NeuroRighter™ User`s Manual
Contents
1. box then filtered according to the characteristics of the LFP filter This has no effect if Processing LFPs is not enabled see Processing Settings above Spike Detection Spike detection is the process of finding candidate action potentials from raw data No method currently available is 100 specific and 100 sensitive there will always be false positives and false negatives in a practical experimental setup In the NeuroRighter software spikes are detected by first calculating an estimate of the noise level for each channel o A threshold is calculated from this number using the entry T in the Threshold box Any time the acquired data crosses this threshold To a spike is detected The threshold is symmetric meaning that samples greater than To and less than To all trigger spike detection An typical value of T is 5 There are four methods for spike detection currently implemented in NeuroRighter Adapative RMS Fixed RMS Median and LimAda Fixed RMS This method computes o as the root mean squared value of the samples within the first 40 ms of data acquisition Adaptive RMS With adaptive RMS o is computed as the root mean squared value of the last 250 ms of acquired data The window is updated every 10 ms Median Here o is computed as the median of the absolute value of the data in the last 250 ms This is an adaptive method The 250 ms is updated every 10 ms LimAda This method is identical to tha2. Settings for each stimulation type are described below NeuroRighter v0 5 20 BETA Grece File Help Global Properties Spikes I Spk Wims I LFPs I EEG I Ref Stim Impedance Diagnostics Num Channels z 64 Global Parameters Blectrode Screening BNC Output Ch Experimental Current vs Voltage Control Offset Voltage V Channels to Stimulate Voltages V Pulse Widths us Noise Training Curent Voltage 0 000 iE 020406 2 4000 Noise levels have not been trained Stat Experiment 2 03 1 0 1 5 3 2 0 5 0 y En On Demand ie NA 5 Pulses Per Train NumRepests Num Pulses 1 Channel 1 6 X 1 102 Recording Properties Raw Sampling Rate H 25000 Voltage V 10 law Sampling Rate Hz LFP Sampling Rate Hz 2000 Rate Hz 100 00 Blectrolesioning ADG LFP Gain Phase width us 400 E Voltage V 1 00 to Stimulate ain 10 jain 1 a Interphase Length us 0 Stimulate Duration s 10 12 3 Display Filters Open loop Q E Spikes Channels to Stimulate z Rate Hz 1 00 1 A Q Low cut 500 2 Hi a Voltage phase 10 mo E 3 seam bghat 90005 4 Start Lesioning F 5 Order 1 Voltage phase 2 V 100 5 Select None a 6 Phase 1 width us 400 7 X F Y LFPs Phase 2width us 400 S Select Al ie Low cut 1 006 Interphase Length us 0 E Selec None mM High cut 500 Pre phase length us 100 Order 1 Post phase Length us 100 Sp
3. These files record information about the stimulation that occurred during an experiment For each stimulation pulse the time channel voltage and pulse width are recorded Controls There are several ways to interact with the acquired data while it s being visualized or before the recording has begun Below are descriptions of these controls Noise Training The SALPA filter Wagenaar D A and S M Potter 2002 Real time multi channel stimulus artifact suppression by local curve fitting J Neurosci Methods 120 113 120 requires an estimate of recording noise before filtering By pressing the Train button before recording NeuroRighter records 3 seconds of data to determine noise levels on all channels Once the training is complete the SALPA checkbox in the filters section becomes selectable Display When a recording begins the visual display of data shows the A D card s full range factoring in the A D gain For instance with an A D gain of 10 each channel will have a vertical range of 1 V assuming a 10 V card like the PCI 6259 By clicking the magnifying glass with a inside the range is halved Each click of the magnifying glass increases the visual gain by another factor of 2 Similarly clicking the uu un magnifying glass with a increases the range by a factor of 2 The magnifying glass with a inside returns the display to the default visual gain There is also a pause button This but
4. Loop Stimulation is delivered in a pseudorandom order from the specified set of electrodes The aggregate stimulation rate determines the time between pulses e g if the rate is 100 Hz and 10 electrodes are selected each electrode will be asynchronously stimulated at 10 Hz Rate The selected set of electrodes is stimulated asynchronously at the specified rate e g if the rate is 100 Hz and 10 electrodes are selected each electrode will be asynchronously stimulated at 10 Hz Voltage The voltage or current of each phase of the biphasic stimulation pulse can be set independently If stimulation is current controlled this voltage determines the current after accounting for the voltage to current conversion resistor Phase Width The phase width is the length of time for each phase of the biphasic stimulus pulse The two phases can be determined independently For example if the phase width is 400 us the total pulse will be 800 us 400 for each of the two phases Interphase Length A brief period where the stimulation voltage is set to O V or O A can be inserted between the two phases of the biphasic stimulation pulse This has been suggested by some authors to reduce tissue damage or provide different excitatory effects e g see Merrill DR Bikson M Jefferys JG 2005 If the offset voltage is non zero the interphase voltage will equal the offset Pre and Post Phase Length A brief period where the stimulation voltage is se
5. Measurement and Automation tool distributed with National Instruments data acquisition hardware If you use a second board for dedicated LFP acquisition for example if you are using a Plexon system as in Figure 1 case above check the appropriate box and choose the connected device If you are using multiple analog input boards for acquisition of raw spike data for example if you are recording from 64 channels or recording from a MultiChannel Systems preamp you should select the Use Second Board option and select the appropriate device If you are using the EEG functionality of the NeuroRighter system select the Use EEG Channels checkbox and select the appropriate device Stimulation An example of this dialog is shown below Settings Input Stimulation Miscellaneous Y Use Stimulator NI DAQ Device for Stimulator Dev4 v Multiplexor Type Port bandwidth 8Channel 16 Channel D 8bt 0 32bit Stimulation Timing Y Record stimulation information NI DAQ Device Dev4 If you are using stimulation select the checkbox and then the appropriate device Multiplexor Type You will also be required to select the multiplexor type of your stimulation modules or stimulation headstage If you are using the in vivo stimulation headstage you are using a 16 channel multiplexor If you are using the stimulator modules for a MultiChannel Systems preamplifier you are using 8 chann
6. S E io e ee eee 8 Hardware Setting S ncsece cssscasectcacdens os atheensedtde aus aa dicas 8 Processing Settings vainas ede teed vk a 12 Acquiting Data ea sinicccecvnsecess scissa aaie ae aa E aae E aaie aa E EEE SaueencSeansducs Sentence 12 Record Bicis 13 Rawls dd 13 Spike Waveform Tiles iii A A A ARE 13 A O ON 13 StimulatiON TIOS scscsesasercacuesacsceyantscevednasedennsdai sauce aetsegeasdedstenadecmgn sdedsedasaedaedestscesteoadedenarand daba rin 13 COS iii Ai 13 NOISE ici caida ca 13 A OR O 13 li A apeluseveogetens ay resem E bane tees 14 Spike Dd ias 14 RRETOREN GI ING ista traida 16 Stimularea E E anos 16 Global ParameterS iio a 17 OW DeMAand e eae cee Rh E eee te ce eal Real e ceo ts Ae ote tl 18 Open LOOP iinet asinine nia add Renin cas 18 Electrode Screening A ee et aver even 19 BIGCUrOl SIOMIAG A O ievbiaee da desnavivssiaieds chins bisseianeds bateireitank 20 WS ZaP DON EELE ii A A tit 20 Closed loop Learning eres A its 20 Impedance Measurements ccccsessssccececessesenneceeececessesesaeseeeeeceseesaaaeeeeeessesseseaaesesececesseseaaeaeeeessessesaaees 21 Channels tn tae 22 Gurrent Vs Voltage Control iia a A ti n 22 Periods Per Fr Uenty ce pete id A A aia 22 RU A AA A ti 22 A E 23 A NN 23 Startiand Stop FrequenciOs iii A AA AA Ad a AAA 23 A O ON 23 DIABNOSEICS ez cocccs EEEE EEE EE EEEE T te ence A 23 Basic RO atures miroase aT A E A IEE R At 24 SPeCial ETAO E A E A N 24 A AA N E IE OE E AE E EEE T E ee
7. file Follow the on screen prompts Stimulation Hardware Settings The stimulator board has three spaces for resistors R_curr R_m andR_g These resistors determine aspects of stimulation and impedance measurements R_curr determines the voltage to current conversion factor for current controlled stimulation R_g and R_m determine the gain of the current monitor for voltage controlled stimulation R_curr must be present for current controlled stimulation R_m must be present for voltage controlled stimulation R_g is only necessary when monitoring I during voltage controlled stimulation See the picture below for the resistors locations Current and voltage controlled stimulation resistors The resistor R_curr bottom changes the voltage to current conversion factor Resistors R_m and R_g top change the gain of the current monitor output BNC 1 R_curr R_curr is used to divide the stimulator input voltage from the stim in BNC or screw terminal into current for current controlled stimulation The equation is Ohm s law V R e g 1V input gt 1 yA when R_curr 100 kQ R_m and Rg R_m and R_g determine the gain of I the current monitor when delivering voltage controlled stimulation The gain of I is determined by the following equation g R_m x 1 49 4 kQ R_g Changing the values of these resistors can change the stability of the I monitor These resistors have no effect on I du
8. 938 To test a single frequency set the start and stop frequencies equal to each other e g to measure impedance at 1 kHz set the start frequency to 1000 Hz and the stop frequency to 1000 Hz Filters It is occasionally necessary to filter the measured signals to improve the measurement quality This is especially true if the signals are present on a large background of noise Two filters are available a matched filter and a bandpass filter Matched Filter The matched filter will convolve the measured signal with the original sine wave This is the optimal matched filter assuming a Gaussian distribution of noise This is our preferred method Bandpass filter This bandpass filter is a 1 pole filter with 3 dB points at the 0 25 f where f is the frequency of interest This tends to over estimate the impedance in our experience Diagnostics The diagnostics section is provided to help verify that the recording equipment is amplifying with an appropriate bandpass filter and gain This works nearly identical to impedance measurements However unlike impedance testing the measured signals will be recorded by the recording headstage or preamplifier All input sine waves should be voltage controlled With a known voltage controlled sine wave of a know frequency the measured signals from the headstage or preamplifier can be used to determine the system s gain at that frequency When computed at multiple frequencies the system s transfer
9. Frequency Hz Num Channels M 64 BNC Output Ch Experimental 1 All Channels Current vs Voltage Control Noise Training a Vio Noise levels have not been trained Test impedance Cancel Train ee z Send to Matlab Results Ohms Periods per freq 5 0 5 Start Frequency Hz 1 0 a R_curent Ohms 10000015 Stop Frequency Hz 10000 0 Fiecording Properties R ling Rate H 5000 R_Gain Ohms 1002 Use Bandpass Fiter Skee AA E LFP Sampling Rate H 2000 R_Meas Ohms 1005 Y Use Matched Fiter pi Save Data as A DG LFP Gi Voltage V 0 10 Matlab MAT File ain 10 y ain Display Fiters 107 a Spikes Low cut 5006 Q High cut 9000 4 a Order 16 Y LFPs Lowcut 106 00 High cut 500 2 Order 1E g 14 Spike Detection 3 Threshold 5 0 a Pre samples 21 Post samples 52 Detection algorithm Adaptive RMS x v Validation Recording Output File Record J Save raw spike traces J y Record Video Global Properties Start Channel Impedance measurements can be taken from a single channel or all channels in sequence by checking the all channels box Current vs Voltage Control Impedance measurements can be conducted by delivering current controlled sine waves and measuring the delivered voltage or by delivering voltage controlled sine waves and measuring the delivered current The amplitude of the sine wave is always specified as a voltage since this is what th
10. NeuroRighter User s Manual John Rolston rolston2 gmail com Created on Feb 4 2009 Last Modified April 8 2009 The NeuroRighter system was created by John Rolston rolston2 gmail com while obtaining his PhD at Emory University and Georgia Tech It is a fully functional system for acquiring multi electrode electrophysiological data and conducting simultaneous microstimulation The system has both hardware and software components This document will guide you through using the software and hardware to run experiments A separate manual is available that covers acquiring the appropriate hardware and assembling the system Visit this web site for the most up to date circuit diagrams software and manuals http www johnrolston com Also review the bibliography section below for a list of papers about the NeuroRighter system or papers that use the NeuroRighter system Contents OVERVIGW sete Getic sicker voted O AA A e 4 In VIVO Sisi 4 WA WIE FOSS OCU sien eo l 4 Preparing the SYStO Mis cx seeded veces deozsheleenade i 5 CONNECHONS its 5 POWER SUP A end qe de dos 5 A NN 5 Software Install cio Deans leetidenenePouniaes 6 Stimulation Hardware Settings ccccessssccececessesensesecececesseseaaeeeeeeseesseeeaeeeeeesseeseseaaeeeeeessessesaeaeeeeeesseesaea 6 A NO 7 R omand R ene CO O 7 SOM leo o ita 7 Starting NEUrORI BNE Mss rd dai RE a aE aE aE aaa erase 7 Contiguring a 8 DIEE FIAS E 6g A O ee OEA AA ET
11. Referencing box and select the appropriate serial port When conducting impedance measurements select the device that is receiving the V and I outputs of the stimulation interface board ai2 and ai3 respectively Processing Settings Processing settings determine how data is handled after acquisition There is currently only one setting Process LFPs If this setting is enabled LFPs are either acquired directly from an A D card or processed from the raw acquired data If data is being recorded LFPs will automatically be save to disk see Recording below If this setting is not enabled LFPs will not be processed graphed or saved in any circumstance This can be useful to minimize computation and disk usage for recordings when LFPs are not desired A sample of the Processing Settings dialog box is shown below all Processing Settings K Ti Process LFPs Acquiring Data Before acquiring data you should set experimental parameters 1 Select the number of channels NeuroRighter currently supports 16 32 and 64 channel recordings 2 Select the raw data s sampling rate and LFP sampling rates Note If not using a separate card for LFP recording the LFP signals are created by filtering and downsampling the raw data The new signals are downsampled to the specified LFP sampling rate This has no effect if Processing LFPs is not enabled see Processing Settings above 3 Select the A D gain for a
12. ards o The breakout boxes should be connected with the PCI 6259 or similar cards o The National Instruments cards should be connected to each other with a RTSI cable If using an in vitro system ensure that the MCS preamp is connected to the recording interface board via an MCS SCSI cable see figure at right This cable powers the preamp and carries recorded signals to the interface boards For an in vitro system one stimulator module should be plugged into each of the preamp s four banks of headers for a total of four modules see image at right Ensure that the 15 pin for MCS MEAs is grounded Power Supply Ensure that the batteries are charged prior to system use When the system is not in use turn the power supply s toggle switch to Off When the system is ready to be used switch the supply to On IMPORTANT It is good practice to have all headstages preamps etc connected before turning the power on Connecting or disconnecting components while powered can have unpredictable results Software Ensure that the NeuroRighter software is installed on your desktop computer the same computer with the National Instruments cards The software can be downloaded at http www johnrolston com Software Installation To install the NeuroRighter software download the compressed archive from http www johnrolston com this is usually a ZIP file Decompress the files to disk Run the setup exe file not the MSI
13. e National Instruments D A emits but the voltage is converted to current through R_curr if the stimulation is current controlled see Stimulation Hardware Settings Periods per Frequency Each sine wave is presented for the specified number of periods to help estimate the average amplitude of the measured wave However to improve results the minimum duration of any test wave is 100 ms R_curr When measuring impedance with current controlled stimulation NeuroRighter requires the value of R_curr Knowing this the software can then calculate the delivered current and use that to compute the measured impedance R mand Rg When measuring impedance with voltage controlled stimulation NeuroRighter requires the values of R_m and R_g Knowing these the software can calculate the gain of the current monitoring circuitry and then use this to calculate the measured impedance Voltage The amplitude of the delivered sine wave is specified here If stimulation is current controlled this voltage determines the current after accounting for the voltage to current conversion resistor Start and Stop Frequencies The impedance spectrum is measured over the specified range of frequencies The actual frequencies measured begin with the start frequency and then every multiple of 1 5 thereafter in a semi logarithmic fashion For example if the start and stop frequencies are 1 and 10 Hz the tested frequencies are 1 1 5 2 25 3 375 5 0625 and 7 5
14. e National Instruments analog output used to generate stimulation pulses and test waves has a finite accuracy 16 bits with a range of 5 V Therefore very small amplitude sine waves e g 1 mV will have poor resolution To account for this we often use an external voltage divider to divide down a 1 V sine wave to something smaller e g 100 uV Entered the division factor will allow the software to automatically account for this Digital Filter This filter is identical to the bandpass filter used in the impedance measurement section Bibliography Papers describing the NeuroRighter System 1 J D Rolston R E Gross S M Potter Submitted A low cost multielectrode system for data acquisition and real time processing with rapid recovery from stimulation artifact 2 J D Rolston R E Gross S M Potter 2008 Low Cost System for Simultaneous Recording and Stimulation with Multi microelectrode Arrays 6th International Meeting on Substrate Integrated Micro Electrode Arrays SIMEA Reutlingen Germany Find the paper in the conference proceedings http www nmi de images publikationen MEA 202008 20Proceedings 20final web pdf Papers using the NeuroRighter System No content yet
15. eee eee 25 Papers describing the NeuroRighter System cccccccononononnnonnnnnononononnnonnnnonannnnnonnnncnnnnnnnnononnnnnnnanannnnnanoss 25 Papers using the NeuroRighter System ccccccccccccessssssseceeececessesseaeeeceescesseseaaeseeeeecesseaaaeeeeeessessessaaeess 25 Overview The NeuroRighter system has several configurations The main two are the in vivo in the figure below and in vitro setups in the figure below Headstage Custom Interface Boards Plexon Preamp NeuroRighter Software Computer with A D Cards PCI 6259s MCS Preamp Custom Interface Boards Figure 1 Overview of NeuroRighter System Shows the standard in vivo setup with a Triangle Biosystems TBSI recording headstage and custom interface boards Shows a hybrid system using a Plexon headstage and preamplifier Shows an in vitro hybrid system using a preamp from MultiChannel Systems All setups converge to a desktop computer with multiple data acquisition cards National Instruments PCI 6259 or PCle 6259 In Vivo Setup For recordings of awake behaving animals a lightweight recording headstage is used connected to custom interface boards The custom interface boards handle analog filtering power conditioning and stimulation control The boards then interface with National Instruments data acquisition cards installed in a standard desktop computer running the NeuroRighter software In Vitro Setup For
16. el multiplexors These assignments might change in the future To be absolutely certain which type of multiplexor you are using look at the multiplexor s part number and find its documentation online Port Bandwidth Depending on the type of National Instruments card you are using you will select either an 8 bit port width or a 32 bit port width If you are using a PCI 6259 or PCle 6259 for stimulation set the bandwidth to 32 bits If you are using a PCI 6221 set the bandwidth to 8 bits Stimulation Timing If you wish to record stimulation timing information synchronized to your experiment you will need to check this box and select the device on which this recording occurs See the NeuroRighter Construction Manual for pin assignments i e where to connect wires Miscellaneous The miscellaneous tab appears as below Settings EN Input Stimulation Miscellaneous Video Use Cineplex video recording NI DAQ Device for Cineplex Dev3 Plexon referencing E Enable Plexon Programmable Referencing Serial Port for Referencing COM1 Impedance Measurements NI DAQ Device for Impedance Measurements Dev3 If you wish to use the NeuroRighter software to control a Cineplex camera system check the appropriate box and select the correct device If you are using a Plexon preamplifier and wish to control its programmable referencing through your serial port check the Enable Plexon Programmable
17. ere are two options In vivo and In vitro MCS In vivo The in vivo setting maps channels 1 N where N is the number of channels in linear order That is channel 1 the first analog channel recorded from the first National Instruments card will be displayed in the first channel window of the software In vitro MCS The in vitro setting maps channels as they would appear when looking down upon an MCS substrate integrated multi electrode array Hardware Settings Clicking on Hardware Settings opens a dialog box like the one shown below input Stimulation Miscellaneous Analog Input 1 NI DAQ Device for Analog Input Devi LFP Input E Use Separate NI DAQ for LFPs NI DAQ Device for LFP Input Dev1 Analog Input 2 Y Use Second Board NI DAQ Device for Analog Input Dev2 LFP Input Use Separate NI DAQ for LFPs NI DAQ Device for LFP Input Dev1 EEG E Use EEG Channels e separate analog in channels NI DAQ Device for EEG Dev1 Accept Canca There are three tabs representing three types of settings Input Stimulation and Miscellaneous Input Here you select the National Instruments card NI DAQ that will record the first 16 32 channels of analog data e g Dev1 Dev3 etc All installed devices will automatically be listed as options For more information on device numbering see your National Instruments device s literature or examine the
18. function can be estimated NeuroRighter v0 5 2 0 BETA ae a Leto e File Help Global Properties Spikes Spk Wims LFPs EEG Ref Stim Impedance Diagnostics Num Channels X 64 BNC Output Ch Experimental Noise Training Start Frequency Hz 1 0 Noise levels have not been trained Stop Frequency Hz 10000 0 a aia Step between Frequencies multiple 1 5 Recording Properties Input Voltage V 0 010 Raw Sampling Rate Hz Periods per freq 5 0 LFP Sampling Rate Hz All channels at once requires special hardware A DGain 10 LFP Gain Gain dB Extemal Voltage Divider Display Filters Divide by Digital Filter Spikes Low cut High cut Order Y LFPs 1 Low cut Frequency Hz Y High cut Order Spike Detection Threshold Pre samples Post samples Detection algorithm Adaptive RMS X v Validation Recording Output File Record E Save raw spike traces J y Record Video Basic Features These features are identical to those used for impedance measurements Please refer to that section for more information Special Features All channels at once Selecting this requires a way to deliver stimulation to all channels simultaneously This capability is not present with the normal stimulator headstages In our case we use a Plexon Headstage Test Unit which provides a common signal to all electrodes External voltage divider Th
19. he Results box to the clipboard Clicking Save Data as Matlab MAT File saves the data in MAT format useful for later analysis in Matlab u Before taking impedance measurements ensure that the V and I terminals of the stimulator interface board either BNC or screw terminals are connected to the Impedance Device s ai2 and ai3 inputs respectively see the NeuroRighter Construction Manual for more details The Impedance Device is specified File gt Hardware Settings under the Miscellaneous tab Important Impedance measurements are difficult for a number of reasons First impedance values range over several orders of magnitude Therefore some measurements will be very small and likely buried in noise Other measurements will be very large and clip at the power supply rails It is therefore strongly recommended that the actual data be monitored first with an oscilloscope before relying on the computed values An oscilloscope can be used by hooking up the appropriate BNC outputs and executing an impedance measurement As an example take a current controlled measurement of impedance What s measured is the actual delivered voltage If the impedance is very high e g at low frequencies in standard electrodes the voltage required to deliver that current will be very high This can lead to clipping e g if the required voltage is 8 V but the power supply is limited to 6V If the impedance is ve
20. he first phase and the second phase is the negative of the first phase e g if the first phase is 1V the second will be 1V Num Pulses This specifies the number of pulses or pulse trains that will be delivered Voltage This specifies the voltage of the first phase of the biphasic stimulation pulse The second phase is the negative of this voltage e g if the first phase is 1V the second will be 1V If stimulation is current controlled this voltage determines the current after accounting for the voltage to current conversion resistor Rate This determines the stimulation rate at which multiple pulses are given This has no effect if the number of pulses is equal to one Phase Width The phase width is the length of time for each phase of the biphasic stimulus pulse For example if the phase width is 400 us the total pulse will be 800 us 400 for each of the two phases Interphase Length A brief period where the stimulation voltage is set to O V or O A can be inserted between the two phases of the biphasic stimulation pulse This has been suggested by some authors to reduce tissue damage or provide different excitatory effects e g see Merrill DR Bikson M Jefferys JG 2005 If the offset voltage is non zero the interphase voltage will equal the offset Channel The electrode on which the stimulation is delivered is specified in the Channel box For curious computer scientists this is 1 based not 0 based Open
21. ike Detection luso Stop Threshold 50 1 Pre samples 2 Zz Post samples 52 3 0 Detection algorithm E Adaptive RMS y s IIS Zapper Experimental Closeddoop Leaming Experimental 7 V Validation 1 a a a Pulses train 1 21 Channel 1 Probe Electrodes PTS Electrodes 400 600 800 1 a a Recording Time microseconds Voltage V 10 E Output File Record Rate Hz 100 00 J o Phase width us 400 E a E Save raw spike traces J A mn E Record Video Start Stop Start Stop Global Parameters These parameters affect all stimulation types Current vs Voltage Control This setting determines whether stimulation is voltage or current controlled The current for current controlled stimulation is specified as a voltage and delivered as a voltage by a National Instruments D A output This voltage is then converted to current on the stimulation power interface board through the resistor R_curr see Stimulation Hardware Settings above So to deliver a 10 uA pulse for example you would deliver a 1 V pulse with R_curr 100 kQ Offset Voltage The offset voltage is added to the entire stimulation waveform This can be used to account for offsets induced by the electrode s electrochemical shift or to provide a constant bias current On Demand On demand stimulation provides a la carte stimulation pulses or pulse trains All pulses are biphasic with phase widths of equal length The specified voltage is for t
22. nalog input This is a multiplier that determines the range and resolution of your analog data acquisition The PCI 6259 for instance has a maximum range of 10 V and a resolution of 16 bits If the A D gain is 1 the full voltage range is used and the 16 bits are allocated to this full range If the A D gain is 2 the voltage range is reduced by half to 5 V but the 16 bit resolution is now allocated to this smaller voltage range increasing the acquisition s precision Important You want to choose a range that will prevent clipping If the input exceeds the voltage range the data clips and the signals are lost for the duration of the clipping You want to find a good balance between minimizing clipping and having as high a resolution as possible Fortunately 16 bit resolution provides very high voltage resolution even at low gains So an A D gain of 2 or even 1 will easily resolve action potentials 4 Ifyou plan to record the acquired data to disk configure recording options now select an output file and set the toggle switch to record this will illuminate the recording LED You can optionally elect to record video data with an attached Cineplex system and write all of the raw data to disk by checking the save raw spike traces box Writing data to file is covered in more detail below When your parameters are configured press the Start button to begin acquiring data The power supply should have been turned on at
23. nels to lesion is specified here 1 N channels can be selected where N is the total number of electrodes IIS Zapper This is an experimental closed loop application Please review the code thoroughly before using and ask the author John Rolston rolston2 gmail com for help This application has not been thoroughly tested though it has worked for the code s author on several occasions Important data acquisition should be started prior to the closed loop experiment Closed loop Learning This is an experimental closed loop application based on the paper by Bakkum DJ Chao Z and Potter SM 2008 Please review the code thoroughly before using and ask the author John Rolston rolston2 gmail com for help This application has not been thoroughly tested Important data acquisition should be started prior to the closed loop experiment Impedance Measurements NeuroRighter is capable of measuring impedance spectra in real time using the stimulator and its current or voltage monitoring outputs The essential idea is that if a voltage controlled sine wave us used to stimulate an electrode the monitored current can be used to calculated electrode impedance at the sine wave s frequency This is also true when using current controlled sine waves and monitoring the delivered voltage The results are presented in a table under Results and depicted graphically in a plot Clicking Copy Data to Clipboard copies the contents of t
24. ovement artifacts or related correlated noise This has no effect on the LFP channels nor data saved with the Save raw spike traces command It will affect the data sent to the spike detection algorithms Selecting LFP Referencing On accomplishes identical referencing for the LFP channels Analog Referencing If a Plexon preamp is being used analog referencing can be controlled similarly to digital referencing Stimulation Before stimulating ensure the stimulation modules are properly connected see NeuroRighter Construction Manual and Stimulation Hardware Settings above Stimulation commands are available in the Stim tab in the NeuroRighter application Before stimulating set the Global Parameters Then choose a type of stimulation set parameters for that type and start stimulation Available stimulation modalities are e OnDemand single pulses or brief trains e Open Loop continuous stimulation delivered in pseudo random fashion e Electrode Screening cycles randomly through a selection of stimulation parameters e Electrolesioning sends DC current for a given length of time useful for electrocoagulation e IIS Zapper an experimental closed loop application that stimulates when an interictal spike is detected on an LFP channel e Closed loop Learning an experimental closed loop application mimicking the experiment of Bakkum Chao and Potter 2008 A screenshot of the interface follows
25. recordings from neural or cardiac cultures a MultiChannel Systems MCS preamplifier http www multichannelsystems com is connected to custom interface boards These boards provide power conditioning stimulation control and convert the MCS cables to cables suitable for use with National Instruments data acquisition cards The custom boards interface with a standard desktop computer running the NeuroRighter software Preparing the System Connections Before initiating a recording ensure that all cables are properly connected see the NeuroRighter Construction Manual for details MCS 68 pin SCSI Cable Connects MCS preamp to recording interface board SS e This includes e Power cable from power supply to interface boards e Recording cables o Cable from recording headstage to interface board o Data cable from interface board to data acquisition card e Stimulation cables o Stimulation input cable from National Instruments card to interface board MCS Preamp with Stimulator Modules The bottom module has been removed for clarity The SCSI connector cable is Instruments card to stimulator headstage not plugged in o Stimulation output cable from interface board to stimulator headstage o Stimulator power cable from interface board to stimulator headstage o Current vs voltage control cable from National Instruments card to interface board o Stimulation switching control cable from National e National Instruments c
26. ring current controlled stimulation Software Usage Starting NeuroRighter NeuroRighter installs shortcuts in the user s Start Menu in the NeuroRighter folder as well as on the desktop To start the program double click on the desktop icon shown in figure at right ASA aa S NeuroRighter You will be presented with a screen similar to Figure 2 below Icon NeuroRighter v0 5 1 BETA Dale File Help Global Properties Num Channels M 64 Spikes Spk Wims LFPs EEG Ref Stim impedance Diagnostics BNC Output Ch Experimental Noise Training Noise levels have not been trained Train Recording Properties Raw Sampling Rate Hz 25000 LFP Sampling Rate Hz 2000 A DGain 10 v LFP Gain Display Fiters Spikes Low cut High cut Order Y LFPs Low cut High cut Order Spike Detection Threshold 5 0 Pre samples 2 Post samples 52 Detection algorithm Adaptive RMS v v Validation Recording Output File Record ss Save raw spike traces J J Record Video Figure 2 Configuring Settings There are three groups of settings available by selecting the File Menu in the NeuroRighter software Display Settings Hardware Settings and Processing Settings Display Settings Clicking on Display Settings opens a dialog box like that shown below a DisplaySettings In vivo O In vitro MCS Th
27. ry low the voltage required will be very low If the noise is for example 10 mV peak to peak at the delivered voltage is 10 mV this will be obscured by the noise However filtering might be able to recover the desired voltage Second impedance is affected by stray capacitance There are many places where the stimulation signal is carried near other wires and conducting objects after it has left the stimulation interface board Along this path a voltage or current controlled pulse will wind up charging these other objects and wires stray capacitance Since the stimulation current and voltage are measured on the interface board these stray capacitances will be included in the measured impedance Therefore what is truly being measured is the impedance of the electrode and the cables leading to it With short cables this effect is negligible especially when higher amplitude test currents or voltages are used However the effect can be large when using long cables and low amplitude test waves It is therefore recommended that you test a known impedance to estimate your error A good source of a known impedance is the MultiChannel Systems test MEA which has a known resistance and capacitance in parallel However any custom built resistor and capacitor in parallel will do NeuroRighter v0 5 2 0 BETA Dee aes File Help Channel Parameters Spikes Spk Wims LFPs EEG Ref Stim Impedance Diagnostics 1 1
28. t to OV or OA is usually present at the beginning and end of each pulse In our experience this helps control stimulation artifacts If the offset voltage is non zero the pre and post phase voltage will equal the offset Channels The set of channels to stimulate is determined before beginning the open loop stimulation experiment The number of selected channels can be 1 to N where N is the number of available channels Electrode Screening The electrode screening experiment cycles through a selected set of stimulation parameters on a set of electrodes in a random ordering Each selected electrode will be stimulated with all possible permutations of stimulation parameters Each permutation will be delivered the specified number of times the Num repeats box again in a random order The randomization of ordering minimizes habituation effects between stimulation pulses The rate of stimulation is 1 Hz i e one permutation on one electrode every second Channels The set of channels to stimulate is specified here 1 N channels can be selected where N is the total number of electrodes Voltages The specified voltage determines the amplitude of the biphasic stimulation pulse The given number is the amplitude of the first phase and the second phase is the negative of this voltage e g if the first phase is 1V the second will be 1V If stimulation is current controlled this voltage determines the current after accounting for the
29. t used by Daniel Wagenaar s MEABench software http www its caltech edu daw meabench See his documentation for details This method has not been thoroughly tested as have the previous three Referencing Digital and analog referencing of channels can be set through the Ref tab as shown below NeuroRighter vO5 2 BETA y MEME E M 7 Gu quae au aus ele File Help Global Properties Spikes Spk Wims LFPs EES Ref Stim impedance Diagnostics Num Channels z 16 Digital Referencing BNC Output Ch Experimental Spike Referencing On LFP Referencing On Noise Training Spike Reference Channel 1 LFP Reference Channel 12 Noise levels have not been trained Analog Referencing Plexon Only Spike Referencing On LFP Referencing On Recording Properties Spike Reference Channel 1 LFP Reference Channel 1 Raw Sampling Rate Hz 25000 Reset Al LFP Sampling Rate Hz 2000 A D Gain 10 v LFP Gain Display Filters Q Spikes Low cut 5005 Q High cut 90001 a Order 16 Y LFPs Low cut 1 00 1 High cut 5006 Order 18 Spike Detection Threshold 50 Pre samples 2 Post samples 52 Detection algorithm Adaptive RMS Z Y Validation Recording Output File Record E E Save raw spike traces J e sm Digital Referencing Selecting Spike Referencing On will digitally subtract the selected channel from all other channels This can be useful when dealing with m
30. this point or else only noise will be recorded The software however can run whether or not the hardware is powered Recording NeuroRighter saves 4 types of files raw spike waveform LFP and stimulation Not all files are written for all recordings The types are determined by the user Files are only saved if the recording toggle switch is up When recordings are occurring the recording LED will flash between green and red Raw files Raw files are not saved by default To save raw files ensure that the Save raw spike traces box is checked bottom right of software window Raw files include every sample of data recorded The saved data is not filtered regardless of what filters you have set for visualization or spike detection Spike Waveform files Spike waveform files include information on all spikes detected The time of the spike the channel it occurred on and a number of samples before and after the spike threshold crossing are stored The number of samples is determined by the Pre samples and Post samples controls The default is 22 samples before and 52 after the threshold giving 75 samples per waveform 22 pre 1 triggering sample 52 post LFP files LFP files are currently saved by default These files contain the filtered and downsampled data that is visualized in the LFP graph LFPs are not saved if Processing LFPs is not enabled see Processing Settings above Stimulation files
31. ton freezes the display Filters There are currently three filters that can be used while acquiring data SALPA spikes and LFPs SALPA The SALPA filter Wagenaar D A and S M Potter 2002 Real time multi channel stimulus artifact suppression by local curve fitting J Neurosci Methods 120 113 120 removes stimulation artifacts from the raw data allowing better visualization of action potentials To select this filter noise levels must have been trained prior to beginning the recording i e before pressing Start Spikes The spikes filter is a Butterworth bandpass filter with 3 dB points specified in the Low cut and High cut boxes The number of poles is also selectable This filtering takes place after the SALPA filter if applied LFPs LFP signals can be acquired in one of two ways 1 derived from the raw analog input channels then filtered and downsampled or 2 directly acquired from a dedicated analog input A D card as in scenario of figure 1 above In the first case the LFP filter Butterworth bandpass with cut offs specified in the Low cut and High cut boxes is applied to the raw acquired data then downsampled to a frequency specified in the LFP Sampling Rate Hz box It is strongly recommended that a filter always be used when downsampling LFPs in this manner In the second case the data is acquired at the frequency specified in the LFP Sampling Rate Hz
32. voltage to current conversion resistor Multiple values should be separated by commas spaces tabs newlines or colons Pulses per Train Pulse trains can be delivered in addition to single pulses If a value of 1 is provided here single pulses are delivered If larger numbers are specified then a rapid train of pulses is delivered at a rate of 200 Hz 5 ms between pulses Multiple values should be separated by commas spaces tabs newlines or colons Pulse Widths The phase width is the length of time for each phase of the biphasic stimulus pulse For example if the phase width is 400 us the total pulse will be 800 us 400 for each of the two phases Multiple values should be separated by commas spaces tabs newlines or colons Num Repeats The number of times each permutation is presented is specified here Electrolesioning To localize electrode tips for histology it is often suggested to deliver direct current DC stimulation prior to animal perfusion This component of NeuroRighter allows this to be done easily Voltage The voltage of the electrode for the duration of the stimulation is specified here If stimulation is current controlled this voltage determines the current after accounting for the voltage to current conversion resistor Duration The duration for which the voltage is provided for each electrode is specified here Typical values are in the 1 30 second range Channels to Stimulate The set of chan
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