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Acquire & Analyze 2.1.8 User Manual

1. Tile Vertically cM ec eU EE E C A Active Window C T iii o Open Help Pci DAC Informatio D iaa Application Toolbar rc A AAA Protocol Tool ia Create New Graph usais l Lab NOtEDOOK enmaai I ILIUM E D TAI ri Show Event Markerg srerirsretsrescrerssirosevesonisarinirotet esee tabin PONEV K es sabe KORS TO akee orai NOREN A Area Corre cia LE at Lock Edit Mode Toggle iaa DAC TG BAL sti R EEE RR AE EEE Ea Start Chart AQUI a n A A ES Slow PU iii ti E Medi m EE 3 Fast PU o w Mark SAI ETERNI UU IM Graph A A EES Control and Scroll Toolbar nene ene ene neister eNe aE E Eei LA Graph Plot SEU Ni mil NEW iii DI Area Under ii iia a A A Soroll Rig y PR o o OE D S rol EE Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual n SOTO D OW EE ZOOM Kee le CN EY VAPEUR amp ZOOM FOE AXIS E Zoom Auto Y Axis Only ii Al Zoom Recenter at Cursor coccccnononononnnononononnnanononononocoonnnnononononconononnn nono nnnconononnnos E Ree ee al EN EE al NOTIN I i E E T R Zoom In X axis IA A a E Zoom Out X axis EN RE Ouf E iia iii Application St t s Bar A cid Exporting DEA AAA ARA AAA AAA AA MEN Laboratory NOVEDOSA AAA A AA o A PPP O o II recs LOU cris Blue Bar at Top Active Part of error iii HF r ELE I Si de A M i
2. Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual connection just close the spreadsheet save it before you close it Open up the second experiment that you wish to access Repeat the same procedure with the data bar and selecting tissues This time you will not need to reselect the Excel worksheet labels as the program will remember your last selection Go to the Avg Data tab again and select the row s to export Repeat this process with as many data files as you need When you are done you can click the Avg button to the right of the Excel worksheet drop down list box at the upper right of the Avg Data tab This will total each column and calculate an average and standard deviation E lal fi lv Tela Ev T Export Settings Filename Sample Data_GraphData xIs y M Data to Export r Other v Current Isc Area corrected values a Eneas Gt Prompt for Note when saving JV Resistance Rt v Export to an Excel Spreadsheet v Isc Calculated v Vt Calculated Set Worksheet Labels No format selected xl sur data 2 Format Names Worksheet Names SMT data 1 New Name New Format Save Name Save Format Delete Name Delete Format ili Ae Physiologic Instruments 12335 6 World Trade Drive e San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Data Bar Values Raw Opens a data g
3. A small message box will appear that requests you to install the parallel port drivers Select the install drivers on boot checkbox to be checked and press Install 8 Completing You may start the program now if you wish If not unselect the check box Click Finish when you are ready You may need to reboot your computer if the screen instructs you to do so After you have run the program installer you will need to run the license unlock installer This is included with all versions starting at the A build version 2 3 114 To run this installer run the program called F Acquire23 XUnlock exe where F is your CD ROM drive Accept all defaults and click finish This will unlock the software so that it can run in data acquisition mode This should complete the installation successfully If it did not for some reason first try again following the instructions closely and if it still does not work please contact our support staff Unless you have an unusual hardware configuration this should now be working If it does not for some reason for example if you are trying to use LPT2 with the DI 720 or your DI 9 Physiologic Instruments 12335 6 World Trade Drive e San Diego CA 92128 Acquire amp Analyze 2 3 User Manual 400 needs a special address other than 180 you may need to install the full Windaq driver CD ROM 10 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Anal
4. Apply Cancel This section consists of two sets of 32 button controls laid out as grids On the upper grid the buttons are labeled with numbers and may be of various colors These buttons will be used to select the tissues whose data will be displayed in the graph The lower grid contains similar buttons except that these may contain graphics symbols and colors or they may be blank These are the symbols that may be plotted to represent individual tissue data Alternatively the tissues can be labeled by numbers Selecting Tissues to Plot In order for the graph to display data from a given tissue the button corresponding to the tissue number must be selected depressed by left clicking over the button Note The number of tissues is limited to 8 in this version of 66 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual A amp A The button is selected when it turns from gray to color and appears to be depressed Standard Windows shortcuts apply to selecting multiple tissues Namely clicking on one button toggles the status of that tissue then pressing the Shift key and pressing a second tissue will cause all tissues buttons between the two to take on the status of the first button Setting Tissue Color Right clicking on the tissue button will open a color selector dialog box for setting the color This will be the color that displays for symbols digits a
5. Event Mark screen before the scheduled manipulation This Event Mark screen contains a countdown timer description of the manipulation to be made a list of tissues to which the manipulation is to be made and buttons to place the Mark in the file and record the event The first tissue to be manipulated appears in the large icon on the left of the form When the user presses the Mark button or Spacebar a Mark Event is recorded for the first tissue the countdown timer is set to the specified interval between marks and starts counting down the tissue indicator updates to indicate the next tissue to be manipulated Upon reaching 0 the countdown timer will automatically place a mark in the file for the tissue and reset for the next mark or close the form if there are no more tissues to be marked Sequential Variable The alarm is used to sequentially apply the same event mark to multiple tissues but with varying times between marks on different tissues This alarm acts much like the Sequential alarm except that the Mark button or Spacebar must be pressed for each tissue mark to be recorded The form closes when the manipulation has been made to all specified tissues Pop up Menu There is a pop up menu that will Seconds appear if the user right clicks the Minutes mouse on either the edit or the view Bap fas curae protec Hours Copy to Manipulation 61 Physiologic Instruments 12335 6 World Trade Drive San Diego CA
6. T Phusiatagic Acquire amp Analyze Version 2 3 User Manual PHYSIOLOGIC INSTRUMENTS INC 12335 World Trade Drive Suite 6 San Diego CA 92128 Tel 858 451 8845 Fax 858 451 6012 Email physinst aol com Web http www physiologicinstruments com Acquire amp Analyze 2 3 User Manual Table of Contents TABLE DE CONTENTS cssccsnctescascacevensiscesccsnsvecscsnccctvecusssacabinssdeesiosdacesiecanasianseessiosdacevaspusnssaascan s 1 INTRODUCTION caia 6 INSTALLATION cinta 8 HARDWARE streets 8 DataO DIE720 Series E 8 e 8 SOFTWARE Si is 8 ACQUIRE amp ANALYZE 2 3 INSTALL FOR DO 9 FULE WANDA GO INSTALL EE 11 QUICK STAR Eon 12 OVERVIEW M 12 DATA ACQUISITION PROCEDURE eene Ie I e e n en nnnn nnn nnn nnn nnn nan n n n n s s p nsn p s pn pp Ip Vua 12 DATA ANALYSIS PROCEDURE serios ib tt 14 APPLICATION REFERENCE GUIDE soccicnsariairani n din Ee 16 APPLICATION WINDOW areo riode eese ao OAR EAE aE TEE AE E TEES RTEA E 16 Application Window Menu BA ANA AA 16 LE 16 New Experian 16 Append EXP is 17 Open EXP imd USO E nS E KK i UREE 18 Close Experiment osse oa 18 KEE E 18 SEN 18 Graph Print SEW asa ii 18 oce A E E E E E 18 ds 18 lu NN II ia 19 ou di T 20 Eben 20 A a e PU o aoa orem ne E 21 E POINTS EE 21 E FOOT F
7. 180 Instantaneous 240 Instantaneous 300 Instantaneous Inl xl Method Joe Stk Conc Qty Unit_ Description Add by Weight Add by Weight Add by Weight Add by Volume Using the Data Grid For users that are accustomed to modern spreadsheet style grid editors you may want to note that the value of the cell will not get saved until you leave the cell In other words if you wish to change the Original Time value for example you click on the cell you wish to change edit the value and then leave the cell If you attempt to make any other operations before leaving the cell with the value that you want to update it will not save this value Notice in Edit Protocol 57 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual this close up view that the row selection icon has changed to a pencil instead of an arrowhead to the left of the cell displaying 160 seconds indicating that you are currently editing a cell To verify that you have saved the cell contents make sure the pencil icon no longer appears Toolbar buttons Create New Protocol Create a new protocol library file Open Protocol Open an existing file from disk Open for Viewing Only This feature enables opening a second protocol for viewing and copying Save Protocol Save current edit protocol library Save As Protocol Sav
8. The first three buttons open only one panel at a time and correspond to the Manipulation Libraries panel M the Protocol panel P and the Event Log panel E The next three are combinations of two of each panel These three buttons correspond to the Protocol Design MP Experiment Run PE and Event Log Edit ME phases of an experiment Manipulation Libraries M Displays only the Manipulation Libraries editor panel 53s Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Protocol P Displays the Protocol editor panel Event Log E Displays the Event Log editor panel Protocol Design MP Displays both the Manipulation Libraries and Protocol editor panels It is used for creating and editing manipulations and creating editing experimental protocols Experiment Run PE Displays the Protocol and Event Log editor panels It is useful for viewing both the protocol and the recorded events during an experiment Event Log Edit ME Displays the Manipulation Libraries and Event Log editor panels It is used for editing the event log In this display the manipulations libraries can be used to quickly update events in the log file Using the manipulations libraries to add events provides consistency to the recording of events enabling better search capabilities for subsequent analysis Editor Panels Below the main toolbar is the editor region of t
9. that have been accessed by the A amp A application Clicking on one of these files will open that data file without having to sort through your Windows folder hierarchy A Graph Print Setup xj Tissues Plot Points EX EE E ESESE 0 BE axis Color Label Freq fi Plot Title Save As Default 19 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual 2 Add Printer Edit Menu Copy Currently the Copy feature copy to Windows clipboard is available but not the Paste To use the Copy feature 1 2 3 When using the data grid windows select one or more rows with the mouse which will then appear highlighted Type CTRL C This will copy the selected data to the clipboard The clipboard data can now be pasted into a text file created with Notepad or WordPad in comma delimited format also compatible with Excel 20 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Zoom Menu The following commands permit manipulation of the graphics display They are listed here and explained in detail under the Graph Toolbar beginning on page 47 a Zoom All Zoom All Ctrl A Determines the minimum and maximum data Zoom Auto X Axis Only for all tissues to be displayed and then adjusts Zoom Auto Y Axis Only the X and Y axes so that all the
10. the bar width also can be changed by pressing the left mouse button while the cursor is just outside either side of the box and then dragging the box to a new width An enunciator will appear to display the box width A Acquire and Analyze 2 1 Experiment 1 Isc yA vs Time Sec Bl xl File Edit Zoom Experiment Acquire Analyze Tools Graph Setup Window Help 81 x EIB El ea ees a a ml lala elalalalralalealalalealal 3 4 32 Data Bar Lines Data Bar Toggle Button X 41 38 Sec Y 3 38 pA Ready DI 720 Instrument VCC Series Voltage Clamped 00 02 21 No Protocol Tissue rea cm2 7 28 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Area Under Curve If this menu option is checked it will activate the Data Bar and also display a horizontal line having three positioning handles The Area Toggle Button is see above screenshot also synched with this menu option The line is used to determine the slope such as during the initial response to a drug and for setting a baseline for calculating the area under a curve e g area under current vs time is the net charge transferred To use this feature to carry out a linear regression open up the Data Bar Values Averaged dialog and select the Linear Regression tab Each Tissue will have a default slope and intercept already computed from the points that lie within the part of the graph selected
11. the list until the list is done It is possible to stop in the middle of an experiment if you need to make an adjustment to the tissue or chambers In this case you may want to re start the protocol in the middle of the list If that is true click on the row of the next alarm which you want to fire off Now re start the data acquisition click white running man on the toolbar or use the menu option The dialog will appear with the time of this alarm incremented to account for the time that the experiment has been stopped If you want the alarm to start up right away you can use Current You can alternatively specify your own value or use the previous schedule When you click on each radio button the Actual column in the protocol editor grid will change reflecting the new schedule if you accepted the change now After you find the right time click OK and the experiment will start running again with the reminder alarms firing at the scheduled Actual time A Reset Protocol Start Time x This screen allows you to set the start iR of the next alarm Subsequent alarms will be shifted in sequence Display units in sec v Scheduled Time Current scheduled auto update D Curent auto update C User specified 0 H C Revert to previous actual schedule C Use original schedule Cancel Protocol Table Row Selection Button Buttons down left side of pane select the entire row 59 Physiologic Instr
12. 92128 Acquire amp Analyze 2 3 User Manual grid This menu has two functions The first is to enable the user to switch time units from seconds to minutes to hours so they can match the time displayed in the graph window along the X axis Note that you must have the splitter enabled and have a valid protocol library open in both the View and Edit grids in order to have the Copy to Current Protocol option enabled The second is to provide a protocol item copy capability If you right click in the Protocol View grid on one of the row entries you can copy that row to the current Protocol Edit grid Similarly if you click on the Edit grid you can copy that row back to an open Manipulation library if you have both editors currently displayed the MP button Note that you must first select a row in the Manipulation library before the Copy to Manipulation option is available Event Log Editor Displays the Event Log editor panel A ARA Laboratory Notebook k MIP E Pe el Event Log Time fs Solute Tissues Method Kon Element4 112345678 A 82 Fast Speed 123456 Change Potentiorr 1 Change Potentior 2 35 62 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual A ne OR RIES A TC E E 0 00 Fast Speed C 0 00 Change Potentiometer on C 0 00 Change Potentiometer on 3 Tools Delet
13. BER IMP E Pdf S Gl el sl al Manipulation Libraries Default Solute Method Side Stock Element 1 Add by Weight Serosal 10 uM Element 2 Add by Volume Mucosal 20 uM Element 3 Remove Add 100 uM Element 4 Remove Add 100 uM Element 5 Other 10 uM Open Library Click to Open and existing library Select a library from the list and press the Open button Save Library Save an open manipulations library to disk Save As Library Save an open manipulations library to a new filename on disk Add Manipulation Select a library name by clicking the left mouse button on the appropriate library Press the Add tool to open a form for entering the manipulation data Delete Manipulation Select the manipulation and press the Delete tool Alternatively right click the mouse on a manipulation and select Delete Pop up Menu Right clicking on the Manipulation Libraries editor panel pops up the following menu 55 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual New Manipulation Creates a new manipulation entry New Manipulation Edit Manipulation Edit Manipulation Remove Manipulation Permits editing on grid or opens the input box for editing the fields AS Gopy to Event Log Remove Manipulation New Library Deletes the selected manipulation from the Open Library current library after copyi
14. In but along only the Y axis See also page 50 E Zoom Out X Axis Same as Zoom Out but along only the X axis See also page 50 El Zoom Out Y Axis Same as Zoom Out but along only the Y axis See also page 50 Bl scroll Left Scrolls the data to the left by 1 3 of the screen See also page 50 Scroll Right Scrolls the data to the right by 1 3 of the screen See also page 49 H Scroll Up Scrolls the data up by 1 3 of the screen See also page 49 D Scroll Down Scrolls the data down by 1 3 of the screen See also page 49 Experiment Menu Menu commands under this heading all Properties pertain to the currently open experiment Laboratory Notebook gt Manipulations x Protocol Properties l SR Even log Opens the Experiment Properties dialog for the active experiment This form Protocol Design Experiment Run has two tabs one labeled Experiment Event Editing and the other labeled Tissues The Experiment Tab permits the user to enter and edit the name and description of the experiment and identify the author The Tissues Tab enables the user to select from which tissues the system will record data To collect data for example from tissues 1 6 these buttons must be depressed on this form as shown in the following screen snapshot Data acquisition from any tissue can be turned on or off during the experiment Turning off tissue channels that are not be
15. a locked padlock in red When unlocked this will appear as an unlocked padlock in orange DAC Toolbar The DAC Toolbar buttons are available for only data IL NI acquisition Start Chart Acquisition Starts data acquisition Menu Acquire Run n Stop Chart Acquisition Suspends the acquisition of new data E Slow Pulsing Changes acquisition speed to slow mode as set in Setup Chart Pulse DAC Si Medium Pulsing Changes acquisition speed to medium speed mode Ed Fast Pulsing Changes acquisition speed to fast mode w Mark Event Clicking this button opens a dialog box to make a mark and notation in the data file that describes an experimental manipulation and the tissues to which it applies Pressing Done on this form places a time mark in the record that displays both on the graphics screen and the event log Graph Toolbar The graphics toolbar is the second row of buttons just EZ Hil m tal Li n This is a new feature and thus may not appear in all screen snapshots in this manual yet 47 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual underneath the main application toolbar These tools apply to the current graph window that is selected at any time only Control and Scroll Toolbar The first toolbar manages graph control and scrolling buttons PA Graph Plot Setup Opens the multi tabbed gr
16. and when the clamps are in Remote mode If not then adjust the trim pot for the Remote interface as described in the user manuals for the VCC MCX R37 test point TP2 and VCC600 voltage clamps front panel Remote trim pot so that the instrument s read 0 0 mV under these conditions A checkbox is provided if checked to cause the measured offsets to be subtracted from future measurements made during the experiment If it is not checked the data will not be corrected from the measured offsets Typically this should remain checked x Type 2 da de Js lbe EA ER 0 000 0 000 0 000 0 000 0 000 0 000 v 0 000 0 000 0 000 0 000 0 000 0 000 v Apply Reference values when acquiring data Reference OK View Gains This dialog displays the current A D sampling gain per tissue channel If the Pulse Setup dialog is set to Autogain for either voltage or current the gains may not always be the same on each channel See the Setup Menu under Pulse Setup for more information on how the gain settings work A D Gain Per Tissue K x Start Stop Chart Acquisition Used to initiate acquiring data The menu line toggles between Start and Stop so it serves the dual purpose of starting or stopping data acquisition The first time this is selected the program checks to see if a Reference has been taken If it has not data acquisition is aborted and the Reference Screen is opened Once the reference is taken or if a Reference has
17. axis Inside each major tic is a Minor Tic The of minor tics displayed will vary and are not labeled but represent a small axis increment similar to markings found on rulers Use standard unit values 1 2 5 10 This is intended to match traditional analog oscilloscope behavior and impose a grid to the axis based on simple values 1 2 5 or 10 Depending on the scaling of the graph this could be less than 1 0 1 0 2 0 5 or greater than 10 100 200 500 Note that when using this feature results are computed automatically and the axis range may not be what you might think it should be In that case you can always turn the standard units feature off and override the default behavior with specific Min Max Origin Major Tics and Step Unit values typed into the boxes Scroll this axis when acquiring data When the data acquisition mode is running checking this checkbox on will automatically scroll the axis to the left as new data points begin to fill up the screen and start to go off screen to the right This allows you to track the most recent progress of your data sampling without manually zooming or scrolling Scroll with Zoom X when acquiring data The scroll only scrolls it leaves the zoom scale the same To keep a continuous display of ALL data points recorded so far you can check the scroll with Zoom X feature Center axis Re centers the location of X axis up and down the screen along the Y axis Autoscale un
18. bar that can be positioned to encompass data of interest The user can quickly select and average the data within a movable window and then export to a comma delimited text file compatible with Excel and other spreadsheet application software programs There is also an option available to perform a simple linear regression on selected portions of the data set which should help to quickly observe trends in your data to help direct your experimental decision making process For example l Select Analyze Tools Data Bar from the main application menu right click on the graph window and select Data Bar on the option list or click on the corresponding mil toolbar button This will draw a pair of vertical blue lines in the data window The width of the bar can be set by selecting Setup Data Bar Settings from the application menu Set the Bar Width to about 180 seconds 3 min Checking the Lock checkbox fixes the width to avoid accidental change When not locked the bar width also can be changed by pressing the left mouse button while the cursor is just outside either side of the box and then dragging the box to a new width Select Analyze Tools Data Bar Values Averaged to display the Data Bar Values dialog box There are four tabs The first tab Avg Data should be visible Press and hold the left mouse button inside the Data Bar Drag the bar to a desired location over the data and release the mouse button The average of all data
19. by the data bar A Acquire and Analyze 2 2 Sample Data EXP Isc yA ys Time Min E 81 x File Edit Zoom Experiment 4 Analyze Tools Graph Setup Window Help WIES IS Aem SgS 1 2 mim gi jam aiaieiaigialalisiaiaia Area Toggle Button X 1 98 Min Y 98 91 pA Right Node 00 02 16 83 7 y 0 519 154 Ready DI 720 Instrument VCC Series Clamp Mode 00 00 00 No Protocol Tissue rea cm2 1 Move the data bar to the part of the curve you wish to study Click on the tissue number The Set Line button will become enabled Click on this button and the line will be set for that tissue Look in the graph window now for the single blue line that roughly fits the data in the part of the graph that you have selected with the Data Bar Notice there are three squares on this line By selecting the right and left most squares you can adjust the endpoints and angle of the line The 230 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual middle square moves the line without changing the angle When you have a fit you like you can export the data to the clipboard by selecting the line s you wish to export they will turn a dark color and then typing CTRL C A Acquire and Analyze 2 2 Sample Data EXP Isc yA vs Time Min File Edit Zoom Experiment Acquire Analyze Tools Graph Setup Window Help EJ xj jE Si J 31818 sl la ma ani e
20. data will be Zoom Recenter at Cursor displayed This provides a quick way to see the Zoom Window data and readjust the axes to include all points melo Zoom Out Zoom In X Axis E Zoom Auto X Axis Only Zoom In Y Axis Same as Zoom All but only along the X Zoom Out X Axis horizontal axis Zoom Out Y Axis Scroll Left E Zoom Auto Y Axis Only Scroll Right Same as Zoom All but only along the Y Scroll Up Scroll Down vertical axis E Zoom Recenter at Cursor Redraws the graph centered about the cursor without changing axes scales To implement this press the Zoom Center button and then click the left mouse button on the graph at the point the graph is to be centered about Ex Zoom Window Press Zoom Window and then press the left mouse button on the graph and drag the boundary to encompass the region you want to expand al Zoom In Zooms in along both X and Y axes Makes graph appear twice as large by halving the size of each major tic interval See also page 50 al Zoom Out Zooms out along both X and Y axes Makes graph appear twice as small by doubling the size of each major tic interval See also page 50 el Zoom In X Axis Same as Zoom In but along only the X axis See also page 50 21 Physiologic Instruments 12335 6 World Trade Drive e San Diego CA 92128 Acquire amp Analyze 2 3 User Manual E Zoom In Y Axis Same as Zoom
21. information line at the bottom of the graph window Tl Soroll ren Clicking the Scroll Left tool causes the plotted data to be shifted to the left a distance of 1 3 of the graph width Scroll Right Clicking the Scroll Right tool causes the plotted data to be shifted to the right a distance of 1 3 of the graph width H Scroll Up Clicking the Scroll Up tool causes the plotted data to be shifted upwards by 1 3 of the graph height n Scroll Down Clicking the Scroll Down tool causes the plotted data to be shifted downwards by 1 3 of the graph height m manages the ANA ARA ARRE AR zooming features al Zoom All Zoom All determines the minimum and maximum data for all tissues to be displayed and then adjusts the X and Y axes so that all the data will be displayed This provides a quick way to see the data and readjust the axes to include all points amp Zoom Auto X Axis Only Same as Zoom All but only along the X horizontal axis E Zoom Auto Y Axis Only Same as Zoom All but only along the Y vertical axis E Zoom Recenter at Cursor Zoom Center redraws the graph centered about the cursor without changing axes scales To implement this press the Zoom Center button and then click the left mouse button on the graph at the point the graph is to be centered about 49 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire
22. points within the bar will now be displayed in the data grid on the Avg Data tab Click the Export Settings tab Click the filename browse button to select a file in which to save data If you would like the data to be corrected for tissue area check the Area corrected values checkbox When finished click the Avg Data tab 14 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual 5 Clicking the small diskette icon on the Data Table toolbar will save the current values displayed to a comma delimited ASCII text file at the Windows path location you specified in Step 4 This delimiter may be changed using the menu item Setup Preferences This file can be opened with Notepad or imported into Excel or another statistical analysis package 6 Allor portions of the raw data may alternatively be exported to a file by selecting Analyze Tools Export Raw Data from the menu 15 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Application Reference Guide The following provides a more detailed description of the graphical environment menus and controls Application Window Application Window Menu Bar The menu controls see screenshot of menu bar below are described in detail When applicable the associated Toolbar icon accompanies the description File Edit Zoom Experiment Acquire Analyze Tools G
23. software program will not be able to control the clamp mode Left click the Reference button Observe that the LED indicators on the front panel of the instrument change as the computer commands the clamp to switch to OPEN mode to VOLTAGE CLAMP mode and finally to the mode selected via the Pulse Setup dialog box page 37 The table should now be populated with data All values should be less than 0 1 page 25 If any of the boxes show up with a red or yellow color that is a warning that the reference is out of range and you should check your clamp setup and run the Reference again There are three preset rates for acquiring data slow medium and fast These default rates can be changed by the user page 37 For now select Acquire Medium Pulsing or press the middle g yellow signal light icon on the toolbar Select Acquire Start Acquisition or press the running man icon on the toolbar The collection of a data point is indicated by the word Pulsing at the left hand side of the application status bar and by an audible beep provided that a sound card is installed on the computer speakers are connected and volume is on After a few data points have been collected they will auto zoom on the Y axis so that you can see the range of the data being taken The data points will auto scroll on the X axis as they run off the right edge of the screen If no data is seen right click on the graph and select Tiss
24. the 67 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual button will change with each click and indicated on the button Note changing the line width also changes the size of the point drawn Assigning the Symbol To Plot Just like color and line width may be set for each tissue the user can also assign a symbol to each tissue The symbols assigned to each tissue are shown in the grid below the tissue numbers To assign create or edit symbols Dbl click a symbol in the lower part of the Tissue Selection box to open a symbol editor The symbol shape may be edited on the grid by using the left mouse button to fill in pixels the right mouse button to clear them Once edited the symbols may be saved to disk Alternatively new symbols may be loaded from disk Grid The grid is a set of rectangular boxes drawn on a spacing given by the Step Size for the X and Y axes The options for displaying the grid are e None Don t display the grid line e Dashes Draw the grid using dashed lines e Lines Draw grid using solid lines Lines This box provides display options for how individual data points from each tissue are to be connected e None No connection between adjacent data points e Dashes Dashed line connects points e Lines Solid line connects points Plot Provides options for how each data point should appear e Points Displays the data points as smal
25. with Windows 98 you can install following the same steps as the XP install except that there will be no Zeeman drivers step Instead the program will be installed using the Autoexec bat file to call the firmware loader If you are using Note This card requires an ISA slot on the computer motherboard If your computer does not have an ISA slot new computers since about 2001 DO NOT this is the wrong hardware for you You should instead have the external parallel port version DI 720 8 Physiologic Instruments 12335 6 World Trade Drive e San Diego CA 92128 Acquire amp Analyze 2 3 User Manual the DI 400 with Win2K you will not see the Zeeman install step but there will not be any changes to the autoexec bat file either Acquire amp Analyze 2 3 Install for DI 720 The first screen of the installer appears 1 Setup Acquire and Analyze Welcome Click Next to continue 2 Select DI 720 External DAQ and click on Next 3 Select Destination Location Unless you need to change this location for some reason select the default C Program Files Acquire23X and press Next 4 Select Start Menu Folder Unless you need to change this name for some reason select the default Acquire and Analyze 2 3 and press Next 5 Select Additional Tasks You may create a desktop icon or quick launch button here if you would like 6 Ready to Install Press Install 7 Zeeman parallel port drivers 2K amp XP only DI 720 only
26. your work for example it is very convenient to keep the data grids and Lab Notebook windows on one monitor while your main application takes up the other monitor you may have run into problems of leaving some application windows on the second extended Windows display desktop You should check your Display properties to determine if you have this capability if you are not familiar with it Usually this requires specialized hardware such as a high end video graphics card If you do use more than one monitor but not always you may occasionally run into a situation where you have left your tool windows over on the 2 monitor screen which may not always be available If this is the case you will need to retrieve them because their screen coordinates have been saved for the old desktop which is now currently not available First click on the Update button to the right of the label for Multiple Monitor Support This will count the number of monitors you have attached Next click on Retrieve Lost Windows This will then locate A amp A windows that are currently off screen and reset them Obviously if you never need to worry about multiple monitors you can skip this part 42 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual The Mark Event Countdown field allows you to specify the default number of seconds you wish to have as a warning before an alarm expires during data acquisitio
27. Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual A Acquire and Analyze 2 2 Bl x File Edit Zoom Experiment Acquire Analyze Tools Graph Setup Window Help Application Toolbar EX ll El ja E F B a A mi a 0 0 eleleleleleokelelelel A Sample Data Isc yA ys Time Min Graph D TH Toolbar ned H X 2 68 Min Y 103 13 pA 4 Application Status Bar EIN X 3 83 Min Y 296 47 0 7 Ready DI 720 Instrument VCC Series Voltage Clamped Osec No Protocol liz Above you see a sample screen shot from the latest version of A amp A The top pane dark blue is plotting short circuit current Isc vs time and the bottom pane brown is plotting resistance TER vs time The graph colors symbols gridlines axis parameters and displayed tissues may be set for each pane Any number of individual panes may be defined and displayed Other features include zoom controls experiment protocols event marks data extraction and export tools and quick data summary tools To better view the details of this image you can use the zoom control on your Adobe Reader cs Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Installation Hardware DataQ DI 720 Series Connect the power supply to the DI 720 as indicated in the DataQ Instru
28. SCN501 EXE which may or may not be in your taskbar process list The second button will stop the application Close EXE Click on both of these and then close Now try to run the program again AAA 41 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Preferences The Preferences menu option brings up an editor that allows you to modify certain default behaviors of the main application window and features These features are Default display precision Hover coordinates Beep when pulsing Multi monitor support Event countdown Export file column delimiter character Decimal placeholder for European users preferring commas Default data bar width Pulse timeout The Default display precision controls your significant digits display formatting for axes labels and data fields throughout the program If you want ballpark figures or do not need a lot of precision keep the default value of 3 or reduce this If you require more accuracy you can increase this number The Hover coordinates show the current X amp Y position of the mouse cursor when in the graph window The hover decimal places control the number of digits displayed in the hover coordinates Beep when pulsing toggles the Windows beep at each new data point You will need to have speakers attached to your computer in order to hear the beep If you are accustomed to using more than one monitor for
29. User Manual Tissues 4 Area Correction Toggles on and off the area correction mode When this mode is on it will correct the acquired data values for current resistance and conductance for the actual area that can be set in the Experiment Properties dialog This menu option is synched with the corresponding toolbar button fal Data Bar Values Averaged Displays the Data Bar Values dialog box which has four tabs Avg Data Linear Regression Curve Area and Export Settings see below screen snapshot The first tab Avg Data is visible by default when the tool is activated This tab contains the average of the data values for each tissue that lie within the Data Bar see also the section Data Bar on page 28 The number of data points included in the bar is shown in the last column xl S mann dad h Time Start 00 00 10 Time End 00 00 11 00 00 10 00 00 10 00 00 10 00 00 10 00 00 10 Top 00 00 10 Above the tab area is a toolbar Selecting or deselecting the IVGR buttons will enable or disable the display of that property The disk icon is used for exporting data see description of fourth tab The Top button is used to keep this window floating on top of other windows or disabling this so that other windows can cover it 31 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual The second tab accessible by pressing the r
30. ain range you can pre select a particular gain to fit your range before running If you are not sure you can use Auto Gain The advantage of the lower gains is a wider range Measurements that are digitized over a wider range that are small in magnitude will be less accurate The advantage of the higher gains is that the small values are scaled to a better range and the data will be recorded more accurately However if there are extreme or outlier points that skip temporarily or permanently outside of this smaller range the amplifiers saturate hit a maximum value and any value larger than this is seen as the maximum value rather than the actual correct value Fortunately this can be detected immediately The algorithm used in deciding what gains first looks at the recorded current and voltage values to see if they are in saturation For example using the dummy tissue membranes which has a resistance in Test mode of about 296 Ohms if you set the Step Change value to be 10 mV you will likely get a current saturation with a current gain of 8 The digitized value of this measurement comes into the computer at the maximum end of the range This is a saturation case and so the gain is stepped down to 4 If it is still too high it is stepped down again until a gain of 1 is reached If this is still saturated or if both the high and the low pulse responses saturate the data point is thrown out will not be recorded or displayed in the plot wind
31. al Application Toolbar The main application window toolbar first row of buttons is split into two sub bars on sliders The first is called the Protocol Toolbar and the second is the DAC Data ACquisition Toolbar Protocol Toolbar The Protocol Toolbar buttons are available for both El El 1 na data acquisition and analysis El Create New Graph This button causes a new instance of a graph to be displayed That is an additional graph is placed with in the main widow The data that is graphed depends on which graph is active has the attention when the button is pressed The new graph will display Current vs Time for all tissues for the experiment of the graph that has the attention For example if data from two different experiments Exp 1 and Exp 2 are being displayed and a graph of Exp 2 has the attention last graph in which the mouse was clicked pressing the New Graph button will display a new graph of Current vs Time for all tissues for the data of Exp 2 l Lab Notebook Opens the Lab Notebook window for creating and using protocol lists for alarm reminders and to help track the addition and or removal of certain materials to from the tissue chamber reservoirs during the experiment D Show Event Markers Toggles the Event Markers on or off Double clicking on any one of the event markers at the small square at the bottom of the line will open up the Event Log Editor for that mark If you need t
32. al lapsed time fas Seconds DI C Shift experiment by user specified time E OK i Open Experiment Opens and existing data file for analysis Displays the Open Experiment dialog to select a data file to open Close Experiment Closes all graphical instances of the data file and removes the data from memory Currently only one experiment can be open at any given time In order to create a new data file with the data acquisition mode you must first close any currently open experiment Save Experiment Performs a complete Save of the data file to update configuration parameters and save any changes made to the Event Log etc Measured data are saved as soon as they are acquired Save Experiment As Permits the user to save the data as a new file name via the Save dialog Graph Print Setup Permits customizing the print colors for each tissue and the axis Here you can also specify a plot title and the frequency of how many data points are labeled with the corresponding tissue digit number Print Displays the standard Windows printer dialog to output the active graph to a printer Exit Closes all experiment files stops data acquisition saves the current configuration and closes the program 18 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual MRU Files Underneath the Exit menu option is a list of Most Recently Used files MRU for short
33. amp Analyze 2 3 User Manual E Zoom Window Press Zoom Window to enlarge a visible portion of the data Positioning the mouse at one corner of the region of interest and then pressing the left mouse button to drag a rectangular outline until it encompasses the area to be enlarged define the Zoom In area Releasing the left mouse button will cause the screen to be redrawn al Zoom In Press Zoom In to enlarge the data by a factor of x2 for both x and y coordinates al Zoom Out Press Zoom Out to double the extents of the X and Y axes R Zoom In X axis Zoom In X zooms the X axis without affecting the range of the Y axis The range of the X axis is reduced 2 fold R Zoom In Y axis Zoom In Y zooms the Y axis without affecting the range of the X axis The range of the Y axis is reduced 2 fold Ej Zoom Out X axis Zoom Out X zooms the X axis without affecting the range of the Y axis The range of the X axis is increased 2 fold El Zoom Out Y axis Zoom Out Y zooms the Y axis without affecting the range of the X axis The range of the Y axis is increased 2 fold Application Status Bar The bottom line see below screen snapshot of the main A amp A window contains information displayed in separate boxes about the current state of the application These include the status of the data acquisition system and whether it is currently acquiring data BLANK type of voltage current clam
34. and Current Gains control the Full Scale Range FSR capability of the analog to digital converter A D in the data acquisition unit The A D of the data acquisition system at a gain of 1 for example has a FSR of 20 V 10V to 10V The VCC then has it s own setting to convert the real measured value at the tissue to this FSR Assuming the VCC instrument gains are set to V 10 mV mV and I 10 mV uA effective measurement ranges in real tissue values seen by the software in response to the gain setting in this dialog box are as follows Gain Voltage Current 8 t125 mV 125 pA 4 250 mV 250 uA 2 500 mV 500 uA 1 1000 mV 1000 uA e Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Exceeding these limits will result in errors in recorded data The Auto Gain setting circumvents this by continuously checking for these limits and adjusting the gain on each channel to maximize resolution without saturating the A D input For both Voltage and Current Gain Auto Gain auto detects an appropriate gain setting for each channel independently If you choose to use this mode and want to know what the gains are set to per channel go to the View Gains option on the Acquire menu just below Reference This displays the gain setting on each channel for both current and voltage measurements If you happen to be certain that your measurements will always fall within a cert
35. aph setup form see This form may also be quickly accessed by double clicking the left mouse button over the graph area Dbl clicking over the X axis causes the form to open ready for adjusting X axis parameters Dbl clicking over the Y axis causes the form to open ready for adjusting Y axis parameters Dbl clicking elsewhere on the graph opens the form for changing general graphic parameters Hil Data Bar The data bar is a moveable and resizable set of vertical lines that enclose data points for each tissue being graphed The bar therefore defines a window in time The width of this window may be set by two methods Press the right mouse button over the bar and select the menu item Setting Enter the bar width in seconds If you would like to set the bar width and prevent accident change place a check in the box labeled Lock The bar will now have a fixed width that is not changeable by the methods indicated below Other features on this form allow the user to change the bar color and width of the lines forming the bar In addition one can change the manner in which the bar moves by selecting Center Bar on Mouse Click Selecting this feature causes the bar to be centered about the mouse cursor position when its left button is clicked The bar width may be changed by dragging either of the bar s defining boundary lines To do this move the mouse cursor just outside either left or right boundary lines Press and hold
36. ay from axes 72 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128
37. been previously determined then the Start Chart Acquisition button starts the experiment clock timer running and data acquisition begins at the currently selected pulse rate 3 Where X indicates the number of channels 2 6 or 8 205 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Slow Pulsing Selects the slow rate of acquiring data as defined on the Menu Setup Chart Pulse DAC dialog box For example if the value for Slow is 20 seconds one data point will be acquired on all active channels every 20 seconds Medium Pulsing Selects the medium rate of acquiring data If the value for Medium is 5 seconds one data point will be acquired on all active channels every 5 seconds Fast Pulsing Selects the fast rate of acquiring data If the value for Fast is 2 seconds one data point will be acquired on all active channels every 2 seconds Mark Event Opens a Mark Event dialog to open Alternatively you can use the F12 key to bring up this dialog On this dialog the user may enter a brief description of the event select the tissues to which it applies and place an event mark in the data file by clicking on the Mark button The event mark is a vertical dashed line having a square box at its base Moving the mouse cursor over this square displays a small box containing a description of the event Dbl clicking over this box open the Event Log with the line marker at
38. cognized the hardware yet If this is the case you can attempt to J Connect to Instrument at Startup connect to the instrument by pressing the Connect to Instrument button If this still does not work or you know Connect to nstument you need to run the DI 720 loader again you can press the Run Loader Run Loader button The 720 Loader program opens up in it s own command window and you will need to press a Cancel key to continue to close this window after the loader runs The Connect button will pop up a message box notifying you if the connection fails If it succeeds there will be a status message in the lower left hand corner of the application window saying DAC Initialized If you are still unable to connect you should double check that you have the data acquisition hardware properly connected to your computer on the correct port and that the power cable is connected and the unit is turned on Check this and run again If it is still not connecting and you had previously run the program recently you may have a hung process or crashed program If this is the case go to the xi application directory something like C Program LA stop pa Files Acquire23X in your Windows Explorer locate the program called StopAcq23X exe and E run it There will be two buttons to stop processes and one to close the program The first button will Stop Acquire222 exe stop the data acquisition program DI
39. cular application A Total Pulse Duration not editable This represents 3 B C B Duration This represents the width of each pulse segment labeled B on the pulse diagram Interval This represents the short pause between pulses Number of Steps This is not an editable parameter currently DC Clamp Level Affects the overall offset of the pulse Step Change Height of pulse in millivolts Period Slow User settable to specify the frequency of pulsing Period Medium Similar to H Period Fast Similar to H n TAHA 238 Physiologic Instruments e 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Pulse Setup X A Total Pulse Duration 520 ms F DC Clamp Level oo mv B Duration 200 ms G Step Change pm m C Interval ms H1 Period Slow 2 _ ies Note A 3 B C H2 Period Medium os Cancel H3 Period Fast r Clamp Mode Voltage Gain Current Gain Open Circuit m Nl CB Voltage Clamp CA B C C 8 C Current Clamp Auto Gain Auto Gain Ready In addition to the pulse height and timing parameters there are a few options to be aware of e Clamp Mode default is set to Voltage Clamp e Voltage Gain default is set to 8 e Current Gain default is set to 4 The Clamp Mode controls the mode of the VCC clamp device see Operating Instruction Manual for the VCC for more information on these settings The Voltage
40. data f you get an error message such as DISO1NT DLL not found you need to verify that you have a valid parallel port in your computer and that it is set to LPT1 The software assumes that you are using LPT1 If you have a computer that does not have a parallel port you can buy a PCI slot parallel port card for less than 50 from most large computer electronics warehouses Check to make sure it supports bi directional modes EPP ECP and that it is set to LPT1 using the Device Manager 12 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 10 11 12 13 Acquire amp Analyze 2 3 User Manual Set the Tissue Area value in cm if you would like the data on the screen to be corrected for the area of the tissue If the area is set to 1 0 or if area correction is disabled the data on the screen will read the same as on the digital panel meters Click Save Changes to close this dialog box Now we need to take a zero reference reading to calibrate the measurement Select Acquire Reference from the main menu Check the box Apply Reference Values Before proceeding further check to ensure the tissue is now correctly set up in the chamber and the voltage current clamp should be set up powered on and placed in either voltage or current clamp mode Turn on the REM remote local switch amber light for each channel selected for data acquisition above If this switch is not turned on the
41. dow Menu Cascade Cascade Tie Horizontally E Tile vertically Tile Horizontally Tile 4 Page Tile Vertically Tile 4 Page v 1 Experiment 1 Isc uA vs Time Sec E Physiologic Instruments e 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Active Window List These options rearrange or select the open graph windows Help Menu About Acquire About Open Help File This option displays the application about screen see DAC Information below with the version and a link to our website You can also access system information about your computer Open Help File Displays this manual DAC Information Displays some basic values corresponding with your version of the data acquisition board see below x Acquire and Analyze Version 2 1 8 Data acquisition and analysis for transepithelial transport http physiologicinstruments com Copyright C 2005 Physiologic Instruments Inc System Info 44 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual A DAC Information 720 BBA PM AVER 1 10 Hardware Interrupt 0 Hardware Revision Input Buffer Pointer 268436646 Input Buffer Size 0 Input Channel SH Last Calibrarion 807415072 45 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manu
42. e ASA A TER 21 Ex Zoom Auto Y Axis Only tara 21 E Zoom Recenter at CUTSOT x EErEE ERES iS 21 E Zoom Windi ia 21 al ZOOM AN 21 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual al Oy 010 4 E DINNER EE R Zoom In X Axis el Zoom E Y ARIS A iia el Zoom Out E EN lal Zoom Quite Y AKIS td tata a Scroll E ik see cst eei NEUEN eI ATAT fece EN ardor E a SCE UP eC D ER E Leg EE Leieren PT T Laboratory Notebook PD E API Prot iia EE Eege Protocol TMG ge EXP ds Event EON ate iii Acquire MI aio Diigo eM A e A A PP a A Start Stop Chart ACUSA as KE e A Medi Pula F st PS toa MARE Uria An lyze Tools Mei od gen Bcc TIE TODO ii Area ao CIN os RPP o o o O I m A Mr cul Data Bar Values Ara Data Bar Values RW acusa pbnoNemd et aa Raw Data A o p Um Export Data Bar VA osos Export Raw rc ur du mM P Create New decim Graph View Editor AM Graph View MRU Estaba SEP MENU rs Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Graph Plot ciii Eeer LE EE TMS SNE Settings ent ege A a Ee IN Window Men E ccc ii ida Tile TE ol ER
43. e Selected Event Select the row of the event to be deleted by clicking the button to the left of the event and then click the Delete Button Event Table Row Selection Button Edit Fields A right mouse click on any of the following fields opens that field for direct editing Time Solute Tissues Method of Application Side of Tissue Quantity if applicable Unit Chamber Volume Final Concentration Description 63 Physiologic Instruments e 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Graph Window The graphics windows are used to display data recorded by the A amp A system These data can be from an experiment in progress or from experiments previously performed These graphs are child windows ofthe main A amp A program form This means that they are always contained within the main form and resize when the main form s size is changed Title Bar The top blue bar on the graphics form is the title bar This bar displays the title of the experiment the parameters being plotted in terms of units e g current vs time will display as uA vs min and the complete file pathname The color of the Title Bar is dark blue when the graph is selected active and light blue when it does not currently have the attention Graph Window Pop up Menus There is a pop up menu that is available if the user right clicks in the Graph Window There are three differen
44. e current library under a new name View 2 protocols in split screen This tool splits the protocol pane to permit viewing a second protocol Connect Protocol to Experiment Causes the loaded protocol to be associated with the experiment Pressing this button enables alarms specified in the currently open protocol to appear in the main experiment window as markers The times specified in the loaded protocol may have to be adjusted for the current experiment time In this case an input form will open to permit this timing adjustment Note that if there is a valid protocol schedule attached to an experiment the Status bar at the bottom of the application window will show the title of the protocol When you start or re start taking data there will bea few options that you have to set the actual time that the alarm sequence will fire off at see the screenshot below The time that shows in the Scheduled Time column corresponds to the Actual Time in the protocol editor This represents the time shown on the horizontal time axis in the graph window that the next alarm will fire off at If you have not selected any rows when you connect the protocol the first row will appear in yellow The yellow highlight represents the 58 Physiologic Instruments e 12335 6 World Trade Drive e San Diego CA 92128 Acquire amp Analyze 2 3 User Manual next alarm to fire As the alarms fire off this highlight will move down
45. e letter E such as 2 0E 4 to represent 0 0002 Unit The units that apply to the quantity may be chosen from a drop down box or typed into the field Units entered via the drop down method may be used in other parts of the program to calculate concentrations etc Description This field may contain any specific comments the user wants to make regarding the manipulation 60 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual About the Alarms The alarm feature is implemented when a protocol is associated with an experiment The alarms are designed to assist he investigator in making the proposed manipulations in a timely fashion Three types of alarms are available as described below Instantaneous The alarm is used to apply a single event mark to one or more tissues The alarm opens an experiment Event Mark screen about one minute prior to the scheduled manipulation This Event Mark screen contains a countdown timer to the scheduled event time description of the manipulation to be made a list of tissues to which the manipulation is to be made and buttons to place the Mark in the file and record the event or delay activating the event Pressing Spacebar executes the Mark button Sequential Fixed The alarm is used to sequentially apply the same event mark to multiple tissues with the same specified interval between marks The alarm opens an experiment
46. elat Editor POS j MET Y M RS Manip lation Cibraties BHO sae e iii Protocol Editor MET A O E RE S S TR die A A E situate T e s O p EET Graph Window Pop up Memes Standard Pop Menu eT X Axis e CA estet ote X etx heise mae eae een Y Axis Pop Up Mi asi Graph PlotSet p Diallo MEE lun ISSUES MP Selecting Tissues to Plot c Setting SS CO AR A Setting Line VY HEIL su assis vse T Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual le ET 68 E E TEE 68 A O fc SM cL LUC Co et 69 Show tic ee ur deca ao etd A I a 69 eege 69 Show axes labels Show unit labels ooooocococccccoconananananononocananananononococonanananonaninic ns 69 TEE 69 He A 69 Save BE EE 69 ABUS A I M MR ER E 69 AXIS hu T E 69 Min Step Unit Unit Maj Tics Min Tics Max Otem 69 Use standard unit values 1 2 E EE 70 Scroll this axis when acquiring data li 70 Scroll with Zoom X when acquiring data 70 CCCI A EI as eau 70 ET Ee EC 70 Force ALL graphs to this axis setting reinicia jasa dida nica ads 70 E A E 71 Auto Zoom this axis when acquiring data 71 Graph Window Status Bar Ad 72 APESTA NT E Cu N 72 M m Physiologic Instruments 12335 6 World Trade Drive San D
47. eriment the event log may have events exactly as laid out in the protocol events that vary only slightly from the protocol events added on the fly and not found in the protocol and events that may lack all detail and await later editing to add the detail The Event Log portion of the editor allows the investigator to edit any and all the salient data describing the experiment to fill in gaps on detail and add specific descriptions or notes E Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Screen Layout A ARA Laboratory Notebook K loj x MIP E d ella i el Manipulation Libraries Klump Solute Method Side Stock Klump 1 Add by Weight Mucosal 1mg Klump 2 Add by Weight Mucosal 2mg Klump 3 Add by Weight Mucosal 3mg Klump 4 Add by Weight Mucosal 1M Klump 5 Add by Volume Serosal 3 Event Log MIETEN NT mE os 162 0 Fast Speed 123456 108 0 Change Potention 156 0 Change Potentiom 235 Blue Bar at Top Active Part of Screen Displays the type of panel that is currently active If this is the Protocol panel then it also displays the currently active or loaded protocol if any Tool Bar Below the Blue Bar are six tool buttons that determine which features of the form will be displayed Each button is labeled with a single letter or with two letters representing the panels that are opened
48. ese are experiment planning tools that aimed at developing an experiment protocol Using a the lab notebook offers several benefits e It organizes the experimental method thereby making experiments within a group more consistent and easier to compare e It provides a consistent description for the experimental manipulations e It enables use of special alarm features that help enforce uniformity among experiments See also the section Laboratory Notebook for a description of how to use this form 23 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual The Lab Notebook submenus are Manipulations This opens the editor with only the Manipulations screen showing This screen provides a means of defining common experimental manipulations and storing them in user libraries For example one manipulation might be to add a chemical such as amiloride to block sodium ion entry into certain epithelia When performing this manipulation the experimenter needs to designate the name of the event the method by which it will be added the side to which it s added the concentration of stock solution the amount to add and the final concentration in the bath For amiloride this might be amiloride added with volume to the mucosal side from a 10 M stock solution The amount added might be 50 uL in 5 ml for a final concentration of 100 uM Protocol This opens the editor wi
49. g the Specify Range option Options are available to encompass the entire experiment or just the data that falls within the Data Bar If you wish to use the data bar range option the data bar must be set prior to opening this dialog box The data may be area corrected upon export by checking the Area Corrected Values box When you are ready click OK to write the data to the specified file A Export Raw Data i Data to Export Tissues Time Range v Current v V Voltage From To m c DIS anb she 00 01 48 00 01 55 zinea EISEN ceste Yt Calculated 25 26 27 28 23 30 31 32 C Use Experiment Range iso bal Parme Use Data Bar Range Export Target Dther Esport to Excel Export to Text File V Arsa conected values Include Protocol Sample Data RawData xls S HEU DK Cancel 51 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Laboratory Notebook Overview The Lab Notebook provides a way of organizing an experiment before it is run The three most important aspects are 1 The ability to create a set of Manipulation libraries A Manipulation is a fundamental unit of experimental action such as adding or removing certain drugs or solutions to or from the Ussing chambers 2 Grouping these manipulations into a list of experimental Protocol A Protocol is a sequence of Manipu
50. he dialog The contents of this region will depend which of the six editor modes is currently selected M P E MP PE ME For the first three options only one panel is visible For the last three options two panels will appear one above the other Editors There are three types of editors each with their own toolbar and layout Manipulation Libraries Editor The Manipulation Libraries editor panel can keep track of various experiment issues such as adding a drug at a certain point This section is a work in progress and not fully synchronized yet with the other aspects of the program Future versions of A amp A are planned to provide the ability to create custom pulses such as IV curves and custom graphs that will be able to compare different experiments rather than just different tissues Manipulation Toolbar Contains toolbar buttons specific to the Manipulation Libraries editor 54 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Create New Library Click to create a new manipulations library Type a new file name in the File Name box and press Save The file extension will be automatically be made MAN The file name should be suggestive of the contents of the library For example a library could be created that is specific for the compound forskolin and contain additions of only that agent to different sides of the tissue and at different concentrations
51. heet checkbox For reports many times it is useful to be able to compare steady state averages from several different experiments To do this open the first saved experiment data file from which you wish to store the results of Move the data bar to the portion of the graph that you want to summarize Select the tissues you want to discuss with the Tissue Toolbox Now open the Data Bar Values Average dialog Select the Export Settings tab see below Now check on the Export to an Excel Spreadsheet checkbox Choose a filename unique to your analysis perhaps something relating to the manipulation you were studying Next click on the Set Worksheet Labels button This opens up a dialog see the Setup Excel screen snapshot below that allows you to choose worksheet names in a template fashion that can be re used again in the future When you are satisfied with the format labels press OK This will open up a spreadsheet Now go to the Avg Data tab Select the row s that you wish to export Select the label of the worksheet that you wish to export to Click on the disk icon upper left corner Now close the experiment but do not exit the application or you will lose the Excel connection If you do lose the Excel SigmaPlot is another popular charting application However it does not currently provide a development SDK whereas Excel allows us to talk with the spreadsheet application to generate starter worksheets 2355
52. hout running off the top or bottom edge of the screen If this is not checked the user can manually zoom as desired Me Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual A Graph Plot Setup x Axis Type Current lsc y Step Unit Unit Maj Tics Min Tics Min Max E 7117394341 fi 1 5 p M fi 0 5 fi 13 288260565 Se Step Unit Width of Major Tic Origin es 7882605658 Use standard unit values 1 2 5 10 IV amp uta zoom this axis when acquiring data Center axis Autoscale units DK Apply Cancel Graph Window Status Bar At the bottom of the graph window is a status bar with four panels The first displays status messages such as Force if the current plot is set to force other plots to match it s X Axis settings The second and third panels display the X and Y position of the mouse in the window 1f Hover Coordinates are enabled The fourth panel shows the current linear regression if the Area Under Curve option is selected Force X 4 79 Min Y 2 90 pA Middle Node 00 02 38 2 53 y 0 2 54 Graphics Shortcuts There are several keyboard and or mouse shortcuts that are available to common items in the graph window These are e Shift Data with respect to X or Y axis e Move Position of X or Y axis e Dbl Click in Graphics Area e Right Click over X or Y axis e Right Click over Graphics Area aw
53. iego CA 92128 Acquire amp Analyze 2 3 User Manual Introduction Acquire amp Analyze 2 3 combines features of earlier versions of our separately packaged software Acquire version 1 and Analyze version 1 into one program that runs under the Windows M operating systems Windows 2000 and XP This program is designed to collect and display the electrical parameters of an epithelium mounted in an Ussing chamber The design of the software is intended to be used with our VCC MCX line of voltage current clamps Our clamps currently can measure up to 8 tissue channels simultaneously The tools from the Acquire component of the program enable the user to easily record real time data while conducting experiments The tools from the Analyze component provide for storing and managing the data performing simple linear regressions and exporting the data to other applications Version 2 2 and later incorporates a complete re design of the user interface menu structure and dialogs which should provide for a streamlined user experience In addition the Lab Notebook feature provides a method of preparing experimental protocol for conducting experiments to better assist the experimenter in organizing the manipulations posting reminder alarms and a final event log for post experiment reporting See the VCC MCx Operations Manual for more information on this product or check our website at http www physiologicinstruments com m
54. ight arrow key or clicking the Linear Regression tab shows a table of the linear regression data for the data in the bar This may be used to determine the slope of an initial response The third tab Curve Area displays the area under the data using either zero as a baseline or if activated the dynamic baseline see page 28 The fourth tab Export Settings establishes the settings for exporting the data from the other three tabs On this tab the user can specify the path and name of the file into which to accumulate the data and determine which value s they wish to export A note can be added to the export when the diskette icon is clicked via the Prompt for Note when saving checkbox Check the parameters to be saved left group of checkboxes labeled Data to Export and whether area correction should be applied Area corrected values checkbox To export to a text file after setting the desired features return to one of the other three tabs Now a left click on the diskette icon at the upper left of the form exports the selected data select rows with mouse to a delimited ASCII text file The type of delimiter can be set under the menu item Setup Preferences This text can then be imported in your data analysis package of choice such as Excel or SigmaPlot Alternatively you can export directly to a Microsoft Excel spreadsheet format an Excel xls workbook file by checking the Export to an Excel Spreads
55. ing recorded will use less data and lead to smaller data files For a new data file this dialog appears automatically after the filename is selected At this point you will be required to select Save Changes in order to begin data acquisition the Cancel button is disabled After this first time at any later point 295 Physiologic Instruments e 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual during the acquisition this dialog can be opened up again from the menu to make changes For these subsequent calls the Cancel button is also enabled You can also specify a description note for each tissue and set the Tissue Area cm correction factor This corrects the current and the resistance for the dimensions of the aperture of the Ussing chamber There is also a Save As Default checkbox that if this is checked when you press Save Changes it will store the selected tissues and tissue area to appear as a default setting next time you run a new experiment A Experiment Properties Tissues r Tissues Descriptions Active Tissues Tissue FXIESE 5 6 D ap 17 1e 19 20 21 22 23 24 25 26 27 28 29 30 37 32 Tissue Area cm2 fi 5 Save As Default Save Changes Cancel Laboratory Notebook The submenus under this heading all open a common editor for display and editing manipulations protocols and the experiment event log The first two of th
56. its If this is checked on the program decides what unit to use hours minutes seconds etc If this is not checked the current unit is kept Force ALL graphs to this axis setting If there are more than one graph windows this feature can apply settings from one graph to all other graph windows currently open 70 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Axis Type Time y Min Step Unit Unit Maj Tics Min Tics Max E 3 601515 17 Min fi 2 5 fi 62 798485 n Step Unit Width of Major Tic Driain keem Use standard unit values 1 2 5 10 Jv Scroll this axis when acquiring data Scroll with Zoom when acquiring data Center axis Autoscale units Force ALL graphs to this axis setting OK Apply Cancel Y Axis Tab Contains display settings for the Y Axis The settings are essentially the same as the X axis with the exception that the Y Axis has two less checkboxes and one different from the X Axis The difference is the checkbox for Auto Zoom during data acquisition The Axis type is no longer limited to just Time but can cover Current Voltage Resistance and Conductance Auto Zoom this axis when acquiring data If this checkbox is checked on the Y Axis will automatically zoom out to the full scale of the data points as the data acquisition proceeds This way you will be able to see all the data that is displayed wit
57. jelalajalalalalalealal aj n TeTeTR i vi Linear Regression Curve rea Export Settings Set Line 0 53157 155 778 0 996643 24 0000517814 83 1118 0782128 24 0 000433027 68 1617 0 769198 24 X 2 14 Min Y 99 90 pA Right Node 00 02 16 83 8 y 0 511 153 Ready DI 720 Instrument VCC Series Clamp Mode 00 00 00 No Protocol Tissue Area cm2 1 You may wish to increase the displayed numerical precision for comparison with other models This is done in the Setup menu in the Preferences dialog by changing the display precision to a larger value of significant digits shown For clarity you can also selectively hide or show the tissues that you are not studying for this regression model and print the graph from the File menu Print option The R value is the computed accuracy figure of the regression Currently the program performs only a linear regression If you wish to attempt a nonlinear or other sort of model fitting you can export all or part of the data to a text file or to an Excel spreadsheet using the Analyze Tools Export Raw Data menu option This data can then be easily imported into Excel and or other statistical analysis packages Tissue Toolbox Displays a tool for selecting which tissues for which to display data The tool applies to the active graph 30 Physiologic Instruments e 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3
58. l dots These may only be discernable when the line option is set to None The size of the dot can be set for each tissue as described above see Tissues to Plot e Setting Line Width e Symbols Displays the data points as user definable graphics symbols as shown in Tissue Selection box e Digits Plots numeric text at the position of the data point to indicate the corresponding tissue number Label Frequency The value in this box establishes the frequency at which data points will be labeled by symbols or digits When the density of data points is high it is difficult to read the symbol or digit identifier The label frequency can be set to label only every n data point 68 Physiologic Instruments 12335 6 World Trade Drive e San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Labels Each graph axes is minimally drawn in the foreground color see below with tic marks indicating the step size see axes description On top of this additional features may be added as described below Show tic labels Tic labels are the numbers that identify the real value of position indicated by the tic mark For the X axis these indicate the time e g number of minutes from the beginning of the experiment For the Y axis the unit may be current conductance resistance or voltage Show minor tics This determines whether the minor tics between the tics on the axes will be displayed Show axes labels Show unit label
59. lations taking place at certain specific timed intervals Each item in the protocol list has a reminder alarm notifications at the scheduled time and tracks what is added quantity solution and other relevant notes 3 Tracking what was actually performed during the experiment in an event log This information is then available for future reference while going over your results The notebook consists of three editors based on these three most important organizational elements of experimental epithelial transport study e Manipulations Editor e Protocol Editor e Event Log Editor The Manipulations Editor provides for the creation and storage of typical experimental manipulations such as the addition or removal of solutions These manipulations can be added and grouped into saved libraries on disk thereby allowing the user to quickly access individual manipulations or load lists from previous experiments An experimental protocol is a proposed schedule of the sequence of manipulations that are to be made during an experiment These schedules can be created viewed edited and saved with the Protocol Editor To increase the usefulness of the protocol it also contains various types of alarms to assist the technician in performing the experiment While having a well laid out protocol is nice it is still only a suggestion of what is to take place What is important is a log of the actual events of the experiment In an actual exp
60. ments DI 720 manual Connect one end of the parallel port cable to the parallel port interface connector on the back of the DI 720 and the other end to your computer s parallel port Connect one end of the data acquisition cable to the instrument or interface box and the other end to the left DB37 connector there are two on the front panel of the DI 720 box DataQ DI 400 Series Install the DI 400 as indicated in the DataQ Instruments DI 400 Manual The jumpers on the card were set to the appropriate positions prior to shipping These should not be changed without consulting Physiologic Instruments Inc The hardware settings should be JP13 2 3 JP11 2 3 S1 1 4 5 6 7 ON 2 3 OFF Connect the data acquisition cable provided with your system to the 34 pin D sub connector on the DI 400 Connect the other end of this cable to the instrument or interface box depending on your hardware Software If you are using a DI 720 with the parallel port LPT1 and are installing on a relatively new PC with Windows XP or 2K you can now install the A amp A 2 3 software First insert our CD ROM labeled A A Ver 2 3 into your CD drive If for some reason the installer does not auto start then assuming your CD drive is F run F Acquire23 XInstaller exe If you have a download instead of the CD ROM you can double click on the downloaded executable instead to start the install If you are using a DI 720 or the DI 400
61. n using a protocol template from the Lab Notebook Protocol Editor The Export File Column Separator distinguishes between spreadsheet columns for exporting data Comma delimited is the most popular character for this The Decimal Placeholder is for our European neighbors who traditionally use a comma where we use a period to denote the left and right parts of a floating point number The Default bar width is the width in seconds of the data bar blue vertical lines The Pulse Timeout sets the value in seconds for the pulse to wait for a response from the data acquisition unit If there is a problem for some reason the program will detect that the pulse has been hung up however if this is set to a low number and the application is running on a slow computer the pulse may be a false positive detection seeming to hang prematurely when really it just has not completed yet If this is the case the user can increase the timeout value and the pulse should return If there is still a problem it is most likely an incorrect parallel port hardware configuration or a problem with the data acquisition unit xi Default display precision atl Mark Event Countdown sec 10 13 v Display Hover Coordinates Export File Column Separator A A r Decimal Placeholder y v Beep when pulsing Default bar width sec 60 Multiple Monitor Support Und Pulse Timeout sec fio pdate Retrieve Lost Windows OK Cancel Win
62. nd lines when data for that tissue is plotted To use the color dialog see the below screen snapshot There is a default palette of 24 colors If you would like to add additional colors of your own design click the Define Custom Colors button which will expand the dialog to full size as seen below Move the mouse over to the color gradient and select the Hue that you like Note that you will have to move the slider to the far right on the vertical darkness bar in order to get any color besides black Once you see the color you want in the patch labeled Color Solid then click on Add to Custom Colors and the selected color will be copied over to the left side of the dialog in the Custom Colors section This color will then be remembered during the course of the A A application but not after you exit the application However once you have chosen a custom color for your tissue or background the A A application will remember the new color value 2x Basic colors MT FMI Nm WI ie L A f IIE i Ga NENEENN EEE eee ee Bunn M Custom colors Ei 4 ooo gc Sat 0 Green 0 Define Custom Colors gt gt ColorlSolid Lum o Blue o Add to Custom Colors DK Cancel Setting Line Width The line width and size of data point may be set to one of 4 thickness independently for each tissue To change the line width press and hold the Ctrl key on the keyboard and Right Click the tissue button The line width on
63. ng to buffer memory Save Library As Close Library Copy to Protocol Copy to Event Log Select a manipulation and right click on the row in the data grid The pop up menu will have the Copy To Protocol option enabled if you have a dual mode MP with the protocol editor open to a valid protocol This option will copy the selected manipulation to the protocol If the Event Log mode ME is selected the other option Copy to Event Log will appear and the Manipulation can be copied to the Event Log New Library Open Library Save Library As Close Library Manipulation Library file management routines Manipulations Libraries Table This table consists of an expandable library tree listing Columns Solute Intended to store the name of the dissolved solute such as sodium potassium etc Method Intended to track which method was used to add the solution to the chamber Side Serosal mucosal or both Stock The concentration of the solute in the solvent in the original stock solution before adding to the chamber E Physiologic Instruments e 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Protocol Editor Displays the Protocol editor panel screenshot broken into two sections in order to clearly show all of the fields A ARA Laboratory Notebook MiP E Me Edit Protocol Origts Actual s Alarm Solte Tissues D 120 Instantaneous
64. o hide these markers temporarily push this button so that it appears in the up state This button is in the down state show markers by default A Area Correction Same as Menu Analyze Tools Area Correction 7 In previous versions of A amp A the toolbars were originally split into appearing in the application window and the graph window separately They have been combined into one location now which clarifies usage However some screen snapshots in this manual still reflect old versions of the software and will be updated in future releases of this manual 46 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Le at Lock Edit Mode Toggle Toggles the data edit lock mode on and off The intention of this feature is to help reinforce academic research ethics If you choose to not make use of this capability you can simply leave it set in the unlocked state If you choose to use the lock mode you can click on the orange unlocked padlock button Once locked you must type a password to unlock it The default is admin To change this password the administrator must edit the text file located in the application directory in subfolder Images The filename is called admin txt and assuming your students will not know this information this could be used to prevent modification of data values after or during recording When locked this will appear as
65. or the purposes of Quick Starting we will start a new experiment make sure the system is set correctly for the user s hardware setup the pulse parameters perform a reference measurement and begin collecting data Data Acquisition Procedure After setting up your Ussing chambers and electronics you will want to take some sample data To learn how the data acquisition process works it is useful to step through a list of common tasks so that you can understand how the software operates 1 Double click your left mouse button on the A amp A icon on your desktop or in the Windows Start menu 2 Onthe File menu select New Experiment 3 Enter a new filename in the Save Experiment dialog box and select the destination directory for your data When you are satisfied with the filename and path press Save 4 Nextthe Experiment Properties dialog box will appear Is Tissues Find the tab labeled Tissues and under Active Tissues Active Tissues select the tissues from which you will be collecting data Mo isis sfe 8 To select tissues left click on the colored square MEA Y representing each tissue If the square looks depressed that 17 18 19 20 21 22 23 24 means the tissue is selected i e will acquire data on this 25 26 27 28 29 30 31 82 channel and if it looks like it is in the up button position it is not selected In the example figure to the right tissues Tissue Area cm2 0 3 1 3 5 and 7 are selected to collect
66. ow since it is then an incorrect value This appears to work well for in house testing If you happen to be conducting an experiment with a very fast dynamic response over a large voltage range where the gains will likely be changing you may want to preset the gain to a lower value i e not using Auto Gain Otherwise it is a very useful feature in that the computed resistance values are accurate despite gain changes avoids saturation at high gains Incidentally we recommend running your experiments with any overhead fluorescent lighting in your lab turned off as the wires connecting the electrodes from the tissue to the clamp serve as antennas and frequently dynamic response of human tissues can occur in or near the 50 60 Hz range of most wall outlet power sources 40 Physiologic Instruments 12335 6 World Trade Drive e San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Instrument Settings The Instrument Settings menu option brings up an editor that allows you to modify the Voltage Current and Signal gains which you may need depending on the instrumentation configuration and the type of experiment you are conducting Additionally there are two A Instrument Settings x connection utility buttons If for some reason you forget to turn on the Voltage Gain o y power to the data acquisition box or i plug in the parallel cable connector neon 10 to your PC the software may not Signal Gain n have re
67. p setup and the time of the last data point acquired It also displays a message if the data acquisition mode is pulsing for a new data file Ready DI 720 Instrument YCC Series Voltage Clamped 00 42 59 No Protocol Tissue rea cm2 1 50 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Exporting Data The Export Raw Data dialog box provides a means of saving selected data from the experiment into a spreadsheet compatible file The menu command Analyze Tools Export Raw Data will open up the dialog box see below In the Export Target section you can choose whether you would like to export to an Excel spreadsheet must have a valid license for Microsoft Office installed and note this may be slow for large data files or to an ASCII text file as a delimited format recognized by most spreadsheet packages such as Excel or SigmaPlot Select the export filename by clicking the browse button to the right of the displayed default filename Next select the tissues and the data parameters to be exported By default the order of the columns exported is grouped first by Tissue and then by the Data to Export L V G R etc If you would prefer to group the columns first by parameter and then by tissue you can select the checkbox labeled Sort by Parameter The time range of the export data may be entered manually in the boxes after selectin
68. raph Setup Window Help File Menu There are three states to the File menu The first on the left below is what you will see when there is no experiment open yet The second on the right is what you will see with an open experiment The third happens only if you open the application with no valid data acquisition system connected which is like the first one but disables the New and Append features New Experiment New Experiment Append Experiment Append Experiment Open Experiment Open Experiment Glose Experiment Close Experiment 5a ss periment Save Experiment Ds Save Experiment Gs Save Experiment As Graph Print Setup Graph Print Setup Print Print Exit Exit New Experiment Used to start a new experiment data file Displays the Save Experiment dialog box to set the location and file name for the experiment After selecting a filename you will need to specify which tissues you want to take data on corresponding to tissue channels on the VCC clamp the area correction if any store any comments and then press Save You will then need to Reference the channels zero adjustment calibration before taking data 16 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Save Experiment 2 x Save in o Data 8 ex E3 i My Recent Documents Desktop My Documents EdTest EXP E Experiment 1 EXP Experimen
69. rid window containing the raw values occurring within the extents of the data bar see following screen snapshot Data from this grid can be selected and copied to the clipboard CTRL C Data Bar Yalues Raw d x ooo w B e 1 v clr E 2 s 4 s e 2 a 3 10 12 12 13 14 15 16 17 10 19 20 21 22 2 24 2s htimmiss i Y frs ron Iess EET 00 02 31 2 2 f 2 2 j 2 E i gt E 00 02 41 00 02 51 I pe Po CH 00 03 01 E El 00 03 12 00 03 22 00 03 32 00 03 42 00 03 52 el alle e n h To Ts s Te 7 8 8 0 1112 13 19 15 16 17 10 13 20 21 22 20 24 25 26 27 26 29 Tissue mm TE INE TRENT ee 00 00 11 00 00 21 00 00 31 00 00 41 00 00 51 00 01 01 00 01 21 00 01 31 00 01 41 Raw Data All This displays the raw data for the entire experiment rather than just within the bar in tabular form for each tissue The user can select both the tissues to display and the parameters current voltage conductance and or resistance Export Data Bar Values Opens up the Data Bar Values Averaged dialog box to the Export Settings tab Export Raw Data Displays the Export Raw Data dialog box This form enables the user to select tissues time interval parameters and file name to be exported to ASCII text file A m Physiologic Instruments 12335 6 World Trade D
70. rive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual or Excel spreadsheet workbook formats This is useful for transferring specific data to other graphics programs See also the section titled Exporting Data Graph Menu Future revisions of the program will expand this menu with additional types of graphs such as I V curves Create New Graph Opens a new child window within the Create New Graph same experiment that displays the same Graph View Editor raw data Additional graph windows can be used to highlight a different channel or View I Rt Vt calc 3 pane Le part of the data than in the first window or View Current Resistance Tile Vertical to display additional Y axis types current voltage resistance This feature can also be accessed via the toolbar button One useful layout is to have two windows open one displaying current and the other displaying resistance as the data is being acquired The background colors of the windows can be changed to quickly recognize which is which Graph View Editor The Graph View Editor provides a means for tracking a custom screen layout that you prefer to work with For example see below screen snapshots you can create a second plot window with Create New Graph and then switch the Y axis using the pop up menu right click while holding the mouse over the Y axis to Conductance Color the background by double clicking in the graph window and set
71. rotocol this command opens the editor with both the Manipulations form and Protocol form on a horizontally split screen This enables the user to easily view the manipulations as they are added to the protocol 24 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Experiment To assist in running the experiment this command opens the editor with both the Protocol and Event Log on a horizontally split screen This enables the user to easily view the upcoming manipulations as well as review and edit the experiment record Event Editing To assist in editing the Event Log this command opens the editor with both the Manipulations and Event Log on a horizontally split screen This enables the user to easily populate missing events fields from the manipulations libraries Acquire Menu Reference This menu contains all the commands involved in View Gains acquiring the data Start Chart Acquisition Reference v Slow Pulsing Ds Opens a form for taking a baseline reading to allow Medium Puling the computer to correct for slight offsets in the Fast Pulsing output amplifiers for current and voltage Mark Event F12 measurement and for differences in the ground potential between the instrument and the computer For a new data file a reference measurement is required before data collection can begin After the first reference is taken it can also be called up again from
72. s Checking axes and unit labels cause the units to be displayed on the axes Backcolor Left clicking the mouse on the Backcolor box opens a color dialog box to enable the user to define the background color for the graph Note Some back colors will conflict with tissues colors Forecolor Left clicking the mouse on the Forecolor box opens a color dialog box to enable the user to define the foreground color for the graph This color is used for axes and labels Save as Default Checking this checkbox on will save the current settings to a preferences file when the user presses OK or Apply After the program is shut down and then re run again later it will remember your default settings here X Axis Tab Contains display settings for the X Axis Axis Type The axis type for the X axis is currently set always to time This may change in future revisions IV plots Min Step Unit Unit Maj Tics Min Tics Max Origin Various graph axis parameters The Min is the smallest X value leftmost displayed on the screen The Max is the largest value The Origin is where the vertical axis intersects the horizontal axis The Step Unit is the value for the size of each Major Tic A Major Tic is the larger tic mark along the axis A tic label GOs Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual usually accompanies this There are a certain of major tics across the
73. sue Area cm2 1 36 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Setup Menu Graph Plot Setup Data Bar Settings Graph Plot Setup Pulse Setup P Opens a multi tabbed graph setup form see page Instrument Settings 66 This form may also be quickly accessed by double clicking the left mouse button over the graph area Dbl clicking over the X axis causes the form to open ready to adjust X axis parameters Dbl clicking over the Y axis causes the form to open to adjust Y axis parameters Dbl clicking elsewhere on the graph opens the form for changing general graphic parameters Preferences Data Bar Settings The Data Bar Settings menu option brings up an editor that allows you to customize your data bar so that you can use the features more efficiently to produce the sort of graphs and analysis that you need for your experiment post analysis Checking the checkbox Synch all plot windows to current plot on has the effect of matching multiple windows with the same data bar location which can be useful for comparing research results Data Bar Settings E Bar Width Io seconds Lock BarColor PS Line Width m v Center Bar on mouse click Synch all plot windows to current plot OK Cancel Pulse Setup The Pulse Setup menu option brings up the pulse editor see below screen snapshot This allows you to customize
74. t 2 EXP KI SE My Computer File name Experiment 1 EXP a MERA Save as type Acquire Experiments Exp y Cancel Places Append Experiment Earlier versions of the program occasionally would run into a premature ending Most likely newer versions will not have this problem However in case the program hangs or you wish to stop and experiment and return to it later you can open a saved experiment file in Append mode This will allow you to add new data points to the existing file This option will first display an Append Experiment dialog box Select the name of the file to which you want to append data You will need to run a Reference as if you were taking new data if you just started the program If you were previously taking data and closed the experiment and are now appending and the selected tissues are the same in Experiment Properties then you will not need to re reference When you start taking data you will have an opportunity to shift the new data points in time You have three choices no time shift the next data point will appear directly after the last one taken automatic time shift to the current time or you can specify your own shift Pressing OK on this dialog will start the data le Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual A Append Experiment Lapsed Time k x C Continue with no time shift Shift experiment by actu
75. t menus that will appear depending on where the mouse cursor is when the user clicks the right button Standard Pop up Menu If the user clicks anywhere on the screen that is not directly over one of the axes the standard pop up menu appears This has the following options Data Bar Area Under Curve Tissue Toolbox Data Bar Values Averaged Data Bar Values Raw Raw Data All Data Bar Settings Which match corresponding menu options on the main Application Menu Analyze Tools except the Data Bar Settings option which appears on Setup If the Data Bar is not currently being displayed the Data Bar Settings option is not available wv Data Bar Area Under Curve Tissue Toolbox Data Bar Values Averaged Data Bar Values Raw Raw Data All Data Bar Settings 64 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual X Axis Pop up Menu If the user clicks over the X Axis a different menu appears with options that correspond to options on the Graph Plot Setup dialog box Use standard unit values Scroll this axis Scroll with Zoom X Center axis Force all graphs to current X Auto scale units These features are further explained in the section Graph Plot Setup Dialog X Axis Tab Use standard unit values Scroll this axis Scroll with Zoom Center axis Force all graphs to current X v Auto scale units Y Axis Pop up Menu If
76. th only the Protocol screen showing This form defines the sequence of manipulations to be made during the experiment The columns are the same as those for the manipulations form except for the four additional columns Time Alarm Tissues and Description All cells in each row may be filled in on the protocol form or the may be partially filled in by selecting from the Manipulations list Double clicking a manipulation on the cause the last row in the Protocol to be populated with the contents of the manipulation thereby saving effort and error The time will be blank When a time is entered and the mouse is clicked outside the row the table will be sorted to place the manipulation in the correct sequence For each protocol event complete the cells for Alarm and Tissues Description may be filled in during protocol design or may be completed during the experiment Event Log This opens the editor with only the Event Log screen showing The event log is a record of the events that actually occurred during the experiment It is analogous to the lab notebook In an ideal experiment the event log will be identical to the protocol except that the descriptions may be augmented Few experiments are ideal so the event log may differ substantially from the protocol The protocol is a tool to guide the experiment The event log is what happened The Event Log may be edited during and after the experiment Protocol Design To assist in the design of the p
77. the left button and observe the tool tip Bar Width 00 00 00 where the digits indicate the new width of the bar Drag the bar line to change the bar width Once the width of the bar is set the bar may be positioned over the data points by Pressing the left mouse button while the cursor is inside the bar and then dragging the bar to a new location Release the mouse button to update the data display for the new data within the moveable bar If Center Bar on Mouse Click see above has been set then pressing the left mouse button at any point outside the bar will cause the bar to re center about this new mouse position Data contained within the bar may be viewed by selecting Analyze Tools Display Data Values from the menu or by using the Right Click menu when the cursor is in the graphics screen in Area Under Curve Pressing this icon displays a line on the screen with three handles These handles may be used to tilt slide and otherwise manipulate the line While dragging the handles the slope and intercept of the line are continuously displayed on the information line Once set the line may be used to measure slopes initial rates as 48 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual well as the area bounded by the data curve and the line When the adjusting the line the x amp y values slope and intercept of the line are displayed on the left side of the
78. the menu at any point in case you wish to take new references or if the selected tissues change In order to use the reference screen in the software application the hardware unit must first have the remote local switch on voltage current clamp function mode set to Remote REM This allows the program to control the function OPEN CLAMP and mode I V switches on the clamp automatically By definition when the clamp function is OPEN the current measured is zero Similarly when the clamp is set to VOLTAGE CLAMP at 0 0 i e short circuit the voltage measured is zero Therefore values for current and voltage measured under these two conditions respectively serve as a zero reference and should be subtracted from future measurements during the experiment To take a reference measurement click the Reference button on the form The clamp will switch to open circuit to measure the zero current and then to short circuit to measure the zero voltage Finally the status of the clamp will be set to the acquisition mode established under Setup Chart Pulse DAC page 37 The table will display the reference data Reference values should be typically less than 1mV 225 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Note If the DAC menu was set to voltage clamp to zero short circuit condition verify that the meter on the voltage clamps reads 0 0 mV after referencing
79. the Backcolor to be different than the first plot In the below example current in micro amps uA is in blue and conductance in milli Siemens mS is in light brown This way you can quickly identify the plots during data acquisition To save this view for later use with other files select the Graph View Editor option on the Graph menu and then type in some unique name to remember this view i e Current Conductance Next time you run the program you will be able to Load this view from the Graph View Editor or from the Graph View MRU List Graph View MRU List Keeps track of your Most Recently Used MRU graph views that you have created with the Graph View Editor 35 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual x Current Resistance Tile Vertical Save View Current vs time Current Resistance Tile Vertical Load View 18 R 1357 1 amp R 2468 Rt amp Vt calc 3 pane Delete View A Acquire and Analyze 2 2 File Edit Zoom Experiment Acquire Analyze Tools Graph Setup Window Help JE gl siew Seis 1 A aj ajaja ielaigigiaisiaiaiaia A Sample Data EXP Isc pA vs Tin Sample Data EXP Rt 0 vs Time Min E ni x 100 407 Y 10438pA Right Node 00 02 16 83 8 y 0 511 X 0 26 Min Y 297 81 0 Ready DI 720 Instrument VCC Series Clamp Mode 00 00 00 No Protocol Tis
80. the left indicating the row corresponding to the mark All aspects of the Event Log may be edited Changes are stored automatically Mark Event Alarm Type x Tissues 7 14 15 16 2262301624 25126127128 112930131 132 Mark Event Skip Event Delay This Event Only Es mm Delay And Shift ALL Remaining Events 27 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Data Bar Analyze Tools Menu Area Under Curve Tissue Toolbox Data Bar Area Correction If this menu option is checked the Graph Window adds a pair of vertical lines on the graph labeled Data Bar Values Averaged Data Bar Lines in the following screen snapshot Data Bar Ves Raw thereby establishing a data window The Data Bar ees Toggle Button is also synched with the menu Export Data Bar Values option Export Raw Data The data that fall within this window in time can be averaged exported and otherwise manipulated Changing the position of the data window is by pressing the left mouse button while the cursor is inside the box and then dragging the box to a new position in time Releasing the mouse button fixes the data bar at this new time window Set the width of the bar to about 180 seconds 3 min by Right Clicking on the graph area and selecting Settings Checking the box locks the width to avoid accidental change When the bar width is not locked
81. the timing of the pulse that triggers the data acquisition steps The pulse has four components The first segment is determined by the DC Clamp Level Depending on the Clamp Mode this will either be the voltage or the 237 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual current held across the tissue In the case of Voltage Clamp at DC Clamp level of zero the current will be the short circuit current The second and fourth segments are set to equal and opposite values Values of current and voltage measured during these segments are used to determine the resistance of the tissue In other words V IR RSE I ERA R V AI Dus T AV gt Vus Ce Vow A R oaie ze AI If for example we set the step change G to be 5 mV then the difference in the voltage will be 5 mV minus 5 mV which is 10 mV The currents are measured and then the conductance is computed The resistance is the inverse of the conductance These values are then recorded and plotted on the screen depending on which axis type you have selected on the Y axis The picture on the lower right section of the dialog see screen snapshot below is a timing diagram of how the pulse is designed Each letter in this diagram corresponds with the label to the left of the options some of which are editable and some are not Typical default values as shown above may need to be customized for your parti
82. the user clicks over the Y Axis a different menu appears with options that correspond to options on the Graph Plot Setup dialog box Set Parameter Current Voltage Resistance etc Use standard unit values Auto zoom this axis Center axis Auto scale units These features are further explained in the section Graph Plot Setup Dialog Y Axis Tab METI oes Use standard unit values Voltage vt Auto zoom this axis Resistance R Center axis Conductance G Auto scale units Current calculated Voltage calculated 65 Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Graph Plot Setup Dialog The graph area is the region where data from an experiment is displayed The parameters governing the appearance of the graph are controlled by the settings in the Graph Plot Setup dialog box There are three Tabs Plot X Axis and Y Axis Plot Tab The Plot Tab controls general display attributes of the graph Graph Plot Setup x Tissues Right Click Color Ctrl Right Click Line Width OA E POE ERR Salle sgr TREE I RR RS ENG Grid None C Dashes Lines Lines C None C Dashes Lines Plot C Points Symbols Ze Digits Label Frequency fi V Show tic labels J Show minor tics v Show unit labels Nl Backcolor Forecolor Window Name Sample Data EXP Save As Default Tissues DK
83. ue Toolbox or select the menu item Analyze Tools Tissue Toolbox Double check the tissues selected for display 4 NOTE Every now and then the data acquisition unit hangs during pulsing If this happens a timeout will occur You must shut down the program use the task manager if it is stuck and run the boot loader Run720Loader bat in the root of your program installation directory C Program Files Acquire23X for example Once you get a successful load for the unit you should be able to run the program ls Physiologic Instruments 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual 14 To see your data corrected for tissue area press the area correction button on the program toolbar or select Analyze Tools Area Correction from the menu 15 Now let the program acquire data for at least 5 minutes before proceeding Each new data point is saved to disk immediately after measurement Changes to other information such as the experimental record require that you do a manual Save before exiting the program After you have saved your data to an A amp A data file you can always access it again to analyze the acquired data Data Analysis Procedure After you have collected data you will probably want to examine it more closely and or to export data to other programs for producing summary reports and publication quality graphs For this purpose we provide a movable and resizable widow or
84. uments e 12335 6 World Trade Drive San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Time This is the time in minutes as originally scheduled before experiment is run The time is stored in seconds from the start of the experiment The time field in this case refers to a certain Manipulation that needs to be performed at some time interval Actual This is the actual time that the event will take place if there has been a false start Alarm Specifies the type of alarm to be applied There are three types of alarms See the section below for descriptions of how they work Tissues Specifies the tissues to which the manipulation is to be applied Solute Specifies the manipulation solute to be added to the chamber This value may be entered in the field or added from the manipulations pane Method of Application Specifies the method for making the manipulation Methods can be selected from a drop down list or typed directly into the field In general there are three types Adding by Weight Adding by Volume and Replacing and Adding also by Volume Or you may have a special case Side Selects the side of the tissue that the manipulation is to be made The choices are Mucosal Serosal or Both sides Quantity Input the quantity to be added Quantity will only be applicable when a substance is added or a volume is removed from the chamber Values may be entered as decimals and in exponential form by including th
85. yze 2 3 User Manual Full WinDag Install 10 11 12 13 In that case here are special instructions for installing WinDaq Place the CD found in the blue notebook into the CD drive If the setup routine doesn t start automatically run Setup exe from the CD Select Install Software for all other products except starter kits 2 opt OK On the Specify the Product form Select WinDaq Lite Option 1 and OK To Specify the Instrument select either DI 4xx Series Plug In Card Or DI 720 740 730HV Portable Instruments depending on your device Press OK If DI 720 was selected specify the communications mode as Parallel Port Fill in the registration information Select the directory into which the software will be installed following the screen prompts Select the instrument to be used with the WinDaq Lite software DI 400 DI 720 If DI 720 select the parallel port to use typically LPT1 If DI 400 you will need to Setup the Bluewater Driver and take the default settings of 180 and O Select a Program Manager group Select No for the CODAS Click OK 11 Physiologic Instruments 12335 6 World Trade Drive e San Diego CA 92128 Acquire amp Analyze 2 3 User Manual Quick Start The following section steps the user through a sample procedure that should get them up and running quickly Further details may be found by reading the Reference section of the manual Overview F

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Acquire & Analyze 2.1.8 User Manual