PROFILE TAB The Profile tab controls the Z axis depth of your profile Here you can set start and end points step size lag time before measuring lag time between measurements and so on Profiling wi
18. by the installation program This will install the SensorTrace PRO program and a version of this manual in the program group Unisense A configuration utility for the A D converter will also be installed This is called Instacal and will be placed in a program group called Measurement Computing Important If you already have InstaCal on your PC the installation procedure will ask you whether you would like to update or remove it Choose Update GETTING STARTED 1 Connect all hardware in your set up to the computer 2 Start SensorTrace PRO It is placed in the program group Unisense The following dialog appears D Sensor Trace PRO 302 i EE UNISENSE SensorTrace PRO v3 0 2 New experiment Load old experiment 3 Choose either to make a new experiment or load an old experiment click OK a New experiment A dialog appears were you can choose name and location of your new data file b Load old experiment A dialog appears were you can choose the file you would like to open This mode is for working with old data settings or parameters cannot be changed and new measurements cannot be made SENSORTRACE PRO INTERFACE The SensorTrace PRO interface is divided into two main areas The upper area is divided into different tabs that allow the user to access the different functions of the program In the lower area the Strip Chart window is located This shows all the
19. d more about the Comments dialog in the Comments tab 18 section Possibilities during measurements Motor will stop and return to the safe position you Abort are asked whether the program should save the data Keyboard shortcut Esc Motor will rest until restarted or aborted Resume Make a new data file You are asked for a new file AU name You are asked to decide whether you would New file like to keep the settings from your previous experi ment or whether you like to start with new settings Clears all logged data Clear Manual versus automated profiles If you have a Unisense Motor Unit the profiles and number of replicas can be performed automatically using the positions and delay periods described above If you do not have a motor unit you will have to move the sensors manually with a micromanipu lator In this case a dialog box will appear after each measurement that will tell you which depth to go to When you have reached the depth appearing in the dialog box press OK This corresponds to the motor reaching its depth and the wait and measure cycles will begin i Cancel 19 X Y TAB The X Y tab controls the horizontal movements if profiles are made in two or three dimensions As with the Z axis this can be done manually or automatically motor control SensorTrace PRO 2 0 Testing for PRO2 manual xis 1 Sensor 1 221 20 mv USING THE 2D or 3D OPTION AND SE
20. e the maximum number of zones to be used in the calculation Note that the maximum number of zones multiplied with the minimum zone width has to be smaller than the distance between the start and end points The calculation can be very slow if using a high number of zones on a slow computer The minimum zone width is the smallest zone width that the method allows and it should not be smaller than twice the step size in the profile To make the calculation it is necessary for the program to have values for diffusion coefficients and porosity These values can either be measured values obtained by different methods see e g Ullman and Aller 1982 Iversen and Jorgensen 1993 Revsbech et al 1998 or they can be estimates based on literature To set the porosity and diffusion coefficient values Press Ds AND THETA to display the Ds and Theta dialog In this dialog adjust a The number and borders of the zones with different diffusion coefficient and porosity First select the number of zones in the entry box which adjust the size of the table below Then adjust the start depth of each zone b Porosity i To specify a uniform porosity in all depths Enter a measured or estimated value in the Default 29 30 porosity field and click SET POROSITY To enter variable porosity enter measured or estimated porosity values by typing directly in the table If only a subset of the porosi
21. ent see Rules of thumb box below since background and the transport phenomena and processes in one layer affects theory in published the concentration in neighboring layers The SensorTrace PRO papers before software enables the user to model the distribution of production using this tool for and consumption in a one dimensional diffusion reaction system research purposes based on measured concentration profiles Concentration Consumption Bulk water phase Diffusive boundary Straight line layer DBL diffusion onl Surface Concave curve production Sediment biofilm etc Convex curve consumption Depth x RULES OF THUMB If the diffusion coefficient and porosity is constant in a layer the following rules of thumb can be used for a qualitative interpretation of the processes in that layer e If the concentration curve is convex there is net consumption e g respiration if the concentration curve is concave there is net production e g photosynthen thetic production of oxygen If the concentration curve is linear there is no net consumption or production only diffusional transport 26 THEORY Under steady state conditions where solute transport only occurs by diffusion the concentration profile can be described mathematically by the one dimensional mass conservation equation d dc pD R 0 dx where C is the pore water concentration x is t
22. h could also be tested 6 Save solution Press the Save solution button to save the highlighted solution to an Excel file The first time this button is pressed a dialog appears where the name of the Excel file is chosen The following solutions are appended to this file Note the file cannot be open in Excel while saving new solutions to it Unisense encourages users to read the background and theory in published papers e g Berg et al 1998 before using this tool for research purposes For references please see the References section in the back of this manual 33 OUTPUT FILE All data and text entered are stored in an output Microsoft Excel file The worksheets in the Excel file reflect the tabs in the SensorTrace PRO software However for technical reasons two sheets are present with calibration data SensorTrace PRO tabs Excel worksheet Settings Sensors Comments Comments Calibration Calibration data and Calibration Profile Profiles DIRECT EXPORT OF GRAPHS The content of all graphs in SensorTrace Basic can be exported either as graphics or as a data file This option is particularly useful for conserving the data in the visualizations and strip chart E1 Microsoft Excel Testing for PRO2 manual File Edit View Insert Format Tools Data Window Help pe a question for ARNO OP ere NRA NP were RERO RTE 10 Bl U E E E dl gt EE E18 v f 4 Sensor 1 2
23. he depth is the porosity Ds is the diffusion coefficient and R is the net rate of production or consumption If C Ds or R are not constant with depth this equation can only be solved numerically METHOD Several routines for interpretation of concentration profiles have been developed The routine implemented in SensorTrace PRO is based on the method published by Peter Berg et al 1998 The method exploits the fact that given a set of different depth zones with known or estimated porosity and diffusion coefficient a steady state concentration profile can be calculated if the activity rate of consumption or production is given for each depth zone The user must provide estimates for the diffusion coefficient and the porosity in all zones and some boundary conditions for the model before the routine is initiated The routine makes an initial guess of the activity distribution and compares the calculated profile with the actual measured profile Via a stepwise optimization method the activity distribution is refined until the calculated profile does not deviate from the measured profile within some statistical margin for further details see the Technical Details box The SensorTrace PRO activity calculation feature gives the user an interactive interface to experiment with activity calculations from concentration profiles However the program uses a different algorithm from that of Berg et al 1998 see Technical details
24. ick ADJUST ZERO DEPTH This will redefine the zero depth for the current profile and activity visualizations and the activity calculations If you are adjusting the zero depth this way on a profile that you have just made in the program the final output file is not yet generated the zero depth adjustments will be saved to the output file for this profile If you have opened a previously generated data file zero depth adjustments will not be saved to the data file 24 Edit Chart It is possible to edit the setting of the chart display There are many possibilities but it is important to stress that changes are irreversible and this feature should be used with care i This feature is undocumented and any changes made to the chart are irreversible Use with care r a 2D Chart Editor 2D Series Format Grid 30 General Marks Data Source Options Levels Marks Pointer Position PS contour 2D Series jj Frame Filled Transparency 0 E Smooth Interpolate 25 ACTIVITY TAB The shape of a measured concentration profile is determined by DISCLAIMER the transport phenomena and processes activity occurring Unisense strongly at different layers within the investigated system However it is encourages all not a simple task to quantify these phenomena beyond a crude users to read the qualitative statem
25. rs not connected to your system and search for connected A D converters Noisy and fluctuating measurements signals Physical vibrations from other appliances on the table are causing movements of the sensor resulting in instability of the experimental set up and disturbances in the measurements Remove all unrelated appliances from surfaces in contact with the experimental set up and ensure completely stable conditions for the sample Electrical noise in the system You have accidentally set the Backgound Data Acquisition in the Setting tab to Slow 39 Solution 1 Solution 2 Solution 3 Problem Possible cause Solution Problem Possible cause Solution 1 Solution 2 Remove all unrelated appliances from surfaces in contact with the experimental set up and ensure completely stable conditions for the sample Check that the system is properly grounded Connect the provided blue grounding cable to your amplifier and directly into your measuring set up Change the logging frequency of your software You will need to experiment to see which settings produce the best signal Please consult sales unisense com if you require additional support Make sure that your computer meets the requirements of the program Restart the program and make sure that the Background Data Acquisition is set to Normal SensorTrace PRO shuts down suddenly Computer has entered sleep mode Remove sleep mode settings The Motor unit does
26. sensor signals and event marks continuously to provide the user with an overview of the entire experiment These elements are explained on the following pages THE STRIP CHART The Strip Chart graph is permanently visible in the lower part of the SensorTrace Basic interface It allows the user to view sensor signals continuously for the active sensors By default uncalibrated raw sensor signals are shown but if the Calibrated check box is checked calibrated values are plotted but for calibrated sensors only The strip chart hold a maximum of 24 hours of measurements You can change the height of the window by dragging its upper border The SensorTrace PRO interface Comments and calibrations points can be seen as colored marks in the strip chart window By holding the cursor over the mark the associated text is displayed All datapoints in the Strip chart window can be cleared by pressing the Clear button This will NOT affect the data stored in profile measurements Chart time axis The range of the time axis can be changed using the drop down menu Show last min The time range can also be changed with mouse zoom see below Mouse zoom To view specific areas of interest all graphs in SensorTrace PRO can SETTINGS TAB be zoomed with the mouse by dragging a frame from the upper left to the lower right of the area of interest To un zoom drag a frame in the opposite direction After star
27. t up the software will automatically search for hardware To zoom only on the signal axes check the Y zoom only The hardware found will be indicated in the two tables and the checkbox user can adjust the settings THE CHART FORMAT DIALOG Signal axes and series formatting can be modified in the Chart Format dialog which appears when a signal axis is right clicked works only after START is pressed The dialog is divided into two tabs for displaying calibrated and uncalibrated values respectively or Detected Velocity um s COM port 1000 The dialog allows the user to e manually set the minimum and maximum axis value Auto by default ees allocate each sensor to a different signal axis maximum four separate axes change the appearance of each sensor graph Sensors with respect to visibility and thickness of i i The top table shows the sensor instruments and sensors In this raph lines and visibility and size of data ied d table you can enter parameters for the channels and sensor types point marks in addition to the graph color that you are using Sensor Mark the checkboxes for the sensors you will use most instruments and A D converters from Unisense will be recognized by the software and the appropriate number of channels will be preset Type Choose the sensor type from the drop down menu Vis 5 Unit Select an appropriate unit R
28. th depth can be done with or without a motor unit automatic or manual The functions of this sheet are the same whether you do your profiles manually or automatically IMPORTANT The depth scale is positive downwards For example if the zero is set at the sediment surface positive values in the boxes below Actual Depth and New Depth will indicate that the sensor is in or should move down into the sediment ES IMPORTANT The depth scale is positive downwards For example if the zero is set at the sediment surface positive values in the boxes below Actual Depth and New Depth will indicate that the sensor is in or should move down into the sediment The profile tab Motor control SensorTrace PRO 2 0 Testing for PRO manual xis mS This control box allows you to read adjust and redefine your sensor position Actual um indicates the current vertical position of the sensor tip NOTE the Actual position is arbitrary until the user has related the position of the sensor Move ol tip to the position of the study sample see the ol example below Pushing the up or down arrows will move the sensor the distance specified in Increment um and update Actual depth um accordingly Clicking Move moves the sensor to the position set in Depth um SET ACTUAL re defines the motor position Actual um to the position given
29. ther documentation and support is available at our website www unisense com OVERVIEW SensorTrace PRO is a program for making profiling microsensor measurements i e making a series of measurement points with a microsensor along a path and visualizing these measurements The software supports motor controlled automated measurements but it is also useful in managing sessions with manual positioning The software supports up to 16 sensors and the sensor positioning can be managed with a resolution of 1 um SensorTrace PRO is designed with easy data management in mind so all set up information as well as experimental data is automatically saved as MS Excel files System requirements Windows XP 2000 Vista 100 MB free hard disk space 1024 x 768 display or higher A digital Unisense amplifier or A D converter unit e g Microsensor Multimeter For sensor signal via meter A USB port For motor control An RS232 port or room for USB adapter To view output files you should be able to view or import Excel files Other programs For time series measurements of up to 16 channels we recommend that you use SensorTrace BASIC which is available as a free download from our website www unisense com For photosynthetic experiments using the light dark switch technique we recommend that you use SensorTrace PHOTO INSTALLING THE SOFTWARE Start the installation program from the CD Follow the instructions given
30. tween replica profiles In 2D and 3D profiles this is also the height above the sample where the sensor tip will be moved parallel to the sample surface Therefore be sure that the safe position is well above the sample surface Wait before measure s When the position set by the primary parameters is reached the system will wait for a period before it starts measuring This is to ensure that the sensor signal is stable before the measurements start The default setting is 3 seconds but should be set to match the sensor response time Measure period um sets the duration of the measurement in each position Each measurement will be a value integrated over this period of time When making profiles in a noisy environment such as ona ship or in a cold room it can be helpful to integrate average over a longer period i e increase the measure period Making replica profiles Set the desired number of cycles in the Number of cycles After finishing the first profile the sensor is returned to the safe position and another profile is started after a delay period given by Delay between s In Replicates you enter the number of measurements that should be performed at each depth When all parameters are set press START At all times during the experiment it is possible to enter a comment Press COMMENT and Comment the Comment dialog appears E Enter the comment and time stamp and press OK You can rea
31. ty values need to be different set a uniform porosity and modify the subset by typing in the relevant cells afterwards c Diffusion coefficient To use diffusion coefficients calculated from the porosity Enter the diffusion coefficient in free water at the actual salinity and temperature See the Unisense table for values for oxygen diffusion coefficients in the Documentation and Downloads section of our website http www unisense com Default aspx ID 49 Select an equation to calculate the sediment diffusion coefficient with depth from the porosity in the Sediment diffusion coefficient equation box See a discussion of the most suitable equation in Ullman and Aller 1982 and lversen and Jorgensen 1993 Boundary conditions To use independent diffusion Choose coefficient values type a y Top conc bottom conc diffusion coefficient values Top conc top flux measured or estimated Top conc bottom flux Bottom conc top flux directly in the table Press OK when done 4 Specify boundary conditions It is possible to choose between several different boundary conditions see Berg et al 1998 To choose the right set of conditions it is important to consider the characteristics of the profile see examples in Boundary condition examples box BOUNDARY CONDITION EXAMPLES BOX Oxygen profiles in many cases end with a constant concentration of zero as all the oxygen is used
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