Manual (PDF file) - PaynesNotebook.net
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1. Ignore This is another way to do RLI division and perform a manual correction of signal amplitude from bad diodes RLI gt Map Transfers the inverse of RLI to the map This results in RLI division if Correction is selected Make Correction A few diodes do not cohere with other diodes The amplitude is much larger or smaller than the amplitudes of signals in surrounding diodes In this case we can ignore this diode or correct the amplitude manually To manually correct the amplitude first clear all selected diodes Second select a reference diode Third select diodes that should have similar amplitudes as the amplitude of the reference diode 11 Last click the Make Correction button The program scales the traces in the trace window according to the first selected trace from the reference diode Save Map Saves the current map to a MAP file Load Map Loads a map to the internal map from a MAP file Selection Provides four methods to select diodes which can be ignored during analysis The user can key in the value of a threshold in the text box This feature enables the user to clean up a map by removing diodes with less information Max Amp When the lt button is clicked diodes with maximum amplitudes less than the threshold are selected When the gt button is clicked diodes with maximum amplitudes greater than the threshold are selected Amp Latency W2. None fats 0 Dil ia taxis oneal oy Acquisition Analysis vay eo Panel Dices Ho T Trace Slope Load Image Time Course tie ae fi tI ala Saved Traces Mtra mao 7 Compare Hel reie File Control Jnccoasc Se 1 m teisesse Panel acu Lum F Muka Aurraqe Rarseas Right Window Multipurpose f mp Ay Time Course E A Saved Traces In Om RAN denatanza SaveiLoad File Line f Reference Paneer r somniar Mi I Mormatent I 1 Menu Bar 1 1 File Open J save Right winaow Open Opens a data file A window will show up in which the user can select a data file to load Create Folder Creates a folder to store data It is recommended to create one folder for the data collected in one day Exit ESC Exits the program the same as click the ESC button 1 2 Preference Save Preference Save Preference Load Preference Saves most settings to a PRE file Preference files contain stimulation and display File AS l save Right window parameters Appendix I Load Preference Loads most settings from a PRE file 1 3 Save Left Window Save Right Window Saves the left window to an image file The user can change the image format at Main Control Panel gt Image 1 4 Save Right Window Saves the right window to an image file 2 Array Window There are 464 traces representing o
3. Normalized to array maximum y Specifies the property to be displayed Color Scale Color Scale 1 T Contour FIRES MOE Satin as a ma Control Mode Bounds y Black BG ICAA uj T Repeat P Bounds Center Current Pt 160 M upper 1 00 MUN Start Pt 160 Lower 0 00 DUNT oo speed 70 HIRE LTP Movie Record 1 Mp 28 RLI Displays resting light intensity Max Amp Displays maximum amplitudes Spike Amp Displays the amplitudes of spikes Fitting for all diodes needs to be completed in order to display correctly Right Window gt Trace Tab gt Simulation Tab gt Fit All Diodes Amp Latency Displays the latencies to a specified percent of maximum amplitudes Main Control Panel gt DSP Tab gt Main Tab gt Latency Measure Settings Max Amp Latency Displays the latencies to the maximum amplitudes Movie Types Amp Normalized to array maximum Play a movie representing amplitudes normalized to the array maximum Amp Normalized to diode maximum Play a movie representing amplitudes normalized to the maximum amplitude of each diode This type of movie is useful for the analysis of activity propagation Color Controls Controls the color scale bar in the bottom left corner There are four types of color scale bars Color Scale 1 Color Scale 2 Blue to Red Gray Scale The user can 29 select the control mode from one of the two modes Bounds Center Amp In Bounds
4. When checked traces are superimposed 21 Normalize DVI Normalizes AI I so that the amplitudes of traces are set to one This function is useful when the user want to examine the latencies of responses at different locations Normalize LTP Normalizes the reference value prior to TBS to one the reference record Simulation Controls the simulation of the EPSP Display Simulation Save Load component Onset pt 160 HINA Range pt 160 180 F Amp 0 3 l m Tau pt 4 AH Onset E cm Gleak 0 01 HH HA O GsyniGleak pe Sets the start point of the simulated EPSP Range IF step size L Spike Start 169 ena 172 F Auto Fitx1 Axon start o Enajo Fit Pts 40 Fito varies the onset point to minimize the Set All Diodes init Amp Spike Slope Thre 0 sum of square error When the box is FitAli Diodes Cal Whole Vm SPike Amp Thre o When the box is checked the program cleared the onset point is fixed The boxes before the other four variables have a similar function Range Constrains the range of the onset point for fitting Amp Sets the amplitude of the simulated EPSP Tau Sets the time constant in the alpha function Cm Gleak Sets the ratio of Cm to Gleak membrane capacitance to leak conductance 22 Gsyn Gleak Sets the ratio of Gsyn to Gleak synaptic conductance to leak conductance Range Sets the range that the program searches for a set of parameters
5. Y axis scale of analog input signals e g field potential X Scale Controls the X axis scale of all traces in the array window X Shift Controls the shift in the X axis for all traces Nor2ArrayMax When checked the color in the background of the array window is normalized to the array maximum Compare When checked the data in Ref Record and Final Record described below are subtracted and the difference is displayed according to settings described below Increase Decrease Displays increase or decrease in data when Compare is checked Actual Percent Displays actual changes or percent changes Ref Record The reference record number Any record number can be selected Usually this is the record number just before the tetanic stimulation Final Record A record number which the user want to compare with the reference record Average Records When checked a number of records described below are averaged and displayed in the background in the array window and in the Map Movie window This function is available for maximum amplitude only of Averaged Records The number of records to be averaged if Average Records is checked For example if the current record number is 17 and the number of averaged records is 5 the average of maximum amplitudes from record 13 to 17 is displayed If Compare is checked and the Ref Record is 20 and the Final Record is 40 the averages of maximum am
6. during fitting Taking Amp for example when the range is set to one the program calculates the error at the current setting moves the slider to left by one step and calculates the error then moves the slider to right by one step and calculates the error and last picks the one with the minimum error When the range is large the time of computation is longer When the range is small the fitting might get stuck in a local minimum that is not a global minimum Step Size Sets the step size of parameter variation during fitting When the step size is large the program reaches the minimum faster but the precision might not be as good When the step size is small the program needs more time to reach the minimum but the precision is better Spike Start End Auto Specifies the start and end points of the spike component This period is excluded in the fitting When Auto is checked the program sets the spike period automatically The period is defined as the time from the time point when the slope is 50 of the maximum slope to the time point when the slope is 50 of the minimum slope Axon Start End Specifies the start and end points of signals from presynaptic afferents This window is excluded in the fitting 23 Fit Pts Specifies how many points are used for fitting after the onset point Fit x1 One iteration Fit x10 10 iterations Set All Diodes Sets the variables of all diodes to the current set
7. gt Array Tab Max Amp Cha SD The standard deviation of the maximum amplitude before the final record included The number of records included in the calculation is controlled by the number of average records in Main Control Panel gt Array Tab 18 Max Amp Per Cha The percent change in maximum amplitude the maximum amplitude of the final record the maximum amplitude of the reference record the maximum amplitude of the reference record Max Amp Per Cha SD The standard deviation of maximum amplitude in percent before the final record included The number of records included in the calculation is controlled by the number of average records in Main Control Panel gt Array Tab Max Slope Maximum slope within the analysis window Spike Amp The amplitude of the spike component Amplitude The amplitude at the point line the gray line in the trace window SD The standard deviation of the initial baseline before the start point of the analysis window Amp Latency The latency to a certain percent of the maximum amplitude Main Control Panel gt DSP Tab gt Main Tab Max Amp Latency The latency to the maximum amplitude 19 Mode Set what signals are controlled by dragging the mouse in the trace window Optical The mouse controls the x scale of optical signals and the y scale of both optical signals and time course plot Field The mouse controls the scales of analog input signa
8. is the current trial number 0 represents the average of all trials in the record The right number is the maximum trial number in the current record 5 Main Control Panel 5 1 Array Tab Array DSP Baseline Image Color T Trace Background None y Controls the display in the array window r RUI value _ Save Background Data F Diode No Y Scale 100 EP Y Scale 100 Trace Load image X Scale 1 xshife fo T Nor2ArrayMax F Compare Ref Record 1 increase y FinalRecord 1 Actual y r Average Records PP FiE When checked the array window displays traces RLI Value When checked RLI value of each diode is displayed Diode No When checked diode number is displayed Load Image Loads an image file to display as the background The image format is set in Image gt Input Image Format Background The user can select either one of the following modes as the background in the array window None Image RLI Maximum Amplitudes Spike Amplitudes Latency to a certain percent of Maximum Amplitude Latency to Maximum Amplitude EPSP Latency For the latency to a certain percent of Maximum Amplitude the percentage setting is in DSP gt Main gt Latency Measure Settings Save Background Data Saves background information to a DAT file e g maximum amplitudes for each diode Y Scale Controls the Y axis scale of optical signals F P Y Scale Controls the
9. mode the upper and lower bounds are controlled in the Bounds tab below In Center Amp mode the center and the amplitude of the scale are controlled in the Center tab below Contour When checked the spectrum of the color is not continuous Therefore it can reveal the contours of equal values When the box is cleared the spectrum of the color in the scale is continuous Black BG When checked the background is black When cleared the background is white Movie Controls lt Rewind to the start point gt Play the movie Pause Repeat When checked the movie keeps playing Current Pt Control and indicate the current point 30 Start Pt Specify the start point of the movie End Pt Specify the end point of the movie Make Movie When checked the program creates a series of JPEG figures which can be used to generate a movie Speed Specify the speed of the movie Appendix l Settings Saved in A PRE File 2629112 1 The codes for preference control are in MainControllerFileController cpp Version Schedule Flag HHHHo J 0000 Th H Th Th trigger signal DAP e e e e e e e Image X coordinate of CC Identification number D images Y coordinate of CC D images width of CCD images height of CCD images The unit is ms start of reset duration of reset start of duration
10. objects 36 Data Dap MainControllerAcqui Handles interactions between objects involved in data acquisition MainControllerArrayWindow Handles interactions between Main Controller and Array Window MainControllerDAP Handles interactions between Main Controller and DAP controller MainControllerFileController Handles interactions between Main Controller and File Controller MainControllerLtp Handles interactions between objects involved in the analysis of LTP MainControllerSignalProcessing Handles interactions between Main Controller and Signal Processor MainControllerTraceWindow Handles interactions between Main Controller and Trace Window Data Manipulates processes and analyzes the data from one photodiode DataArray Manages all Data objects 472 objects DapChannel Controls one digital output channel DapController Manages all 8 DapChannel objects 37 DapWndow Controls the window displaying the timing of each output channel and the acquisition period Color Color Controls the color in Array Window Trace Window and Map Movie Window WindowExporter WindowExporter Controls the saving of Array Window and Right Window UserInterface UserInterface Controls the graphic user interface The file is created by IU Editor exe UserInterfaceMethods Contains codes for the initiation and display of GUI SignalProcessor Filter Controls the temporal and the spatial filters Po
11. of parameters Init Amp Initializes the amplitude of the EPSP according to the maximum amplitude of each diode Fit All Diodes Fits the data from all diodes until the minimum square error is reached This process might take a long time to finish Cal Whole Vm When checked the program simulates the EPSP to the end of the trace which takes a longer time to fit Spike Slope Thre Spike maximum slope threshold used for automatic spike detection The maximum slope must be greater than this value to be considered containing a spike Without a spike the spike period is not excluded in the fitting Spike Amp Thre Spike maximum amplitude threshold used for automatic spike detection The maximum amplitude must be greater than this value to be considered containing a spike Display Simulation Save Load Save Values Saves values displayed in the trace window to a DAT file Save Time Course Saves displayed time courses to a DAT file Traces Saves traces in the trace window to a DAT file The user can switch the unit between points pt and time ms The following two boxes specify the start and end points Save Fitting Variables Saves fitting variables of all diodes to a FIT file Load Fitting Variables Loads fitting variables from a FIT file for all diodes Save Alpha Vm Traces Saves alpha and Vm traces to a DAT file Save Simulation Properties The values of variable
12. specifies the number of bursts Interval between Bursts specifies the interval between two bursts Stimulator 2 Controls the digital output for stimulator 2 The settings are the same as Stimulator 1 Record Schedule Sets up automated data acquisition according to a schedule Number of Records specifies the number of records When Schedule is checked in the Acquisition tab the program stops data acquisition automatically when the number of records is reached Interval between Records specifies the interval between two consecutive records in seconds 27 Gain Acquisition Gain specifies the gain of amplification at the post amplifier during data acquisition RLI Gain specifies the gain of amplification at the post amplifier during the recording of resting light intensity Note these settings are for analysis only To change the gains the user needs to change the settings of the gain control box a silver metal box manually Trial Controls Number of Trials specifies the number of trials in one record Trials are typically averaged in a displayed record Interval between Trials specifies the interval between two consecutive Trace DAP Map Movie trials 6 3 Map Movie Mode Specifies the display mode of the window There are two modes Map and Movie Map Types dde a Map Mode Map Max Amp y Movie Amp
13. start of start of duration the shutter of the shutter data acquisition stimulator 1 of stimulator 1 The real usually 1 the signal generator Th Th e e start of stimulator 2 d u n terval between umber of pulses interval between uration of stimulator 2 in one b two p mber of points in a trace two points in a trace ms usually 1 ms samp this is just a duration of a stimulus is controller by ing interval urst for stimulator ulses for stim mber of b terval un in terval nber of p between ursts between ulses for stim two b in one b two p ulator 1 ursts for stin n ator 1 ulator 1 urst for stimulator ulses for stin n ulator 2 1 2 31 32 The number of bursts for stimulator 2 The interval between two bursts for stimulator 2 Record The number of records The interval between records in seconds Trial The number of trials The interval between trials Gain The gain for data acquisition The gain for RLI Examination window The start of the examination window in points The width of the window in points Baseline skip window for the polynomial fitting The start of the skip window in points The width of the skip window in points 33 Appendix Il The Structu
14. 6 Trace WindOW vecinal ts 16 A e aa e eine ee E E E ee ERN 17 Mode eck ai e e aa Adah O 19 Pomt Lies t a naan a hee a aa ass 19 Trace eiie i A A a a Si ee Ta ARSS 19 AS 19 Time OUUSE A E A IAE A E IA IE 19 Saved RAC A A 19 AA a EE seule de tocieayea Gaede Saxtaue teeaadeSiclaues A ST 20 PUD NA strc AI 20 MISTS VAY cosa lads be xpos can O O 20 po 6000 215 0 9 a id 21 iv 62 DAP VADs Gc Sa Sie OS RS E ae 25 ETL Output Control A A at ood Ae Sedat eds 25 Acquisition Controls vice haane aie e ao a a ainle a LSG 25 Stim lator l eessen eosi no aor Ea aida 26 SUE A 26 Record Schedule dscici lid iii 26 A EAT eee ee ee eg ee ened 27 Taal Controls ere feels ervare pias e O O aS aeS 27 Gs Ma M OVE sci ca gees Sots ack a A asa e a A eo 27 Mode si A E E 27 MAD PES rra Aen e ara ue HO ee eoan 27 Movie Types cuidada dd 28 Color Controls eener eene an ea a a E a EN lee a E S EE EES 28 Movie Controls ca Gan ee a A IA E 29 Appendix I Settings Saved in A PRE Fille scccssscssssscssssecssssecscssesssssessssssessesees 31 Appendix II The Structure of A ZDA File sssccccccssssssssssscscccsssssssssssscscscssssssees 33 Appendix III Comments on CPP and H Files oomoooonccononocnccnnconcncconocacnnccnnocccccononnos 35 A snapshot of the user interface Menu Bar PhotoZ v 5 22 File Preference Saye Let viincow Save Rant Window trace riai ntegernzas Array Window U Ze im Aqui tna Asta value
15. A AA AA A AAA AAA AAA 6 Sl A sa aaascwotsen coeie a ean nta aca es ied LET nda ede nia aaa SEIE EA 6 A I Ree ROR ne Ont PURGE PA ER CDA ME E TORT TOE cPaE CORE TPA POPST CRIT STE SCT 6 REL Valeo A A A end aoa 6 A A eR e me a ne nr ran rE a een ements 7 Load MASE v sycsesyaauesdogciissavadse a E becaayns ood sone E E TE S 7 Backstound E 7 Save Background Data iia 7 A E 3G ade duwiesy aurdedeedacleuy ae edctotaneaaatee 7 PP Cal Gia tics testes E EA AS T TE binge tite E ESN 7 O E 7 D IMME E E E E EE S 8 INGOT ATT Ay A OO 8 COMPAL ET E ds 8 Increase Decrease aos 8 A A oat Aten Seles teen iit eek Beall ee oe Ati San hed 8 Ref Record anita ts is 8 IA A A bed ten oe Gated eed cous ESAS 8 PCTAC SIRE COL SEG aay ET Se eee SY ae a eee See Sa 8 FOL Averaged Records ad Gusta Re eee Moet ae 9 5 2 DSP Digital Signal Processing Taba a 9 Man Tabarca dd dd 9 COTE CUO a2 cre A A ee 10 PANO O 12 5 3 Baseline Tabs ad 13 Baseline Correction Pes iii 13 111 A a St ees oe A RC 13 Arbitrary MOISES AI AD Sea tote 13 IN VAD AE A avait id ea oid de aes 14 A POSO iia d died 14 A ON 14 O 14 Herri id 14 Output Image Foral 14 Inp t Image Format ll ai 14 White Background manceni ninn eae tacedn eee aeiaea Genet NER SS 14 A A 15 Color Scalesin nnie i a E A EE OE ads 15 Control Mode a 15 UIA PAE EE E REE TA 15 O E EE E 16 6 Right Window Multipurpose sssssessssssoocccceesssssocooceceeesssooocccesesesssoococcsssssssoocccesese 16 0 1 Trace A O 1
16. L e wich EE image in the background of the array window nein E Output Image Format PNG y F White Background when an image is selected as background It also sets the image format for input and Input Image Format BMP output X Position Sets the x coordinate of the top left corner of the image in pixals Y Position Sets the y coordinate of the top left corner of the image in pixals Width Sets the width of the image in pixels Height Sets the height of the image in pixels Output Image Format Sets the output image format PNG BMP JPEG TIFF Input Image Format Sets the input image format PNG BMP JPEG TIFF White Background When checked it switches the background color from black to white 15 5 5 Color Tab Controls the color scale bar in the array window Array DSP Baseline Image Color Scale Color Scale 1 y Color Scale Control Mode Bounas y Bounds Center There are four types of color scale bar Color a E Scale 1 Color Scale 2 Blue to Red Gray Scale Color Scale 1 Color Scale 2 Blue to Red Gray Scale Upper Amp Center Lower Control Mode Sets how the color scale bar is adjusted There are two types Bounds Center Amp Bounds Upper Sets the upper boundary of the color scale bar Lower Sets the lower boundary of the color scale bar 16 Center Amp Sets the amplitude range of the color scale bar Center Sets the cen
17. PhotoZ User Manual v 5 25 8 1 2006 Payne Y Chang Table of Contents Table OF Conti ni A ER Eases auoe sa Eses i L Menu Barinitas 2 A detent dedi wel A 2 PON RO 2 Create Folder ese Bese eh tS I eee Ie Sele la 2 Exit ES C insarcsanengcn inna nenen aAA hae a a aa A aE aT S 2 PA ROTC TNC AAA A E aie aE A OT aan 2 Save Prelerence 20 n a a a aah eg eRe ek a e 2 Load Preferits tates cls Sees a dea a ese 2 1 3 Save Lett MIO di ald egal yi edie ered na AS 3 1 4 Save Right WindOW saccades niet diel ei eee 3 2 ALLAN Wii W ssocaniconenirncaran decana arado da nee daa Rare dada siose Sariei AEREA ENANA craneo dana 3 3 Acquisition Analysis Panel a 4 J LACJUISIO tidad riores pis 4 schedule Borussia da di A 4 A A eciacl arse tees foc E S 4 SIOD Eee A APE Pct POP Re AA a AS 4 Take REI cunda cind adds 4 Record A O O O A A ta ites eed 4 OS 4 A eters estat tes dedicat ca eee are eee eae cena auc 5 a Data rriste Mia ca eck a seek e e E dan tat Te a Liae E aen 5 Saye election e a E T ERa AA EOE ET OEE ET 5 Load Selected raded dd 5 4 File Control Pamel sssccsssinssciesssnsencessescasesoessycecesschesbepecaescopenvodsesdcveessoiasaksnpsatoncassaveksssiereh 5 AlFe Nae Se OE og Os SLO ie RISO EIS Be SONI YS ite IO IS Se AP 5 ADE SMI CEN eae NEER E ac SUES ES SINT NES a Sry Ue eae std ae sods eras eee acts 5 AS Locaton NO Ih Site ete ed eS aS ES teat 6 A O ths teed accu ecu eete S 6 4 5 Toal Nossa dd 6 Main Control Panel nr diia AA
18. ecord Acquires one record or starts a scheduled recording Save Saves data to a ZDA file The structure of a ZDA file is in Appendix II When data have changed the label turns red 3 2 Analysis Go through Data Processes and analyzes all records for current Slice No and Location No The settings of signal processing and analysis are the same as current settings This analysis takes about a minute or two to finish Save Selected Saves the selection of diodes to a SEL file the diode numbers of selected diodes are saved Load Selected Diodes are selected according to one SEL file 4 File Control Panel 4 1 File Name ne 03_01_06 zda The name of the data file currently opened 4 2 Slice No The left number is the current slice number The right number is the maximum slice number in the current folder Clicking the left triangle lt reduces the slice number Clicking the right triangle gt increases the slice number NOTICE The user can also key in a number in the current slice No box directly but it does not go into effect until the user press the Enter key This is also true for other input boxes 4 3 Location No The left number is the current location number The right number is the maximum location number in this slice 4 4 Record No The left number is the current record number The right number is the maximum record number in the current location 4 5 Trial No The left number
19. for the Gaussian spatial filter The unit is the diameter of the photodiode 13 5 3 Baseline Tab image Color BLC Type Polynomial v Polynomial Skip Window five types None Start Point Start and End Start Pomt 155 Number of Points 400 Arbitrary Mode Clamp at Pt 155 HLL Baseline Correction Type Sets the type of baseline correction There are Points Polynomial Arbitrary Start Point The start point of the trace is clamped to zero Start and End Points The start and the end points are clamped to zero according to a line connecting the start and end points of the raw data Polynomial The baseline of the signal is corrected according to a third degree polynomial function The polynomial function is created by fitting the raw data excluding a window set in the Skip Window box The settings of the excluding window are described below This allows the user to exclude the evoked response from the baseline fit Polynomial Skip Window Sets the time window which is excluded in the polynomial fitting The Start Point specifies the start point of the temporal window in points The Number of Points indicates the number of points in the skip window Arbitrary Mode Sets the point to be clamped to zero in the arbitrary mode 5 4 Image Tab Array DSP Baseline Image Color X Position 0 MLL LLL LLM Controls the position and size of the CCD Y Position 0 PER
20. hen the lt button is clicked diodes with latencies to a certain percent of maximum amplitude see Main Control Panel gt DSP Tab gt Main Tab shorter than the threshold are selected When the gt button is clicked diodes with latencies to a certain percent of maximum amplitude longer than the threshold are selected SD When the lt button is clicked diodes with a standard deviation less than the threshold are selected When the gt button is clicked diodes with a standard deviation greater than the threshold are selected 12 Filter RLI When the lt button is clicked diodes with resting light intensity less than the threshold are selected When the gt button is clicked diodes with resting light intensity greater than the threshold are selected Ignore When clicked diodes selected by the above criteria are ignored Array D Baseline Image Color Main Correction Filter T Filter l T Filter Filter Type Binomial y Radius Py IF When checked temporal filter is used during signal processing r s riter cf os IE Filter Type The user can choose either binomial filter or moving average filter for the temporal filter Radius Sets the time scale of the temporal filter The width of the temporal filter is 2 Radius 1 S Filter When checked a Gaussian spatial filter is used during signal processing Oo Sets the spatial constant
21. ls LTP The mouse controls the x scale of time course and the y scale of both the time course and optical signals Point Line When checked the vertical point line gray is displayed x coordinate set by center mouse button Trace When checked traces are displayed Slope When checked the derivatives are displayed Time Course When checked time courses are displayed Saved Traces When checked saved traces are displayed gray traces Vm When checked calculated EPSP is displayed green Alpha When checked the alpha function used to simulate the EPSP is displayed gray The function is used to calculate Gsyn see Chapter two of Payne s thesis Display Controls the display in the trace window Time Course Controls the display of the time courses The trace window can display five types of time courses RLI Amplitude Max Amp Amp Latency Max Amp Latency Amplitude is the amplitude at the point line When File Line is checked a green vertical line indicating the position of current record is displayed When Reference is checked a blue horizontal line indicating the value of the reference record is displayed Saved Traces Saves the traces of current trial to an internal memory When Saved Traces is checked the saved traces are displayed white Trial No represents the trial number of saved traces File Name indicates the file name of saved traces Superimpose
22. lynomialFitting Controls the third order polynomial fitting of the base line correction SignalProcessor Controls general signal processing RecControl 38 RecControl Controls the settings and schedule of recording FileController FileController Controls data input and output DAPIO32 H A header file provided by MicroStar Lab which is required for DAP control Definitions h Contains some general definitions required in several classes Text cpp Controls the transfer from a number to a text DAPIO32 LIB This library file is provided by MicroStar Lab which is required for DAP control ExtermalDependencies Other header and library files included by the C compiler
23. plitudes from record 16 to 20 and 36 to 40 are compared and the differences are displayed 5 2 DSP Digital Signal Processing Tab Main Tab Array psp Baseline Image Color Main Correction Fitter RLI Division F RLI Division T Data Inverse When checked the optical signals are F F P Data Inverse divided by RLI Data Inverse When checked the optical signals are inverted F P Data Inverse When checked the analog signals usually field potential are inverted Measure Window The time window in each trace to analyze the data for example to measure the maximum amplitude and the latency 10 Latency Measure Settings Sets how the latency is measured and displayed in the array window Start indicates the start time in msec Width indicates the longest latency to be displayed Shorter latencies are shown in red and longer latencies are shown in dark blue Latencies shorter than Start are shown in white while latencies longer than Start Width are shown in black of Amp sets the percent of maximum amplitude to which the latency is measured Correction Correction Array aseline Image Color Main Filter When checked the data is corrected by an F Correction RLI gt Map Make Correction internal map Raw data the value in the Save Map LoadMap_ map The initial values in the map are ones Selection
24. ptical signals from photodiodes and eight traces representing signals from analog inputs The color scale bar at the lower left corner is for some modes of backgrounds which will be discussed later The scale bar at the lower right corner is for the optical signals To select deselect one trace left click the trace To unselect all traces right click inside the window T A aeaa ne aM aa a ae EA aret a ea aii e Taea aat vaina mia aa aiy Aa T ra a nm ln o a aana ae am mtae nn nee ms a e ma i a me m 8 m Minna amanina aa maae ea shaa paraan tea em aa a ee temas miasma urana niamm rianan alana oral pain EEEE eerste nite aan me De eee eee nen rns nner nl ae ba mt ahem tt et A A bn e AS A tape ctl tit Seven ee ati A is pa la rin nuria oras A a ee aries ene arte rad A a INEM Sas YN eee ere ll a al rl ob a ir 0 28 mV 0 491 sec To ignore include one trace for analysis shift left click the trace To include all traces for analysis shift right click inside the window 3 Acquisition Analysis Panel 3 1 Acquisition Acquisition Analysis Stop Take RLI Save Y Schedule Box When checked the program keeps acquiring and saving data according to the settings in DAP gt Record Schedule RLI Box When selected the program takes RLI Resting Light Intensity at the end of the recording Stop Stops recording Take RLI Measures resting light intensities R
25. re of A ZDA File The codes for the structure of a ZDA file are in FileController cpp Note that the data are saved in binary format which can not be viewed by a regular text editor Version Slice Number Location Number Record Number Number of Trials Interval between Trials Acquisition Gain RLI Gain Number of Points per Trace Current Time Reset Onset Reset Duration Shutter Onset Shutter Duration Stimulation Onset Stimulation Duration 34 Acquisition Onset Interval between Samples Resting Light Intensity Raw Data Raw Data Channel 1 First point second point the last point Channel 2 First point second point the last point Channel 472 First point second point the last point 35 Appendix lll Comments on CPP and H Files Chapter two of Payne s thesis also contains some descriptions and comments ArrayWindow ArrayWindow Handles the events display and diodes in the array window Diode Handles the events and display inside one diode in the array window Image Controls and manipulates the CCD image Trace Window TraceWindow Handles the events and the display in the trace window It also controls the simulation of EPSP ColorWindow ColorWindow Controls the display in the Map Movie window ColorWindowMovie Controls the playback of a movie in the Map Movie window MainController Main Starts the program MainController Handles general interactions between
26. s for the current simulation are saved to a DAT file 6 2 DAP Tab Controls the data acquisition processor DAP and certain recording settings TTL Output Controls Sets the onset and duration of digital outputs It also displays the timing of digital outputs and the acquisition period The duration of acquisition blue not an input box is controlled by the Acquisition Controls box described in the next section 25 Trace DAP MapiMovie TTL Output Control ONSET DURATION m sec Reset o 100 Shutter o 1210 Acquisition 200 1000 stimulator 1 300 1 Stimulator 2 300 1 Channel Descriptions Reset Shutter Stimulator 1 Stimulator 2 Gain Control Acquisition Not in use NLD nm BR Ww ds Not in use Channels used in the DapController object of PhotoZ fillPDOut Acquisition Controls Number of Points specifies the number of points in each trace 26 Interval between Points specifies the interval between two consecutive points in a trace ms The sampling rate is displayed in the bottom of this box Stimulator 1 Controls the digital output for simulator 1 e g single pulse or theta burst stimulation Number of pulses specifies the number of pulses in a burst Interval between pulses specifies the interval between two pulses within a burst Number of Bursts
27. ter of the range for the color scale bar The range of the color scale bar is from Center Amp to Center Amp 6 Right Window Multipurpose 6 1 Trace Tab Trace DAP Map Movie Trace Window Displays traces selected in the array window Control left click and drag controls the scales in x and y axes according to the last trace right click and drag moves traces Value None hd Display Simulation Mode Optical y Time Course in the trace window shift right click resets the scales in x and y axes middle click sets the x coordinate of r Point Line l Trace T Slope l Time Course r Saved Traces r Vm T Alpha Saved Traces F Superimpose T Normalize DI I F Normalize LTP Value 17 the point line gray Selects the quantity to be displayed in the trace window The quantities are described below None No value is displayed RLI Resting light intensity Max Amp Maximum amplitude Max Amp SD Standard deviation of maximum amplitudes It indicates the fluctuation of maximum amplitude for a number of records specified by the number n of average records in Main Control Panel gt Array Tab The reference record and n 1 earlier records are included in the calculation Max Amp Cha The change in maximum amplitude the maximum amplitude of the final record the maximum amplitude of the reference record Main Control Panel
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