Home

OmniPlex User Guide.book

1. Clicking on the Average CPU column header will sort applications in order of decreasing CPU usage which allows you to quickly focus on any applications that might be using excessive CPU W 1 CPU Usage Appendix Page 46 C WmiPrvSE exe C FULLSHOT exe E perfmon exe E svchost exe LacalSyste Description 328 WI Provider Host 7032 FullShot 9 5 3252 Resource and Perfor 446 Host Process for Win Status Running Running Running Running Threads g 19 23 OmniPlex Neural Data Acquisition System Appendix J PlexControl Keyboard Shortcuts The following keyboard shortcuts can be typed as either upper or lower case characters T Toggles display of the currently selected view s toolbar N Go to the next channel P Go to the previous channel O Display the currently selected view s Options dialog S Toggles display of snapshot versus live data space Redraw view Version 1 8 Appendix Page 47 Appendix Appendix K Hardware Pinouts and Connections Digital input card The DI card has two input ports A and B where A 1s the lower port See the sec tion Digital Input Card Configuration on page 7 191 for information on how to configure each port to operate in either mode 16 individual data bits or mode 3 16 bit strobed word input and for high true or low true logic The two ports are identical except that the RSTART level triggered recording input is only
2. r n On Draen Eni Sorting R a os ee Pee i we Pe pee ia EFN F Tej aF Beia Chapa Tepe Spike Chanrele H ChaindGoming Sage Evast bed Fecri Erailsj same bry Frag FFF Gan 1 Wirata Leregih F Pre Threshold mI Sort Start 4 Sow Ered 3y LEDE Chanral i iirria Appendix Page 22 OmniPlex Neural Data Acquisition System Version 1 8 Docking a window As you are dragging a window you will see sets of blue arrows appear at the four sides of the main PlexControl window indicated by red circles below and a four way arrow in the center of the nearest window indicated by a red square below HA Pioi Pelerrcil E Be Wee Caly Coige Daa Window Bun Hale Li or el oF OR ee eee ae le eee ee ec TSE m Tank 10x SOK Chanrai 1 Waveho J leer ne 7 3 i on Pr P PC m J po _ en 5 J 7 ES Pee an iit ole a le caa i aia i Fn Hes yy Create View Layout for Sour 7 A Aronia Lonligune All Source Wy Start Recording Cute ae Pigs oth Pris H mS R e an i _ ee ee WL Stop Data Acquiiticn Ee a po an T E ea a a lt aS ge ee ee a ee Tes A Pee aE ia oe min ran sites a E ama y W aii T Erech res al ait e eee asea T i aren P ici ET ahpa net prerrerrverrevrrrny eter enter rd AEAT NAA ated toatl ta 4 j AAAA EAS Aah hbi sae ma A Comin BR Pes Hogan Sen Mi Continues ME
3. Appendix Page 38 OmniPlex Neural Data Acquisition System To enable Enhanced PCA select Global Options in the Configure menu F PlexControl PlexControll Data Window Run File View Display Configure Help O co ce bed amp Auto Contfigure All Sources Select the Feature Space tab and enable Use Enhanced PCA Version 1 8 Appendix Page 39 Appendix Global Options General Feature Space Snapshots Control Restrictions Recording Files Recording C Dimension Feature PC Y Dimension Feature PC Dimension Feature PC3 For Trodal Display s Axis Show Max Show Min Y Pods Show Max Show Min Note that enabling Enhanced PCA will not affect any existing PCA or sorting parameters The next time you take a spike snapshot or click the PCA button in the toolbar the PCA calculation will use the new setting ial Channel 1 Clusters _ oy Perform PCAo on ailin C urrent Snapshot Channel 1 TIP 2D Polygon sorting method If you are using the 2D Polygon sorting method you will need to delete the existing units and create new ones Appendix Page 40 OmniPlex Neural Data Acquisition System TIP Increase magnification in PCA view Enhanced PCA sometimes results in clusters with a different overall scaling so that you may need to increase the magnification in the PCA view Version 1 8 Ap
4. CO DO2 DO3 DO4 DO5 DO6 DO7 DO8 DOY DO10 DO11 DO12 DO13 DO14 DO15 DO16 NC NC CO DGround NC DGround NC DGround NC DGround NC DMI PO NO NO oOo RO i NO o1 NO ep Appendix Page 52 OmniPlex Neural Data Acquisition System Connector labeled DIGITAL OUT 17 32 Version 1 8 Pin 1 p gt Sl cal sl oe o N o gt cn a oo PO NO IS NO ep Pin Function 1 DO17 DO18 DO19 DO20 D021 D022 D023 D024 D025 DO26 DO27 DO28 DO29 DO30 DO31 DO32 NC NC M N DGround CO NC DGround NC DGround NO l NC DGround 3 o1 NC Appendix Page 53 Appendix Other AuxAl outputs The four BNC connectors labeled AO 1 AO 2 Line and Line 2 are not cur rently used by OmniPlex and are reserved for future use Appendix Page 54 OmniPlex Neural Data Acquisition System PLEXON the five line symbol CinePlex DigiAmp MiniDigi Offline Sorter OmniPlex PlexBright PlexStim and Radiant are registered and unregistered trademarks of Plexon Inc Dallas Texas USA Other product and company names mentioned are trade marks or registered trademarks of their respective owners Version 1 8 OmniPlex User Guide Neural Data Acquisition System OmniPlex User Guide Plexon Inc 6500 Greenville Avenue Suite 700 Dallas Texas 75206 United States o
5. SPK Clusters x fei 7 Bt Be a Pca cA OFT PB Sa SPK Waveforms H SPK Clusters 3D 3D Clusters Properties SpreadSheet SPEC Continuous SPK Clusters Note how all the channels show No PCA This is because the initial calculation of the PCA projection requires a spike snapshot similar to the way in which auto thresholding requires a SPKC snapshot To take a spike snapshot click the Forward Snapshot button in the toolbar SPK Clusters ES 7 BBE Pee gt pra A Ont BS i Start Forward Snapshot Collection All Channels While spikes are being collected into the spike snapshot the status bar displays Collecting Spike Snapshot ontinuous MM SPK Activity Firing Rates OmniPlex Neural Data Acquisition System 6 You can monitor the progress of spike snapshot collection in more detail by hovering the cursor over the Spike Snapshot tab at the lower left of the PlexControl window Bnameids or SPK Channel 64 Units 7 After hovering the cursor over the tab for a moment the Spike Snapshot view will pop up E Fle Wew Dgy Comge Date Window Run Help eee at of 2 eMUUE Oss BOE ns ove see eS ga QOX SK Chammell Welma i SPK Wasetooms 3 i Version 1 8 137 6 Additional Sorting Methods 8 The blue bars indicate the progress of snapshot collection when each channel s bar reaches the right side the bar turns green to
6. 154 OmniPlex Neural Data Acquisition System Version 1 8 SPK Channel 1 Waveforms e A TEA Bt fal Gb lt 7 Mag 1 70 aan St k TIP Toggling between live and snapshot modes You can also press the S key on the keyboard to toggle between snapshot and live modes Clicking Show Snapshot results in all the other displays being toggled as well you cannot view live spikes in one view while viewing the snapshot in another Basically you are either in a mode of working on live spikes or working on the spike snapshot Note that the continuous displays are totally separate and unaffected by whether live or snapshot spikes are being displayed in the spike and PCA views It is important to remember that switching between live and snapshot modes is purely a PlexControl user interface behavior to allow you to interact with the snapshot data at your leisure All the processing in Server continues uninterrupted 155 6 Additional Sorting Methods 156 in the background filtering spike detection and sorting and so on all continue as before using the current thresholds templates etc When you switch to displaying the spike snapshot all the spike and PCA displays stop animating because they are now displaying a fixed set of 500 spikes by default the same spikes that were collected when you previously clicked on Col lect Forward Snapshot These were also the spikes that were used to calculate th
7. o Crmabe Views Liye for Source CEEE mj 5 datometcally Configue Al Scour h Shut kessi rg Cute ii ai ah ia a a i i n aT Pee Pe Pee me 7 ee Shop Date Aguen Frapante WE nere Fab In Dewi hannal Typa ek Pagina Gro Jupri Enabled Alecord Enabled Sani plieg Freq File Tes Dtply Configure Oot Windoe Aue Hep ie amp oR AE a ES APENE g oe me a h hew Alva Task Ow 2 SPR Charmell Wyeelums zix wn Aprin a fs Create Whew Lappi Tor Mae Tiwa at Er i bikomeieciiy Contigure 2 Sources LU Han Aeconding Data a Sop Gate 2c quition Piparin F Dx SPE Gonen n Carica Enk Sorting Chana Tape Speke Chartres H Chami Gauging E rust bed Recon Eresipbed i A e a i n aaa T wl ath tamping Frag 05 me cS ye ve va iii w is Gan mm Weah Length At Pre Threshold Mm i T oe hr K hha ae aes 6 Pls r nT i nr z ppa z oO tae h a Sort Start J Tort Ered y CT eee Se Chapel i birria On the other hand if you drag a window and release while the cursor is in the center of the four way arrow set then the dragged window will be added as a tab within the window This is particularly useful in that you can drag an individual tab from one window into another For example we could drag the Activity win dow tab from the bottom right window containing the continuous views into the window which contains the multichannel spike and PCA views
8. Appendix Page 25 Appendix E SPK Activity ix A EH Rt ort a OO Tt Ie Ph J m E m m Je A Ag m rate aF ow a i a TE SPK Waveforms PE Clusters 3D 3D Clusters Properties SpreadShee WEB Continuous SPK Activit HX 155 15 00 15 00 mw 1 5 0 i mi i F D E ESA i WE Continuous fatal Continuous Peak Histogram Snapshot ed Continuous id Continuous fA SPK Firing Rates Appendix Page 26 OmniPlex Neural Data Acquisition System Sometimes it requires a bit of thought and experimentation but virtually any win dow layout can be achieved by a sequence of these operations he I iha ime Cp Liyan lir Meie a en eee ALEL AES T E eee E EN apila Loe ee ey ADe iaki han Ipa 1 eee E E i i e eee ta a ree fi i Lomas Lab a am El SS scarce Corp a eae ae marw zim E TL OTTA l Sep t kria l L I T ERIE hy ia Led yy i Li i Pepe hae 1 T P aere Tya diwa CR Se ind rd ht LR aai ii Bese od Peak 4 ani B BE EI Seer leg a T i ast j l l Bist tt fed Piel ie ii Wea l ee ee Pre Tanna i Tan See J ae in ee bi T o m wian i Mamre Tee A r d iri a baa od Bese od Feu lt 4 Traki iim Bii Tinn ae buaii Coe a ial 7 fie te See i Se T 2 OP el l hh vee Ciy Lyan Li Fes im ne H a i WE iha omi im an TETT Le AES T AEAF z i Lade Boe iFilm D in 5 To Eee oe T T
9. Master RangeinY 0 388 to 1 000 Slave Adjust Automatically Use same for all Channels F Shift Right Click changes X and Y ranges independently Every few seconds the PCA display will adjust the magnification and pan as needed to keep the PCA clusters fully onscreen You can only adjust the magnification and panning of the PCA display while you are zoomed in but if you have the Use same for all channels option enabled your changes will be applied to all the PCA displays This usually works well but if the PCA clusters on different channels are substantially dif ferent in size and position you may need to uncheck Use same for all chan nels and adjust each channel s PCA display individually 148 OmniPlex Neural Data Acquisition System 6 4 Step by Step Defining Units for Template Sorting using PCA Con tour Drawing You are now ready to define units for template sorting by drawing contours out lines around 2D PCA clusters instead of by waveform crossing as you did previ ously Keep in mind that you can define any unit on any channel by either method you could define unit a by waveform crossing then unit b by con tour drawing Once you have defined the unit the method used to create the unit definition is no longer relevant 1 Make sure the PCA display is zoomed in on a single channel and that clusters are clearly displayed as described in the previous section Display the toolbar for the P
10. 95 4 Basic Spike Sorting 4 1 Overview 96 Now that you have learned how to configure OmniPlex to correctly detect spike wavetorms the next step 1s spike sorting Spike sorting is the process of deter mining for each detected spike waveform on each channel which neuron near the corresponding electrode tip fired For example the electrode for channel 5 might be picking up action potentials from three nearby neurons call them SPKO5a SPKOSb and SPKOSc Informally we would say there are three units on channel 5 Spike sorting is in effect a classification problem where incoming unsorted spike waveforms are sorted into classes a b c etc each class corre sponding to one neuron Most spike sorting algorithms are based on the assump tion that each neuron produces action potentials whose shape is sufficiently distinct from the shape of other neurons spikes to allow reliable classification The two elements of spike sorting It should be emphasized that there are two distinct procedures involved in spike sorting The actual sorting of incoming spikes is done in Server and once config ured is a process that generally requires little or no user intervention But first PlexControl must determine the spike sorting parameters that Server will use for example how many distinct units are there on each channel and what are the sorting parameters for each of those units OmniPlex supports several methods for both defining the sorti
11. Data Acquisition 10 x DataPool kb s PDOPs s Pool Index es 8 Config 0 000 0 0 SAMs oo eee a a Main 0 0 0 0 14 Restart Server as described in Step 1 wait for the pxs file to load and for the green progress bar to finish then continue to Step 15 15 Server now has auto loaded a pxs topology configuration file either one that was used in a previous OmniPlex session or one that you just created in Step 3 through Step 14 above using the Topology Wizard In either case from now on when you start Server from the desktop by default it will automatically load the last used pxs file TIP 9 When to use Topology Wizard aN You only have to use the Topology Wizard to create a new pxs file when the hardware configuration of your system changes for exam ple adding more boards to a DigiAmp or adding a new card to the chassis TIP Press Ctrl key to prevent auto loading of pxs file If you ever need to prevent the auto loading of the last used pxs file for example for troubleshooting you can hold down the Ctrl key before double clicking on the Server desktop shortcut 1n this case you will be starting from scratch and will need to either load some other pxs file or use the Topology Wizard to create a new one as described in Step 3 through Step 14 Version 1 8 25 1 OmniPlex System Overview and Startup 1 7 Step by Step Starting PlexControl This section assumes that you have already started Server as described in the
12. Mode 3 strobed word Logic Levels Logic Levels Data Data High true High true Strobes Strobes High true Low true High true RSTART High tue C 7 3 1 Digital input modes Mode 1 configures the port to recognize each event input pin as an independent digital input channel Up to 16 separate individually timestamped event channels can be sent into a port that is configured for mode 1 When the voltage on the event channel s input pin goes high or goes low depending on the high true low true setting a timestamped digital event on that channel will be generated For port A in mode 1 these will be channels EVTOEVT16 for port B in mode 1 these will be channels EVT17 EVT32 In PlexControl single bit events are shown as a single contiguous range from channels 32 192 OmniPlex Neural Data Acquisition System The single bit event channels contain no additional information beyond their timestamp and channel number Mode 3 configures the port to monitor a strobe bit on a designated pin When the strobe bit goes high or goes low depending on the high true low true setting then a 16 bit word value is read from the same 16 inputs that are read as separate channels when in mode 1 Strobed digital events are channel 1 shown as Strobed in PlexControl in the Other events source on the DI device and for historical reasons are represented as digital event channel 257 in the recorded file i Prop
13. sss AERLELELELELLELELLLELELELLLE Eui s s 2s ss s EEREELELELELELELELELLLELLLE Li POPP CeCe E NYT sana nnennnene F F Set All Selected Channels Like Topmost Selected Channel Set All Higher Numbered Channels Like Selected Channel Select All Set Values for All Channels og Jz UP TTR O Cl ee eee eee 2 rl E OOETET cc cceseceseseseseseseseseses ess A PPPOE Druan errr rere rere rere Perr a re a eee 81 3 Spike Detection 82 3 4 2 3 4 3 TIP set All command can also be used for other columns The same technique of selecting the column header and then using the Set All commands can be used for the other columns for exam ple enabling or disabling checkboxes within the Rec columns of recording options Changing the value of the threshold in the per channel properties view The properties view at the left side of the screen which displays the properties for the currently selected source and channel can also be used to inspect and adjust the threshold value Click within the cell to display a set of up down arrows just as in the multichannel Properties Spreadsheet WB Source 4 On Device Global Filters Channel Type Analog Channels a4 Channel Grouping Single Enabled Record Enabled Sampling Freq 40000 Gain 250 Waveform Length a00 Pre Threshold 200 Sort Start 0 Sort End 800 sort Method Template
14. 31 AIGND or SENSEI 32 AIGND or SENSEI 33 AIGND or SENSEI 34 AIGND or SENSEI 35 NC 36 DGND 37 AIGND or SENSE 20 AIGND or SENSE 21 AIGND or SENSE 22 AIGND or SENSE 23 AIGND or SENSE 24 AIGND or SENSE 25 AIGND or SENSE 26 AIGND or SENSE 27 AIGND or SENSE 28 AIGND or SENSE 29 AIGND or SENSE 30 AIGND or SENSE 31 AIGND or SENSE 32 AIGND or SENSE 33 AIGND or SENSE 34 AIGND or SENSE2 35 NC 36 DGND 37 The remainder of this section contains information on grounding input pull downs and other topics which can be skipped on a first reading For each channel group there is a common reference input AISENSE1 for AI 16 or AISENSE2 for AI 17 32 that can also be accessed through the 37 pin D sub connectors The acquired signal is the difference between the channel input AI n and the AISENSE input for that group of channels This differential recording helps reject common mode noise that can be picked up in the cabling between the signal source and the analog inputs and also helps reject artifacts due to fluctuations between the ground level measured at the signal source and the ground level measured at the analog input card AIGND Note however that the default configuration requires that the device providing the signals be sround referenced This means that both the AI n and AISENSE input signals coming from the
15. In general many users find that circling clusters in PCA space 1s easier than try ing to find a good location to cross waveforms in the main spike window In the main spike window spikes sometimes overlap over much of their length and the display can be quite busy especially at high firing rates while in many cases the corresponding PCA clusters are more distinct and easier to work with since the first two PCA components tend to emphasize those parts of the spike where waveforms are more clearly separated and the drawing of each spike in the PCA display consists of only a single point However the choice of one unit definition method over the other can be very data dependent so it 1s best to view both the spikes and the PCA clusters before deciding how to proceed Version 1 8 153 6 Additional Sorting Methods 6 5 OmniPlex Concepts Snapshot Mode versus Live Display So far we have collected a spike snapshot for the purposes of working with PCA clusters However we haven t actually looked at the spike snapshot itself Omni Plex in fact allows you to toggle all the spike and PCA displays between either displaying the live incoming spikes the default mode which we have used for all examples so far and displaying the spike snapshot Toggling between live and snapshot modes can be done using the same button from any of the spike or PCA views toolbars SPK Waveforms ee el D pon 7 SE BE Show Snapshot RORE i
16. OmniPlex calculating the sorting parameters from a set of waveforms In this edition of the User Guide we will only cover a subset of the sorting meth ods and unit definition methods others will be described in separate sections at a later date You can also contact Plexon technical support support plexon com for more information 4 1 4 Automatic spike sorting In addition to methods for manually defining units OmniPlex provides an auto sorting algorithm based on the valley seeking method which automatically cre ates unit definitions from a spike snapshot Automatic sorting also known as unsupervised unit classification can be a challenging problem especially in cases where the spike waveforms do not have clearly distinct unit specific shapes or are noisy and additional automatic sorting algorithms will be sup ported in future versions of OmniPlex Even in cases where automatic sorting does not provide a perfect first pass solution it can be valuable especially at high channel counts in that it gives you a set of initial unit definitions which you can then adjust and improve manually 4 1 5 OmniPlex spike sorting as a toolbox It s easy to be a bit overwhelmed by the variety of spike sorting and unit defini tion techniques that are available in OmniPlex but none of them taken individu ally are overly complex Some methods are especially easy to use when defining units manually e g line sorting while others are more su
17. Recording Files Recording Control Colors Start Recording Pause Recording From GUI Only Occurrence s of an Event Ater 1 Occurrence s of an Event CinePlex Data Source 11 CinePlex Data Channel Any Value 1 After 0 Stop Recording Resume Recording From GUI Only From GUI Only After Occurrence s of an Event After Occurrence s of an Event Source 11 CinePlex Data Source 11 CinePlex Data Channel Any Channel Any Value 1 After 0 T Immediately Pause after Starting Recording Note every Resume Recording starts a Frame After Stopping Allow Restart Recording to a New File ok _ _cancel_ 3 The four actions start stop pause and resume can each be independently controlled either from the standard buttons in the main toolbar From GUI Only or triggered by a specified digital event For any action which is to be event triggered click the After Occurrences of an Event radio button Version 1 8 195 F Additional Features and Procedures Here is an example for a common usage scenario where we want the following behavior e Clicking the Start Recording toolbar button will create a new recording file but not record any data yet e When the RSTART line on the DI card sees a true level by default a ris ing edge but this is configurable in the DI device options actual record ing o
18. SPK Gource 26 hannel Type e Chamet on SPK Gource 26 SPEC Channel i Cortrucus 2 Gil ore Mag L71 1 a ie i bt ih aie Version 1 8 157 6 Additional Sorting Methods NAB opr BET SPK Clusters Snapshot ee Note that since the spike and PCA views do not animate while in snapshot mode display options such as Fade Rolling and Erase do not apply How ever when the PCA display is zoomed into single channel mode you can still use the interactive magnification and panning functions and the PCA point size setting is still applied 2 You can now perform all the same unit definition commands that you used while in live mode including waveform crossing and PCA contour drawing When you select waveforms to be used to form a unit template all units are being defined relative to the same set of waveforms In comparison when you define units by selecting waveforms from live data the pool of waveforms available for selection is constantly changing so in this sense defining all units based on a snapshot is more consistent 3 While in snapshot mode you can use the mouse to explore PCA clusters and interactively view the spike waveform corresponding to any PCA dot To do so place the cursor in the PCA view hold down the left mouse button and move the mouse The PCA dot nearest to the cursor is highlighted in color 158 OmniPlex Neural Data Acquisition System Version 1
19. 3 If the wideband signal looks like this where it only occupies a small fraction of the available amplitude range gt WB Channel 1 Continuous W WWE Channel 1 Continuous Peak Histogram Snapshot ied Continuous Version 1 8 35 1 OmniPlex System Overview and Startup 36 then you should first try increasing the volume level of the PC s Line Out or Headphones Out using the Windows volume control or audio mixer Volume Mixer Headphones High Definition Audio Device Applications Ei i E E Headphones System Sounds When increasing the test signal level using the PC s volume control try to set it to a level such that the largest peaks of the wideband signal occupy about 1 2 to 2 3 the vertical range as shown in the WB Continuous view WB Channel 1 Continuous i Sees he i Os 10s E ERA T TTT E Continuous The goal is to increase the wideband signal level high enough that it can be digitized accurately while at the same preventing it from clipping the A D con verters that is exceeding their allowed maximum input range See Appendix A Signal Amplitudes and Gain for more detailed information on this topic Note that maximum positive voltage limit before clipping corresponds to the top edge of the black background area just below the time labels while the OmniPlex Neural Data Acquisition System greatest negative voltage limit is the bottom edge The gray row of spike tick ma
20. 6 1 Step Dy Step Line Sorting ieee icdecrcerei caeecarsiesassceetnetacsaachaniaanncothcomcceiedonneovaerencnes 126 6 2 OmmniFlex Concepts POCA varecietsctrcaiervnseredcereniaatvenrxorescieer EENE EAEE 132 6 3 Step by Step Taking a Spike Snapshot and Viewing PCA Clusters cccccseseeeeees 135 6 4 Step by Step Defining Units for Template Sorting using PCA Contour Drawing 149 6 5 OmniPlex Concepts Snapshot Mode versus Live Display cccsecseeeseeeeeeeeeeeeees 154 6 6 Step by Step Defining Units using Spike Snapshots cccccccsseeecsseeeeeeeeesseeeeseees 157 6 7 Step by Step Automatic Sorting Automatic Unit Finding ccccseeeeeeseeeeeeeeeeeeees 163 oa Sep es 20 Porvoon SOG deresriceeic eterna aeniveeemenneei 171 o E OmniPlex Neural Data Acquisition System 125 6 Additional Sorting Methods 6 1 Step by Step Line Sorting 126 As opposed to template sorting which is based on an error criteria sum of squared errors between a spike and a template line sorting is what could be called a geometric sorting method Since you used waveform crossing to select bundles of waveforms which were averaged to form sorting templates you are in fact already familiar with the basic idea behind line sorting In line sorting you draw one or more crossing lines on spikes in the main spike window as in tem plate sorting but the crossing lines themselves are what is sent to Server to per form the
21. Channel 1 on WE Source 4 Name WEO1 Enabled Record Enabled E Threshold 10 000 Use of the arrows and direct editing of the numeric threshold value is as described previously Dragging the threshold line in the SPKC view You can also adjust the threshold value graphically on a display of the continuous spike signal SPKC To do so click on the SPKC Continuous tab to display the SPKC view if it is not already visible OmniPlex Neural Data Acquisition System Version 1 8 SPEC Continuous iid WE Continuous hed SPKC Continuous SPKC Channel 1 Peak The threshold is only displayed when the SPKC view is in single channel mode so double click on the desired channel to toggle the view into single channel mode T pm P oS pm ao F la F zr j Laer 7 APT eRpe Preps e L i ke anion Li i ia Os 55 hail al i a WB ergs be SPEC Channel 2 Connon SPKC Chonnet Ve Remember that you can use the toolbar buttons to adjust the magnification and sweep speed so that the SPKC signal is is easier to see and work with Here we have increased both the magnification and the sweep speed 83 3 Spike Detection Fe SS Se Ae OPT PEE Mag 2 25 A HP QT Oe TET T LS Us TTT TT ITTF ed WE Continuous Sd SPKC Channel 2 Continuous FJ SPKC Channel 2 Peak Hisi When you move the mouse cursor over the blue threshold line it changes to an up down cursor to ind
22. Data Acquisition System 6 3 Step by Step Taking a Spike Snapshot and Viewing PCA Clusters This section will describe how to use 2D PCA as an alternative to waveform crossing for defining units for template sorting All the other techniques that were discussed in the section on template sorting still apply we will merely be using a different method to select the spikes which will be averaged and used as the tem plate 1 If you are not currently using template sorting stop data acquisition and set the sorting method to Template then restart data acquisition SPK Source 6 On Device Channel Type Channels Channel Grouping Enabled Record Enabled Sampling Freq Gain Waveform Length Pre Threshold Sort Start Sort End Name Enabled Record Enabled Threshold Basic Sorting Spike 64 Single vf 40000 250 800 200 0 800 Sort Method Template Channel 1 on SPK Sour oe ee Line Hs Box Band 2D Polygon 2 If necessary set the gain and thresholds as described in previous sections so that you have incoming spikes on all channels If you have any defined units on the currently selected channel delete them using Remove All Units as described previously SPK Channel 1 Units Version 1 8 ag 1 ected Remove All Units cP Bet Pt ars ont pea 135 6 Additional Sorting Methods 3 5 136 Click on the SPK Clusters tab to display the multichannel 2D PCA window
23. F Additional Features and Procedures 7 You will be prompted to confirm the reset OmniPlexServer This will reset all Server settings to their defaults are you sure 8 Click Yes to confirm the reset You will be prompted to shut down Server OmmnPlexServer A Please shut down and restart OmniP lex before proceeding 9 Click OK then close Server 10 Run Server and then PlexControl as usual All software options and user interface layouts are now restored to their default settings 206 OmniPlex Neural Data Acquisition System Plexon Inc Appendix Appendix A Signal Amplitudes and Gain cccccccccceseseeeeeeseeseeeeueeeeeeseeeeeessaeeeeeeaaes 2 Appendix B Separation of Spikes and Field Potentials using Digital Filters 4 Appendix C PlexControl Spike Display MOde S cccccccsseeeeeeeeeeeeeeaeseeeeeeeeeeeeeees 9 Appendix D Advanced User Interface Features ccccccsseseceseesseeeeseeneeeenenseeenens 21 Appendix E DigiAmp Analog Highpass Filter and Referencing ccccseeeeeeeees 28 Appendix F Auxiliary Analog Input Aux Al cccceeccccsseecceeeeseeeeecesseesseseeesaaees 30 Appendix G More on Thresholding Aligned Extraction cccccssececseeeeeseeeeenaeees 34 Appendix H Enhanced PCA Feature Space cccccceccccsssseeeeeeeeeeeeaaeeeeeeeeeeeneas 38 Appendix Lowest Latency Operattion ccccccssssccceeseeeeee
24. In other words enter unit editing mode and add a unit by drawing a contour around a cluster in the zoomed 2D PCA view But now rather than the contour disappearing once Version 1 8 171 6 Additional Sorting Methods you have finished drawing it as was the case in template sorting the contour remains onscreen EA BY Bet D gt eta a OFT PF AAA Parzen Mult 1 0 4 e u eee SE SPK Waveforms SPK Channel 1 Clusters 3D 3D Clusters es Properties SpreadSheet 4 The feature space contour is sent to the sorting device in Server and each incoming spike is projected into PCA feature space and tested again the contour Points which fall inside a contour are sorted into the corresponding unit You can define additional units by drawing their contours You can use 172 OmniPlex Neural Data Acquisition System the Show All Show Current button to control whether all the PCA contours are shown or only the contour for the currently selected unit SPK Channel 1 Clusters ee St ED pca cA OPT BH GAB Parzen Mult 1 0 a SPK Waveforms I Version 1 8 173 6 Additional Sorting Methods 5 Once you have created a contour you can adjust it if desired You can move it by dragging it by the small square handle the cursor changes to a four way arrow while you are moving the contour Za SPK Waveforms SJ SPK Channel 1 Clusters 3D 3D Clusters Ez Properties SpreadS
25. Memory 81 The row of small windows under CPU Usage History displays the history of CPU usage for each core in the system As a rough rule of thumb if any one core exceeds 75 for an extended period or the total usage CPU Usage bar exceeds 50 you should watch out for performance issues such as drops or user interface stuttering Note that you can resize the Task Manager to make the per core graphs easier to view You can also click the Resource Monitor button to view more detailed performance information Appendix Page 45 Appendix tk File Wlonitor Cheer iea Resource Miomir Help CPU Memory Disk Network E i CPU Usage Image imiPrvS Ere FULL SHES T ewe permon exe svchost exe Localiyvste SBbc ere System Interrupts Cham exe DM Pees menete explore exe iexplore exe System EXPbOTen exe mechostexe netswcs SpplicationWebServer SyilemivVVeb Server exe rmvSCP APIS 2x2 CSS ERE tarkmgr sne SOF ard arene lQHpl ore EHA Ingpl ore exe ass ene miehost exe bo colienvid WO Tdpad exe olin ost cwe suchost exe DoomLaun PlexContra lene wehost exe NEDO Se El swehostexe LocalServic mplayer ewe ihosta RPCSS FEV ICES EEE ncratray exe agent exe aud lady ewe COFSS RHE 4o04 1597 THO ag Desoiption WII Provider Host Full Shot 9 5 Resource and Perfor Host Process Por Win OFI Software Anti hin Deferred Pro
26. Recording the WB data alone results in recording rates of approximately 64 channels 80 kb s 5 MB sec 300 MB min 256 channels 80 kb s 20 MB sec 1 2 GB min Recording both WB and SPKC will double the above figures and should in gen eral be avoided although OmniPlex is capable of doing so as long as you are careful to not run other performance intensive applications on the same machine at the same time The default recording behavior for OmniPlex is to record all channels on all sources except no WB or SPKC channels This gives the smallest files but has a number of potential drawbacks for example 1t becomes difficult to impossible to re threshold the data in Offline Sorter the threshold cannot be lowered towards zero To avoid these problems but at the same time trying to avoid unnecessarily huge file sizes the question then becomes whether to record WB or record SPKC The trade offs are as follows Recording the wideband signal insures that the original digitized signal unchanged by any digital filtering or other processing is available for later use This allows for widest range of offline processing to be done For example you wish to try a lower cutoff frequency for the spike highpass filter you must have the WB signal However 1f it is desired to be able to use the WB data to regener ate the exact same SPKC data as was generated by OmniPlex during the experi ment then the offline application must support all of
27. SPKC Ch EM FP M Ried AT Cont SPK Act if Firing Ra The Activity display is a sweeping time based display like the continuous views but instead of continuous signals vertical tick marks are display in rasters each tick indicating the timestamp of a spike or other event Just as with the continuous 198 OmniPlex Neural Data Acquisition System views you can change the sweep rate and the number of channels that are dis played as described previously The Activity view displays ticks for all OmniPlex sources which consist of time stamped events in the following top to bottom source order e Spike channels 1 N e Keyboard events 1 8 e DI event channels 1 32 e Strobed events e RSTART start or unpause recording event e RSTOP stop or pause recording event e CPX1 CinePlex events As with the continuous views the vertical scroll bar allows you to move up and down through the set of channels In addition you can adjust the amount of space that is used for the channel labels at the left by dragging the vertical separator line e e E in ry A BR OR AAT J m Eeu T There are also options for customizing the display in the Activity view s Option dialog Version 1 8 199 F Additional Features and Procedures 200 Activity View Options Channel Grid Size Rows 16 Columns 1 Show Channel Number Labels E Allow Toggling to Show Snapshot Show Time Scale The
28. To pan reposition or drag the display place the cursor anywhere in the PCA display hold down the Shift key then hold down the left mouse button and move the mouse to pan the display Release the Shift key and left mouse 146 OmniPlex Neural Data Acquisition System button when you are done The X Y axes show the new position of the origin in PCA space i A Ret Fad En ee _ C 22 SPK Waveforms Fa SPK Channel 1 Clusters 30 3D Clusters FE Properties SpreadSheet Note that the X axis represents PC1 the first PCA coordinate which repre sents the direction of largest variance in the original spike data while the Y axis represents PC2 the second PCA coordinate which represents the direc tion of second largest variance Version 1 8 147 6 Additional Sorting Methods 20 Optionally the PCA display can automatically adjust the magnification and viewing position so that the clusters can never go offscreen 2D Cluster View Options Columns 8 Zoom with Chain Arrange Channels in Row Major Order Show Channel Number Labels Allow Toggling to Show Snapshot Drawing Waveform Points Point Size When Zoomed 2 Update Mode for Live Data O Fade Fade Rate Slow F Fast Rolling Fade and Rolling Modes showing most recent 500 waveforms Erase Erase Every 10 secs Erase Mode Standalone Master _ Slave Range Control j f am Standalone Rangein X 1 000 o 1 000
29. WB Channel 1 Continuous SA we Channel Cogtin FY Peak Histogram Snaps SW SPKC Co OmniPlex Neural Data Acquisition System 6 Now that the properties for the WB source are displayed in the Properties view single click anywhere in the Gain row m Plexon Mini DigiAmp Record Enabled E amoung er 40000 a ll Sorset Sotend O 0 maverorm Length a _ Threshold a500 You will see up down arrows appear at the right end of the Gain row Version 1 8 1 OmniPlex System Overview and Startup 42 WB Source 3 On Device Plexon Mini Digi mp Channel Type Analog Channels b4 Channel Grouping Single Enabled Record Enabled sam oh bake Freq 40000 J Waveform Length Pre Threshold 200 Sort Start 0 Sort End 800 sort Method Template Channel 1 on WB Source 3 Name WBO1 Enabled Record Enabled E Threshold 15 000 Click the up arrow once to increase the gain from 50 to 250 If you see clip ping in the WB Continuous view as shown at the start of Step 2 click the down arrow to return the gain to the original value of 50 On the other hand if the signal level is still too low this is very unlikely when using a strong signal such as the audio from a PC you can try increasing the gain one more step to its maximum value of 1000 Remember if you see clipping in the wideband signal reduce the gain one step at a time until the largest peaks of the signal fit comfortably withi
30. actual sorting of incoming data When defining units for line sorting you can draw more than one crossing line per unit definition and incoming spikes must pass through all the crossing lines to be sorted into that unit This is a very intuitive way to interactively specify and refine a unit definition 1 OmniPlex requires that data acquisition be stopped before the sorting method is changed Stop data acquisition as previously described then click on the Sort Method entry in the Properties window at the left SPK Source 6 On Device Basic Sorting Channel Type Spike Channels 64 Channel Grouping Single Enabled Record Enabled sampling Freq Gain Waveform Length Pre Threshold Sort Start 0 Sort Fad 4 Channel 1 on SPK Sou yn Fi l i Enabled Box Record Enabled Band Threshold 2D Polygon OmniPlex Neural Data Acquisition System 2 Note that Template sorting is currently selected Click on Line to switch to line sorting SPR Source 6 Channels A Channel Grouping C Somplng Frey 00 a ee Waveform Length 800 Pre Threshold 200 a Record Enabled Threshold Version 1 8 127 6 Additional Sorting Methods 3 Restart data acquisition Note that since the sorting method changed all existing unit definition are deleted and all spikes on all channels are unsorted again 4 Enter unit editing mode and then add a new unit using the waveform crossing method as previously described for temp
31. analysis you should consider reducing the waveform length and or the post threshold interval See Appendix G More on Thresholding Aligned Extraction for details on aligned extraction which is an alternative extraction method which can give results superior to standard thresholding in many cases 94 OmniPlex Neural Data Acquisition System Plexon Inc Chapter 4 Basic Spike Sorting Bh We ee A 96 4 1 1 The two elements Of SPIKE sorting cccceeeccceeseeeeeeeeeceeceeeeeeeceeaeeeseaeeessaeeessaeeesaeeeeees 96 4 1 2 OmniPlex spike Sorting MEthOdS ccccccsssseeccceeeceeceesececeeeseeceeeeeeeseauseesssageesseas 96 4 1 3 OmniFlex nit definition FO tS ia icisissinsriiedirinideeiidielnsaniaiereiodiena 96 AA Siko SONN sesca 97 4 1 5 OmniPlex spike sorting as a toolbox ae ee 97 4 2 Step by Step Unit Definition using Template Sorting and Waveform Crossing 98 Be e a E a a PAE A E P A N A E E A T 100 4 2 2 Changing the fit tolerance for a unit cc ccecceccceeeeeeeeeeeeeeeseeeeeeeeaeeeeseaeeeeseeeeeeeeas 104 4 2 3 Changing the default for the initial fit tolerance ce ccccecseeeeeeeeeeeeeecaeeeeeeeeeeeeeeeas 107 Be The SPOG Th tice pees rtrd aac pe bile ead ee larciesieldeenciocgc 108 ee icra tiesto cessed snore aiei 111 HER SMB E E fo ea a eee E eee E eer ener var weer en AT E ttre ey ee re Mere enone rere 111 ALT POREC OFF SAIS UL eena ETGT 112 S OE OmniPlex Neural Data Acquisition System
32. any change in the magnification check to make sure that the selected channel is visible you may need to use the scrollbar to bring it into view Chain Control To understand how Chain Control works remember the topology diagram that is displayed in Server which shows chains of hardware and software devices feed ing data downward along chains ending in the Main Datapool where it is read by PlexControl Here we are interested in the chain of sources from the DigiAmp through the spike separator thresholder and spike sorter you can think of this as the spike chain OmniPlex Neural Data Acquisition System Version 1 8 Three of the sources in the spike chain have their data displayed in views in Plex Control continuous wideband WB data from the DigiAmp is displayed in one continuous view continuous spike data SPKC in another continuous view and sorted spikes SPK in two other views the multichannel spike view and the cur rent channel spike view The idea behind chain control is that changing the mag nification in one view will automatically change the magnification is other view which also have Chain Control enabled The usual case where you would use Chain Control is to cause a magnification change in any spike view SPKC view or the two SPK views to affect the other spike views To do so simply enable Chain Control in the views which you want to respond to magnification changes from other views for the same sourc
33. as described in steps 1 and 2 Then hold down the left mouse button on the first channel and drag downward until range of channels up through the last highest numbered Version 1 8 79 3 Spike Detection channel is selected and release the left mouse button to complete the selection Ss sCORRROEEE 4 Right click to display a menu 40C oa E Beena Set All Selected Channels Like Topmost Selected Channel AC Se Be o 2415 Set All Higher Numbered Channels Like Selected Channel Select All Set Values for All Channels 0 IF ig ig iF 5 Click on Set All Selected Channels Like Topmost Selected Channel The threshold values of all the channels are changed accordingly 80 OmniPlex Neural Data Acquisition System Version 1 8 coencco ns eg See eco oe soe ease aas You can set all channels to the same threshold value using the following technique First set the threshold for channel 1 as desired as described in steps 1 and 2 Next left click on the Threshold column header clicking on a column header in the Properties Spreadsheet always selects that entire column 1 iit Now right click and select either of the Set All commands all channels will now have the same threshold as the value you set for channel 1 hold Num Units Rec Spks Rec SpkCont Rec FP snuunnnnnnnn nn s cccccncscne OE K 1 k a 1 an i i b b b
34. cases the time required to load continuous channels from the result ing PLX file into an application or Matlab script can be prohibitive PL2 typically reduces this load time by a factor of hundreds or even thousands due to its more efficient storage and indexing scheme compared to PLX Besides Offline Sorter and NeuroExplorer PL2 files can be read by existing Mat lab and C C programs with little or no modification using a backwards com patible file reading API Refer to the documentation for the PL2 SDK for more details Before recording files in the PL2 format first make sure that the applications that you intend to use with those files support the PL2 format If you are using an older version of an application you may need to update it to a newer version which can read PL2 files OmniPlex Neural Data Acquisition System 5 1 3 What to record OmniPlex allows you to record every channel of every source that is available in PlexControl see the list in the discussion of sources and Server topologies However even though the PL2 format greatly reduces load times for large files it is usually not a good idea to record everything unless your recordings are short or you have a specific reason The main contributors to file size are wideband data WB and continuous spike data SPKC both of which consist of 40 000 samples of 16 bits each per second per channel or 80 kilobytes per second per channel plus a small amount of overhead
35. define a unit 6 Click and drag to draw a line across any spikes that you wish to invalidate Version 1 8 161 6 Additional Sorting Methods 7 All spikes in the snapshot which intersect the line are removed from the snapshot 8 You can continue invalidating waveforms if you wish until you have finished cleaning up the snapshot as desired Once the snapshot is satisfactory you can use waveform crossing on the snapshot to create unit templates for template sorting or draw sorting lines for line sorting as previously described 162 OmniPlex Neural Data Acquisition System 6 7 Step by Step Automatic Sorting Automatic Unit Finding Version 1 8 Another use for spike snapshots is automatic sorting which might be more accu rately described as automatic unit finding or unit definition Automatic unit find ing can be performed while PlexControl s displays are in either live or snapshot modes but the actual unit finding algorithm always creates unit definitions based on the spikes in the snapshot These unit definitions are then sent to Server and used to sort the live incoming data just as with manually defined units 1 To see how automatic unit finding works first make sure that you have collected a spike snapshot and have toggled into snapshot mode as described in the previous section 2 If the PCA view is not already in single channel Zoomed mode double click on a channel in the multichannel PCA view to
36. device in the topology In this context a source is simply all the channels of data produced by a hardware or soft ware device Here is a more detailed description of the flow of data through the devices in the topology for one of the channels of data in a typical system as shown in the pre vious topology diagram e Input channel 1 of the DigiAmp receives an analog signal from a headstage connected to an electrode The DigiAmp outputs continuously digitized data for this channel at a 40 kHz sample rate on channel WB001 which is sent in 8 OmniPlex Neural Data Acquisition System parallel to three destinations the Spike Separator and FP Separator devices and the Main Datapool e The Spike Separator performs highpass filtering on its input data outputting the result on channel SPKC001 which is sent in parallel to the Main Data pool and to the thresholding device Version 1 8 9 1 OmniPlex System Overview and Startup e The FP Separator performs lowpass filtering and downsampling to a 1 kHz sample rate outputting the result on channel FP001 which is sent directly to the Main Datapool e The thresholding device which extracts spikes from the continuous highpass filtered data on SPKCO01 using the current thresholding parameters for that channel outputting the result on channel SPK001 which is sent to the sort ing device e The sorting device fills in the unit numbers for spikes on SPKOO1 using the sortin
37. div 80 00 pSadiv SE SPK Wavefor A SPK Channel 1 3D SPK Channel 1 FE Prope Version 1 8 133 6 Additional Sorting Methods There are several uses for PCA in spike sorting First we can manually draw boundaries around visible clusters as an alternative to waveform crossing as a method of selecting waveforms For example we can indicate that we wish for all the spikes corresponding to the points in a PCA cluster to be averaged to form a template Second we can use them as a visualization method for assessing the results of spike sorting For example SPK Channell Waveforms v A X SPE Channell Clusters i ASE A BEE SD Mag 1 70 P oe BBE EAST 4 D pc cA on BH Third we can use PCA as a basis for a sorting method where we manually draw contours around visible clusters in the PCA feature space in order to define units then perform the real time sorting by projecting each incoming spike into PCA space and testing it against each of the contours Fourth PCA is suitable for use by a fully automatic spike sorting algorithm which identifies clusters in PCA space and generates either templates or PCA contours from them Each of these uses will be described in the following sections OmniPlex also sorts an improved version of PCA called Enhanced PCA which yields improved cluster separation and compactness in many cases For more information see Appendix H Enhanced PCA Feature Space 134 OmniPlex Neural
38. een HP NIU A A ou oan iin SPKC Peak fd WB Continu E Peak Histogra Sd SPKC Conti TIP Click on tabs to display their labels If the tabs are not displaying their source abbreviations WB SPKC etc you can click on the tabs to cause the source abbreviations to appear After the first time you click on a tab it will maintain its labeling 5 Note that a toolbar is not displayed this is because each view can have its own toolbar which can be hidden or display To display the toolbar for the SPKC view left click the down arrow at the upper right as you did with the WB view 6 If you wish you can drag the tabs into a different left to right order for example to move the FP Continuous tab next to the SPKC Continuous tab To do so place the cursor on the tab that you want to move hold down the left mouse button and drag to the left You will see the tab labels change as the Version 1 8 55 2 PlexControl User Interface tab you are dragging steps left one tab position at a time Release the left button when the tab you are dragging reaches the desired position FP Continuous Os WEB Continuous ma SPKC Continuous Peak Histogram Snapshot nd FP Continuous Activity W Firing Rates FP Continuous Os ntl inncan Peak Histogram Snapshot Activity ff Firing Rates If you accidentally drag the entire view as shown by a large shaded re
39. for the currently selected unit this is the same as what is displayed in each subwindow of the Units win dow but larger and with the template waveform displayed This mode is very handy for fine tuning the fit tolerance typically you would start with a a larger tolerance value and then reduce the tolerance until the bundle of waveforms comes into focus without extraneous invalid waveforms For example UN ESE Sa gt or gt te op Show Selected Unit 4 a Sa ON Oe S SPK Channel 1 Waveforms IX SPK Waveforms i lA t Mag 1 70 Ta Se et A BH ED A Mag A E a Unit a Fit Tol 0 057 a ln ni aUn h T Appendix Page 12 OmniPlex Neural Data Acquisition System dum Show Selected Unit 2 X i SPK Waveforms Si Bt Ef amp c Mag Ue ata py TTE DESFILE ES 4 a o mE orr p Version 1 8 Appendix Page 13 Appendix Finally Selected Unit Unsorted shows both the selected unit and all unsorted spikes and provides more visual information than Selected Unit mode a e M fi ga F a mp din m Show Sel Unit Uns i SPK Channel 1 Waveforms 1X SPK Waveforms QL Bt R D 7 Mog While you will probably spend most of your time with this option set to All you will find it very useful to toggle back and forth between the display modes as you are defining and refining unit definitions Note that the Show mode applies to bot
40. is being played into the nose board If you need to troubleshoot here are a few things you can try 4a Briefly unplugging the audio cable from the PC s headphone or line out jack should cause the wav file to be heard from the PC speaker if not make sure you don t have audio muted on the PC 4b If you have verified that the PC is playing back audio correctly try briefly unplugging the audio cable from the noseboard which will usually cause a brief noise transient to appear in the wideband trace display if not check to make sure the noseboard is firmly and evenly seated in the DigiAmp headstage connectors and that the jumpers are in the proper positions as described in the section Power On and Connections above 4c If none of the above steps locate the problem then try using a different audio cable 1 8 stereo Version 1 8 31 1 OmniPlex System Overview and Startup 1 9 Step by Step Setting the Wideband Gain 32 The DigiAmp provides a choice of three global gain values 50 250 and 1000 which are primarily intended for complementing the gain of the headstage so that the total analog gain is 1000 For example if you are using a unity gain headstage G1 then you should start with a DigiAmp gain of 1000 if you are using a G20 headstage then you should start with a DigiAmp gain of 50 The intermediate DigiAmp gain value of 250 is provided for situations where the gain of 50 is too low when using a G20 headstage o
41. is the pxs file which is auto loaded by Server however if you want to prevent the last loaded pxs file from auto loading in Server hold down the Shift key while starting Server The reset procedure can be useful for troubleshooting or 1f you simply want to insure that you are starting from scratch without carrying over and settings changes from a previous OmniPlex Session To reset all software options and settings in both PlexControl and Server 1 2 3 204 Stop data acquisition as described previously In PlexControl select the Reset All Options to Defaults command a PlexControl PlexControll File View Display Configure Data Window Run Help O S ae td or ag i Tasks OPT Global Options Wav Reset All Options to Defaults View Options Re k Start Data Ac i Create View a r Fi a PE bi mt f rir k ril trr ri art ful erik You will be asked to confirm the reset PlexC ontrol OmniPlex Neural Data Acquisition System 4 Click Yes to confirm the reset You will be prompted to shut down PlexControl PlexControl A Please shut down and restart PlexControl before proceeding 5 Click OK then close PlexControl but do not restart it yet 6 Lontigure ata Window Run help a ee aaa ea Define the System PlexNet Options RASPUTIN Emulation Options Add a Device Add a Source Edit Device Options View Options Global Options Version 1 8 205
42. mode to add and delete units on different channels 4 2 1 Adding a new unit 1 Click the Define New Unit button in the unit editing toolbar SPE Channel 1 Waveforms Al Bi ED A Mag 1 70 gt TP ont BBE Define New Unit If you move the cursor over the main area where spikes are being displayed do not click yet you will see that it is now shown as the Add Unit cursor 100 OmniPlex Neural Data Acquisition System Version 1 8 SPK Channel 1 Waveforms 4 a pi da A Mag 1 70 Z or iag HAA E e Define a unit What you will do next is based on the following scheme As incoming spikes are displayed spikes of similar shape which are assumed to be spikes originating from the same neuron will naturally tend to be grouped into visually identifiable subsets or bundles of waveforms You will draw a line across each of these bundles to indicate that those waveforms should be used to calculate a mean waveform that will be used for template sorting In other words the spike wave forms that cross intersect the line you draw will be averaged together and sent to the spike sorting device in Server which will use that template waveform to sort incoming spikes When defining a unit the best place to draw a crossing line is where the bundles of waveforms are most distinctly separated from each other Don t worry if you don t get good results right away OmniPlex lets you delete a template and start over and with
43. pre vious section 1 Start PlexControl either by double clicking its desktop shortcut PlexControl or select PlexControl from the Run menu in Server rpi OmniPlex Server opxDm G1 64wb 32ai pxs File View Configure Data Window Run 7 OFT OFT O Ga tel mt h ne PlexControl PlexLtil Offline Sorter NeurcExplorer Explorer Customize 26 OmniPlex Neural Data Acquisition System If not then select Create View Layout for Sources from the View menu me PlexControl PlexControll a Toolbars Tasks E Sources And Channels a Source Chain E Pro perties Pronerties Soreadsheet or from the Tasks view at upper left me PlexControl PlexControll ndugu You can do this at any time to restore the user interface layout to a default state without affecting any of the actual parameters for acquisition sorting recording etc In other words it is a purely cosmetic operation TIP Do not perform Create View Layout while recording Due to the amount of system activity involved in recreating all the views from scratch especially on systems with high channel counts it is recommended that you not perform a Create View Layout for Sources while recording data Version 1 8 27 1 OmniPlex System Overview and Startup 1 8 Step by Step Starting Data Acquisition 1 Click Start Data Acquisition either in the main toolbar PlexControl PlexControll on it a m a
44. sampling process this capacitance rapidly charges to the level of the applied signal When the multiplexer switches to another channel it takes a tiny amount of settling time for the capacitance of the multiplexer to adjust to the signal level of the new channel However if the new channel is not connected to anything there is no signal to change the value of the multiplexer capacitance and no path for the capacitance to discharge Therefore the value sampled for the un connected channel is approximately the same as it was for the previously sampled channel The added pull down resistors provide a path to discharge the multi plexer capacitance and cause a value near zero to be read for un connected chan nel instead of a value mirroring the previously sampled channel There is a consequence of having the pull down resistors in place The pull down resistor forms a voltage divider with the output impedance of the signal source For example a typical function generator has an output impedance of 50 ohms meaning the signal seen by the Auxiliary I O card will be 3 3 kohms 3 3 kohms 50 ohms or 98 5 of the output value of the function generator The signal will appear to be attenuated 1 5 Sources with higher output impedance will experience greater levels of attenuation If this attenuation is a concern the yellow pull down resistor packs installed in the sockets next to the D sub connectors may be removed Note that a signal will t
45. sigmas In this case the default auto threshold value of 4 sigmas is a good compromise between rejecting low amplitude noise and missing low amplitude spikes 5 Now that you understand what the blue threshold line means in the histogram display you can use the mouse to directly adjust it if desired Click and drag the threshold line when you release the mouse button the numeric threshold values and the blue threshold lines in the other displays will be updated to show the new threshold FTESA a WB Channel 1 Ried SPEC Channel 1 Fa SPEC Channel 1 Continuous Oy Acti att 89 3 Spike Detection 3 4 5 Dragging the threshold line in the single channel spike view You can also use the mouse to drag the blue threshold line that 1s shown in the main spike view This is the SPK window which displays an enlarged view of the channel that is currently selected in the multichannel spike view with a back ground time voltage grid 1 Move the cursor over the threshold line until it changes to an up down arrow cursor then click and drag to move the threshold as desired 2 When you release the mouse button the properties view and properties spreadsheet will display the new threshold value as a percentage and the blue threshold lines in the other displays will update as well Note in particular 90 OmniPlex Neural Data Acquisition System Version 1 8 that the new amplitude threshold is shown on the peak histogra
46. some of them from having worked through the previous tasks 1 Continuous signals in multiple tabbed views at lower right 2 Detected spikes in the multichannel spike view at upper right 3 An enlarged view of detected spikes for the currently selected channel in the main spike view at center left OmniPlex Neural Data Acquisition System Version 1 8 4 Sorted units for the currently selected channel in the units windows at lower left 5 A properties view showing settings and properties of the currently selected source and channel within that source at far left note that what is displayed in this view and therefore which parameters you can access from it depends on which source you have selected either by clicking on 6 A tasks view showing some common high level commands such as starting and stopping data acquisition and recording above the properties view 7 A set of global mini toolbars in a row just below the menu bar and title bar at the top of the screen highlighted in red above 8 For most of the views a per view toolbar which can be toggled on and off highlighted in blue above We previously described how double clicking on any of the multichannel views causes it to toggle into a single channel display and back again When in multi channel mode as in the example shown above each of the displays has a current channel which 1s indicated by the colored selection rectangle frame Clicking on a channel in a view whic
47. start data acquisition again after the file has been loaded However you do not have to stop data acquisition to save the current settings to a pxc file Version 1 8 187 F Additional Features and Procedures 7 2 Step by Step Automatically Maintaining Compatible Sets of PXS and PXC Files 188 Settings in OmniPlex are saved in two files Server saves its topology and set tings in a PXS file and PlexControl saves its settings in a PXC file For many users a single PXS is used and only the PXC file changes from experiment to experiment However other users use a number of different PXS files and the issue of PXS PXC compatibility arises Specifically if a PXC file was created while one PXS file was loaded in Server but at later date the same PXC file is loaded while a different PXC file is loaded in Server incompatibilities some dif ficult to detect can occur If your usage includes such mix and match scenarios you may wish to enable a set of options in OmniPlex which will automatically save your PXC and PXS files so that you know that you have a compatible pair of settings files 1 To enable PXS auto save in Server select Global Options from the Configure menu rpi OmniPlex Server opxDm G1 64wb 32ai pxs Data Window Run File View Configure Help 7 F m li ar f l lemti ese i oy eT IOTI j 1 EX IMEEL SALILA I RASPUTIN Emulation Options OmniPlex Neural Data Acquisition System 2 Ena
48. step by step instructions Items marked with TIP and the Appendices contain shortcuts additional techniques and more detailed information but you don t have to read them in order to complete the step by step tasks successfully The OmniPlex system that will be used for the examples is a 64 channel Mini DigiAmp system with a 32 channel AuxAI card your system may differ in the number of DigiAmp channels 16 256 and the headstage connectors on the Digi Amp 16 channels per connector on the Mini versus 32 channels per connector on the big DigiAmp but for the most part the instructions will apply to any Digi Amp system When the instructions read DigiAmp this should be read as either a DigiAmp or Mini DigiAmp as appropriate for your system 6 OmniPlex Neural Data Acquisition System 1 4 OmniPlex Concepts Devices and Sources Version 1 8 This section describes the types of signals and data that can be acquired and derived by OmniPlex These are shown in the topology diagram in the OmniPlex Server application which shows the flow of data from hardware devices into software processing modules both of which are referred to as devices in OmniP lex terminology and eventually flowing into the Main Datapool at the bottom of the diagram You don t need to start Server to follow this explanation this is only background information to give you an overview of Server s functionality before starting the step by step instruction
49. the Wideband Signal into Field Potentials and Spikes So far you have been working with the wideband signal WB source which after preamplification analog gain is digitized at a sampling rate of 40 kHz The digitized wideband signal for each channel contains field potentials at lower fre quencies plus a spike band signal at higher frequencies Since the field potentials are typically of a much larger amplitude than the spikes the net effect is of spikes riding on the waves of field potentials LA ch n I4 e n siat mewn n M fia S WB Channel 1 Co biel SPKC Channel 1 C FP Continuous Peak Histogram Sn Pei In a live neural signal the spikes would often be even smaller in relative ampli tude compared to the field potentials OmniPlex uses software DSP filters in Server to separate the WB signal into its two primary components e Lowpass filtering with a cutoff of approximately 200 300 Hz yields the field potentials which are then downsampled to a default sampling rate of 1 kHz FP source The downsampled signal can be processed more efficiently and helps reduce the size of recording files As a rule the sampling rate must be at least twice the highest frequency component in the signal and a factor of four or more is preferable 44 OmniPlex Neural Data Acquisition System Ried WE Channel 1 C ied FP CH 1 Co Peak Histogram Note This is an artificial test sig
50. then start data acquisition again See the instructions on stopping data acquisition below Note The Stop Data Acquisition button is to the right of the Start Data Acquisition button Version 1 8 29 1 OmniPlex System Overview and Startup 10 Xx SPKCH Or from the Tasks view select Stop Data Acquisition which is only displayed while data acquisition is running Tasks 10x System A ome Create View Layout for Sources Parameters which you had previously set while data acquisition was running such as gain thresholds etc will be preserved when you restart data acquisi tion 3 Start playback of the test wav file by double clicking on its desktop shortcut The naming of the file may vary from what is shown here e g TestSpike AndFP wav 4 Depending on the signal level from the PC s audio output some activity may now be visible on the traces in the WB Continuous view The colored rectangle identifies the currently selected channel within the wideband 30 OmniPlex Neural Data Acquisition System source by default channel 1 selection of sources and channels within sources will be described later WE Continuous Le hs sl ih ili iis Hin alas ai ts sim We i de a gg a a ace aa a Mg eli LEE We Continuous E Continuous EH Peak Histo If you still see only a completely flat baseline in the WB Continuous view as in Step 2 you may wish to recheck that audio
51. time to Matlab NeuroEx plorer and C C client programs and across a TCP IP or UDP network to remote clients The total end to end latency of OmniPlex from neural signal input to the output from an online client program is approximately 1 millisecond even at a full 256 channels and with multiple sorted units defined per channel 2 OmniPlex Neural Data Acquisition System 1 2 Components The OmniPlex Neural Data Acquisition System consists of the following hard ware and software components e A Plexon DigiAmp or Mini DigiAmp containing 16 to 256 channels of analog preamplification and signal conditioning analog to digital conver sion and a high speed proprietary digital interface to the OmniPlex chassis Version 1 8 3 1 OmniPlex System Overview and Startup 1 2 1 e A rack mountable OmniPlex chassis containing digital input auxiliary analog input link and timing synchronization cards plus one or more BNC break out panels e Acustom configured and performance optimized Windows 7 PC which runs the OmniPlex acquisition and control software and has a high speed link to the OmniPlex chassis e The OmniPlex acquisition and control software consisting of OmniPlex Server PlexControl PlexNet and a software development kit SDK which allows online interfacing to Matlab and C C programs This User Guide assumes that your OmniPlex system has been installed config ured and tested by a Plexon Sales Engineer
52. to Plex Control Matlab C C client programs PlexNet and NEX The list of predefined source types that will be found in a standard OmniPlex sys tem includes e WB Continuously digitized wideband neural data from an A D device such as a DigiAmp e SPKC The result of highpass filtering a WB source 1 e the spike filtered continuous signal e SPK Extracted spike waveforms the result of performing spike detection on a SPKC source e FP The result of lowpass filtering a WB source 1 e the field potentials e EVT Individual digital events e g discrete single bit events or strobed multi bit data words e AI Continuously digitized non neural data typically at a low sampling rate e g 1 kHz e g eye position etc e KBD Similar to single bit digital events but generated by pressing Alt 1 through Alt 8 on the keyboard for manually marking events during an exper iment e CPX Data that is generated by a Plexon CinePlex system and sent to OmniP lex to be included in recordings There can actually be more than one source of a given type in a topology for example WB channels 1 48 could be one source and WB channels 49 64 a sec ond source but in most systems this will not be the case and you can assume for the purposes of this User Guide that when we say for example the SPKC source this means a single source the one that consists of all the channels of data that are output by the Spike Separator
53. to more extensively customize the layout of views and toolbars in Plex Control Floating a window If you place the cursor on the title bar of a window hold down the left button and drag you will undock that window and any tabbed views that are contained within it If you then release the window while it is not attached to the edge of any other window it will become a floating window that covers the windows beneath it Here is an example RRS pew Dho Lenine pata Wdye Pun Hin Tr 7 020 foe ELETT pang anp 4 ce eh oar oe wae Show aivi A x 7 SPM Charmed 1 nee i mam bnsa ee a eres al e r F zal iia aa in a a a sa ar prt os en ey alia T i ate ath a Fe ae Praca z h re a i a piisi rA hi P arasia ta a diais a i a a a ma ice a a sie ie ei a a ah ilii F iaa iaa an aiia ai wn aa dikes ae dines a 288 ee Pee ee ee ee Se ee ei oo pare le lie aah Poe nm i ppm pm ae EER voy OAM LT MA SACRE MAANA AAE ARIANA ARBAB BAAN A ie ncn HUA AAMAS mn Version 1 8 Appendix Page 21 Appendix Fea Yew Depa Centgue Ds Mads Bue Hep ae ae Oe ee E are LEUL ig ptem 4 Create Yisa Leani tor Mae rt Be el at oe e a Wh FE ga oy ata rm aga ni Shewa Ml Valid af s 70 i SPK Varelan HE Wuna L Bune Contigune 2 Soner hg Hart Aeconding Data Ls Sieg Cats Acquedion en as Fa Tep pa my V a A i J r Piperin 20 SPK Gonos ai i j z T A
54. using the Sweep Faster and Sweep Slower buttons in the toolbar OmniPlex Neural Data Acquisition System SPEC Continuous P Fa GD Ac ORT PRT Mag 1 00 TINS Tl i ee 7 i i Sweep Faster ail 0 05 0 55 gt SPEC Continuous A FB Ac Ft BBA Mag 1 00 TE LSIAT 2 Os 105 m i 205 E ee eee eee ee Sweep Slower E The time scale along the top edge of the continuous view is redrawn to show the new sweep speed 2 3 3 Changing number of channels displayed in a view continuous channels You can change the number of channels displayed together in a view with the More Channels and Fewer Channels buttons in the toolbar Version 1 8 59 2 PlexControl User Interface SPKC Continuous iA Fab D Js Ac St BB Mag 2 00 cates ol Le Ze More Channels mm E We Continuous B SPKC Continuous FA Peak Histogram Snapshot FA Peak 60 OmniPlex Neural Data Acquisition System Version 1 8 SPEC Continuous A Fat a aS Ae OPT BBA Mag 2 00 i BAR LE hc c To J3 E Pak P hil WE Continuous ied SPEC Continuous Peak Histogram Snapshot Peak Histo If you are viewing fewer than the total number of channels you can use the scrollbar and scroll arrows at the right side of the view to scroll other channels in and out of the view T 50 m7 7 50 mi ODA E E A A E A T 50 mf 7 50 mf ODA UE E T 50 m7 7 50 mf 61 2 P
55. which you encircled are averaged and used to define a new unit template for the current channel You can see incoming Version 1 8 151 6 Additional Sorting Methods 152 spikes being sorted using this template in the main spike window the Units window the zoomed PCA window and the SPKC window 4 View Depi Colgue Das Winders mua Hap ip E a 2 0 he eee ee onre BEE nE a a um Show Ali valid i ee Tata AOX 5 SPE Chane l Wye LM SPR Chari Chien x e BA BBS Akg in mei ree LET RR ees Fito tan I Cre Jey E T di Core EPL Wg Star 10 Dot a ite piii p ylis Ox Template EEE weto BM SP Charmed Custers J620 Custe BA Properties Spreeditenet SPC Chnra l Costin sala aT Pla Enti j E Hi ki IE i x TRAT OLE LoL Li E E mi ee eee Just as with defining new units by waveform crossing you can continue to add more units by circling additional clusters delete or replace units etc Note that while you are seeing the sorted and unsorted spikes being projected into the 2D PCA display the actual sorting is being done by template sorting and is controlled by the template and the fit tolerance When the sorting method is template sorting a fit tolerance slider is displayed in the PCA unit editing toolbar just in the main spike window This can be used to adjust the tolerance for the currently selected unit while viewing clusters without having to hop ov
56. with threshold timestamping is that it does not use an unam biguous feature in time voltage space of the spike as the reference to which a timestamp 1s attached The obvious choice for such a reference is the largest peak within the spike OmniPlex s aligned extraction thresholding algorithm uses this approach Here is an example of the difference between standard threshold crossing top and aligned extraction bottom Note how the waveform bundles and the cor responding PCA clusters are more well defined when aligned extraction is used Appendix Page 34 OmniPlex Neural Data Acquisition System Besides the improved timestamping accuracy and jitter reduction the more well defined clusters improve the performance of the automatic unit finding algorithm Aligned extraction can be enabled in the device options for the thresholding device in Server 12 32 Chs Edit Device Edit Device Options Show Device Characteristics Add New Source To Device Remove Device Version 1 8 Appendix Page 35 Appendix Thresholding Configuration 0 15 Default threshold Timestamping Mode Use time of threshold crossing Use time of largest peak same side as threshold D Use time of largest peak either side of threshold Use time of first peak same side as threshold The first setting is standard thresholding while the next two are two varieties of aligned extraction The tim
57. zoom it You should now see something like this SPK Channel 1 Clusters Snapshot IX Sn B SPK Channel 1 Clus 3D 3D Clusters R Properties SpreadShe 163 6 Additional Sorting Methods 164 3 5 Click on the Automatically Find Units button in the toolbar E FA Bet Fal a PEA mT ar OPT A Ri A EA Select unit The automatic unit finding algorithm sorts the spikes in the snapshot by looking for clusters of their projected PCA points then averaging the corresponding waveforms for each sorted unit to create a new unit template In other words the unit finding is performed in PCA space then the results of the sorting are used to produce template unit definitions for the actual template sorting of incoming data SPK Channel 1 Clusters Snapshot IX Mea E Unit c Fit Tol 0 040 Parzen Mult 0 7 amp S 3 p eek Waveforms Sn 9 SPK Channel 1 Clus 3D 3D Clusters Properties SpreadShe You can use the Show Snapshot button to toggle back to viewing the live data to see the results of the unit finding which was performed based on the snapshot being applied to incoming spikes OmniPlex Neural Data Acquisition System Version 1 8 gt SPK Channel 1 Clusters IX ES 4 GBT Fa n ZE SPK Waveforms P SPK Channel 1 Clusters 30 3D Clusters EE Properties SpreadSheet If you are not satisfied with the results there are two diff
58. 8 and the corresponding spike waveform is drawn inverted black for white and white for black in the main spike window This can be an useful and rather entertaining way to learn about the corre spondence between spike waveforms and PCA for example outliers that are far from the center of a cluster usually correspond to rare difficult spikes which could be the superposition of multiple spikes or other anomalies Another useful function is which is available only in snapshot mode is spike invalidation When the main spike window is in snapshot mode and unit edit mode you can use the invalidate tool to remove waveforms from the snapshot The main use of invalidation is to remove spikes that are clearly outliers stimulation artifacts superpositions etc After doing this you can define units using the remaining spikes in the snapshot without the corrupted 159 6 Additional Sorting Methods or outlier spikes polluting the results To invalidate waveforms in the snapshot click on the Invalidate button in the unit editing toolbar SPK Channell Waveforms Snapshot i xX EE aiiai A Ee EN Define a unit P i waveforms zl 5 The cursor changes to indicate that you are ready to mark waveforms for invalidation You can think of this as the inverse of defining units by waveform 160 OmniPlex Neural Data Acquisition System crossing in that the crossed waveforms will be removed rather than used to
59. A E BY oH Mag 1 00 MAS Se SPK Waveforms P SPK Clusters Appendix Page 10 OmniPlex Neural Data Acquisition System Version 1 8 This mode is useful for removing the clutter of unsorted spikes but be careful since it also omits all the spikes that almost but not quite match a template mak ing your sorting look unrealistically clean However it is a good way to see whether each of the units 1s distinct from the others The Unsorted mode shows as the name implies only the spikes that do not match any template This mode gives a more pessimistic view of your sorting results Lh oke eS SPE Channeli Waveforms XxX SPR Waveforms ft 7 Bet Pat ao lt Mag 1 0 GSE Sa gt cow gt te nb Show Unsorted x ORK Appendix Page 11 Appendix Ideally the only spikes that you see in this view should be ones that are not valid matches for any defined unit In practice you will likely see some that should have been matched to one of your templates In this case you may wish to try increasing the fit tolerance for the relevant unit however be aware that due to noise and issues such as superposition there will always be some small percent age of spikes that you can visually identify with a specific unit but which cannot be sorted without increasing the tolerance so much that there are also invalid matches to that template The Selected Unit mode displays only the sorted spikes
60. CA display and click the Edit Units button SPK Channel 1 Clusters BA E Dec z on Bet Edit Units 2 The unit editing toolbar is displayed Click the Add Unit button SPE Channel 1 Clusters EH All Bet FE Go pra lt 7 ORT BS AE FS Select unit Parzen Mult 0 7 2 A lal Define New Unit Version 1 8 149 6 Additional Sorting Methods 3 The cursor changes to the Add Unit cursor indicating that you can draw a contour around a PCA cluster SPK Channel 1 Clusters ll Set Fak Go Pca lt 7 OFT Bt Select unit 4 Hold down the left mouse button and draw a contour that encloses the most prominent cluster Don t worry if the contour isn t smooth the main thing is to encircle the points that belong to one cluster while avoiding including points belonging to nearby clusters as much as possible 150 OmniPlex Neural Data Acquisition System 5 When you have drawn all the way around the cluster and returned to the approximate starting point of your contour release the left mouse button TIP Use the CTRL key as a shortcut for adding a new unit Just as with waveform crossing you can use the CTRL key as a shortcut for adding a new unit so that you don t have to click the Add Unit button before each unit Hold down CTRL before pressing the left mouse button and drawing the contour 6 The contour which you drew is erased and the spike waveforms corresponding to the PCA points
61. Contrevcus Savery BA Ring Rates If you move the cursor to any of the four outer arrows the window you are dragging will be docked to that edge For example if we dock the window to the right edge Appendix Page 23 Appendix om a e Ieee Yew Depi Confgue Co Weds fin Hep 2 coe ok ET ENSET Mn aS tet ce TETEE EE cep Show vain ae ieg Ox picuasi W v Dx SEK Wels E Spi Z x 5 WOR _C per iriuiie Pi Pe a a i Ph ac Pe aih bai bh Hih bah ioh dah A PEF UO EE ee i i Pi tan Paaa Ph PPh a bod iol i ae Lo i TF r as i mA ine BA F 1 EH Spies Srupchet Retd y We could then use the splitter bars to resize the windows within this layout e ed a cal corp ome Be View Depay Configure Daa Window fut Hep eae A ELTTI reek OTe Be ee jae E Tasg ADK i SPE Chanel Wivels riz PE Wavetone T F ie 89 Spice inapehet Racy fo On the other hand if we release the cursor within one of the four arrows in the four way arrow the window will dock to that edge but nested within that specific window as opposed to the outer main PlexControl window For example Appendix Page 24 OmniPlex Neural Data Acquisition System Version 1 8 Dimplny Cenfiguie Daa Window Bun Hei F a eo eee eo eo ee o and i 1 Tanks Die Wh matan TO SOC Chanel hiaan Gann Tep eh Pee a pe 8 Pee Pe
62. Data Fade Rate Slow Fade and Rolling Modes showing most recent 500 waveforms Erase Every 10 secs Erase Mode Standalone Master Slave Range Control Standalone RangeinX 1 000 to 1 000 Master RangeinY L000 to 1 000 Slave E Adjust Automatically Use same for all Channels E Shift Right Click changes and Y ranges independently 17 When you change the settings you can click Apply to see the effect of the changes on the display immediately then click OK when you are done making changes Here is an example of the effect of setting the point size to 2 pixels and the update mode to Rolling 144 OmniPlex Neural Data Acquisition System SPK Channel 1 Clusters PLA lt A ORT pea z 18 The size and position of PCA clusters can vary considerably so the zoomed PCA display allows you to interactively adjust the magnification and panning position of the display To change the magnification simply single click the cursor anywhere in the zoomed PCA display and roll the mouse wheel gt SPK Channel 1 Clusters IX fe A pla cA ORT pea sl eee eee eee Channel 1 an SPK Waveforms pa SPE Channel 1 Clusters 30 3D Clusters Properties SpreadSheet Version 1 8 145 6 Additional Sorting Methods a Cn G Ad St Fad D e lt 7 OFT m Oe ee ee eee C Ma SA SPK Waveforms BR SPK Channel Clusters 3D Clusters Fey Properties SpreadSheet 19
63. Data Acquisition System you start from scratch To do this use the Delete All Units on All Channels command in the Configure menu PlexControl PlexControll File View Display Configure Data Window Run Help 4 Ty T 7 OPT OFT ar far Nel A View Options a Tasks Global Options ee ag 1 71 System iO Auto Configure All Sources om Create View for Sources Se a ii Automaticall Collect New Snapshot for Source Confiqure Al Collect New Snapshot for Channel Properties SPK Source 6 Take Snapshot for Source Take Snapshot for Channel On Device Channel Type 5 Rename Channels Channels Auto Sort current Source a Opa Auto Sort current Channel Enabled Add New Unit Record Enabled E Sampling Freq 4 5 Gain Waveform Lengl amp Delete All Units on All Channels Pre Threshold 2 0 Refresh Sort Start 0 3 After all units have been deleted this make take a few seconds on high channel count systems make sure that the SPK source is selected you can do this by clicking on either the main spike window or the multichannel spike or cluster views ee alla om a SE Version 1 8 167 6 Additional Sorting Methods 4 Select Auto Sort current Source from the Configure menu to begin the automatic unit finding a PlexControl PlexControll File View Display Configure O S Ned Se Goer Data Window Run Help a a OFT OFT V
64. E pi nE ff Mag 1 70 gt Bee oer FY 106 OmniPlex Neural Data Acquisition System Conversely if the fit tolerance is too low then no units will be sorted as unit a SPK Channel 1 Waveforms 1 x Si Z Bt ED A Mag 1 70 HP ont BBE A A E Unita Fit Tol 0 003 S a i Decreasing the tolerance can tighten up the sorting of a unit but risks exclud ing valid matches increasing the tolerance avoids being too strict but risks cre ating false matches PlexControl provides some useful visualization options that help you to evaluate the effect of your changes to sorting parameters and these options can be used with any of the sorting methods 4 2 3 Changing the default for the initial fit tolerance As mentioned the default fit tolerance for a newly created template is one stan dard deviation relative to the set of waveforms used to create the template You can change this default value in the Spike Snapshot Options dialog To access it click the toolbar button Version 1 8 107 4 Basic Spike Sorting w g a i B A BH if D A Mag 1 70 snapshot Options The Options dialog is displayed Spike Snapshot Options Collection Auto Sort Sources Auto Sort Parameters Algorithm icine cece Use 3D Feature Space Walley Seeking o7 even for Views Parzen Multiplier 0 7 Larger values produces fewer units Initial Fit Tolera
65. J 4 J d i 5 L a i i k Start Data Acquisition a Create View Layout for Sources Load the pxc file that was last used or in the Tasks view me PlexControl PlexControll LTedte view Lae Dut for Sources Load the pxc file that was last used 28 OmniPlex Neural Data Acquisition System 2 After a few seconds you should see signal traces being drawn in the view labeled WB Continuous in the lower right part of the window AX i WB Continuous WB Continuous Peak Histogram Snapshot Continuous Peak Histogram Snapshot ad Continuous m WB Continuous refers to continuously digitized signals from the WB source The vertical colored sweep line shows the current position once it reaches the far right end of the window it wraps around to the leftmost posi tion and overwrites the oldest data in the view Note the time labels on the horizontal axis indicating relative time later you will learn how to adjust the horizontal sweep speed and other viewing parameters TIP Some settings can be changed only when data acquisition is stopped Later you will see that there are some settings which can only be changed when data acquisition is stopped For example OmniPlex will not allow you to modify the spike waveform length or pre threshold length or change the sorting method while data acquisi tion is running In such cases simply stop data acquisition perform the desired operation
66. Js COMPUTER LLA Pi ok c 13 1 OmniPlex System Overview and Startup 2 Make sure that the blue link cable is connected from the AMP LINK card in the chassis to the connector on the DigiAmp The red markings on the cable connectors should line up before inserting the cable 3 y m 3 es a If you ever need to disconnect the blue link cable from either the DigiAmp or the Amp Link card in the chassis unplug the connector by pulling straight out on the connector on the end of the cable Do not pull on the blue cable itself and do not twist the connector Never bend or kink the blue cable 14 OmniPlex Neural Data Acquisition System Version 1 8 3 Make sure that the HST PWR switch on the DigiAmp is off down 4 Ifyou are using a Mini DigiAmp 4a Connect the headstage tester unit HTU to the DigiAmp headstage input connectors 15 1 OmniPlex System Overview and Startup 4b Connect a 1 8 stereo audio cable from the 1 8 line output jack on the front or back of the PC to the 1 8 input jack on the HTU 4c Set the REF jumpers on the HTU to GND Set the left right jumper to LEFT DIVIDE BY 1 000 f iL IE s H WOKO N Q 16 OmniPlex Neural Data Acquisition System 4d Turn the HST PWR switch on up The next steps are for users of the big DigiAmp and Mini DigiAmp users can skip to Step 6 5 Ifyou are using a big DigiAmp 5a Plug the long narrow nos
67. Overview 48 Step By Step Resizing Windows using the Splitter Bars 50 Step by Step Using the View Toolbars and Options 53 Changing the magnification 57 Changing the sweep rate 58 Changing number of channels displayed in a view continuous channels 59 Pausing the displays 62 Continuous view options 62 Use Same Magnification for all Channels 63 Chain Control 64 Chapter 3 Spike Detection Spike Detection by Thresholding 68 OmniPlex Concepts Snapshots 69 Step by Step Using a Continuous Snapshot to Set Thresholds Automatically 71 Step by Step Adjusting Thresholds Manually 79 Vil da 47 67 OmniPlex Neural Data Acquisition System viii OmniPlex Neural Data Acquisition System Plexon Inc Changing the value of the threshold in the properties spreadsheet 79 Changing the value of the threshold in the per channel properties view 82 Dragging the threshold line in the SPKC view 82 Dragging the threshold line in the SPKC snapshot peak histogram view 87 Dragging the threshold line in the single channel spike view 90 Step by Step Changing the Spike Extraction Parameters 92 Dead time 93 Chapter 4 Basic Spike Sorting 95 Overview 96 The two elements of spike sorting 96 OmniPlex spike sorting methods 96 OmniPlex unit definition methods 96 Automatic spike sorting 97 OmniPlex spike sorting as a toolbox 97 Step by Step Unit Definition using Template Sorting and Waveform Crossing 98 Adding a new unit 100 Changing the fit tolerance for a u
68. RT If you need to record very short trials say less than 10 seconds each then instead of using RSTART RSTOP to start and stop recording use the following technique record the entire series of trials including the dead time between trials continuously without stopping but use digital events e g EVT001 and EVT002 to mark the exact start and end of each trial within the recording You can then use offline tools such as Neu roExplorer s interval features to extract the data corresponding to each pre cisely event bracketed trial As with all recording it is strongly recommended that you make a short test recording to confirm that event triggered recording is working as expected before proceeding to recording important experiment data Version 1 8 197 F Additional Features and Procedures 7 5 PlexControl Activity Display The Activity view displays a raster view of activity on spike and event channels To display it click the Activity tab in the lower right part of the PlexControl win dow T 15 00 mi Continuous SPK jamais I Firing Rates SPK Activity The Activity view 1s displayed SPR Activity IX A Bt E SES LLB Os iT I 7 ii nit mm J il fy all va ih LL my hve mh a MT H i st 1 ii mn a i 1 hi iy eo in y aL mi l mu I T hi nin at A Mi iiil Hy Wit iy W Pinan in mi Wi i iay y AT Hit SSG Rea SPEC C ER
69. Step by Step Adjusting Thresholds Manually ccccscccecsseeeeeeeeeeseseeeseeeeeeeeeeeeaeeeeeas 79 3 5 Step by Step Changing the Spike Extraction Parameters cccccceeseeeeeeeeeeseeeeeeeens 92 OmniPlex Neural Data Acquisition System 67 3 Spike Detection 3 1 Spike Detection by Thresholding 68 In spike detection the amplitude of the SPKC signal is compared point by point against a per channel threshold amplitude value When the SPKC signal crosses the threshold value a segment of the SPKC signal by default in OmniPlex eight points preceding the threshold crossing and 24 points following the threshold crossing for a total length of 800 microseconds is used to define a spike wave form which is then output on the corresponding channel of the SPK source Spike detection operates continuously on the incoming SPKC signal outputting spike waveforms in sequential order as they are detected on each channel Spikes on a channel typically have a larger negative peak amplitude and so the default thresholding in OmniPlex is on the negative side but a positive thresh old can be defined 1f the spikes on a given channel have larger positive peaks The threshold value must be large enough far enough from the zero volts base line in whichever direction to avoid false triggering on low amplitude noise but not so high that low amplitude spikes are missed A common mistake is to set thresholds too low moti
70. WB source that are actually properties of other sources for example the Wave form Length is a property of the thresholder device and Sort Method is a property of the sorting device This is done as a convenience so that you don t have to constantly select sources to change common properties Omni Plex automatically figures out which upstream or downstream source i e downstream from WB to SPKC to SPK relative to the one shown in the Prop erties sub title is meant For example if you selected a channel in the multi channel spike window the Properties view might show something like this OmniPlex Neural Data Acquisition System Version 1 8 Properties iO x ESEA PEENE Basic Sorting Channel Type Spike Channels 4 Channel Grouping single Enabled Record Enabled Fi sampling Freq 40000 Waveform Length BU Pre Threshold 200 Sort Start g Sort End a00 Sort Method Template Channel 9 on SPK Source 6 Name SPROO Enabled Fl Record Enabled A 15 000 Gain is displayed as a property even though the sorting device has no gain control when you change the gain in this case it actually changes the gain in the first device upstream from the sorter i e the DigiAmp Likewise channel 9 s Threshold value is displayed and can be adjusted and editing this param eter affects the thresholding device which is immediately upstream from the sorter However if you select a source for whi
71. You can adjust how tightly the ellipses are fit to the clouds of sorted points from the unit finding algorithm To do so display the Snapshot Options dialog using the toolbar button SPR Channel 1 Clusters Snapshot ele PLA lt 7 St A Gl Al 181 6 Additional Sorting Methods Spike Snapshot Options F Use 3D Feature Space even for 2D Views Parzen Multiplier 0 4 Larger values produces fewer units Initial Fit Tolerances for Template and Band Units Set to a constant value of 0 1 Sett 1 times the standard deviation of waveforms Fit Tolerances for 2D Ellipses 2 times the standard deviation of feature points This value which should not be confused with the fit tolerance for template sort ing controls the tightness of fitting of all generated ellipses except for those that result from cleaning up hand drawn contours You can move and rotate the automatically generated contours just like manu ally created ones Of course you can also modify the Parzen Multiplier and run another round of automatic unit finding as previously described 182 OmniPlex Neural Data Acquisition System 6 8 4 Defining units by line crossing with 2D polygon sorting You can use waveform crossing in the main spike window to select bundles of similarly shaped waveforms as described before to create unit definitions for polygon sorting For example after using automatic unit finding to create the above two unit definition
72. a little practice you will get an intuitive feel for the most effective placement of waveform crossing lines 101 4 Basic Spike Sorting 2 Toadd a unit by drawing a waveform crossing line place the cursor where the line should start press the left mouse button drag to draw the line and release the mouse button at the point at which the line should end 3 When you release the mouse button the crossing line is removed and the template that was created is displayed with small squares indicating the points of the template waveform This is the first defined unit on this channel so it is unit a Incoming spikes that match the new template are now displayed in a unit specific color 102 OmniPlex Neural Data Acquisition System So how does OmniPlex determine which spikes match a template The algorithm for template sorting 1s based on computing an error measure for each incoming spike relative to each template The error measure is the sum of squared ampli tude differences between the spike and the template waveform where the differ ences are taken between corresponding points i e sample values on the spike waveform and the template waveform Also when a new template is computed from a set of waveforms that you selected via waveform crossing a multiple of the standard deviation of the set of waveforms is used as the fit tolerance for that unit by default one sigma In other words for each incoming spike the sum of sq
73. a unit is selected in the Units Window its fit tolerance is displayed as both an editable value in the Properties view at the left and as a value with an adjust able slider in the unit editing toolbar Tasks 2O X SPK Channel l Waveforms xX System om Create View Layout for Sources a Automatically Configure All Sources Start Recording Data top Data Acquisition bropr on SPK Source 6 On Device Basic Sorting Channel Type Spike Channels 64 Channel Grouping Single Enabled Record Enabled Sampling Freq 40000 Gain 250 Waveform Length 800 Pre Threshold 200 Sort Start 0 Sort End 800 Sort Method Template Channel 1 on SPK Source 6 Mame SFKOL Enabled y Record Enabled W Threshold Unita 12 093 0 033 Fit Tolerance gt SPK Channel 1 Units If you decrease the fit tolerance the net effect 1s to make the template matching stricter incoming spikes must more closely match the template If you increase the tolerance the template matching becomes looser the error mea sure between the spike and the tolerance can be larger yet still qualify as a match to the template As an extreme example if you only have a single unit defined on a channel but the fit tolerance is set to the maximum then most or all detected 66 a spikes will be sorted as unit 105 4 Basic Spike Sorting gt SPK Channel 1 Waveforms
74. aa MD Cw Neurotechnology Research Systems OmniPlex Neural Data Acquisition System Version 1 8 April 2013 User Guide gt Plexon Inc E T LE 6500 Greenville Avenue Suite 700 A Eilts BS 4 45 BR Bl Dallas Texas 75206 KYS Technology JSA T 02 2911 5233 CY F 02 2911 6855 E info kyst com tw Caution Electrostatic Discharge Some devices can be damaged by improper handling Use appropri ate electrostatic discharge ESD procedures when handling these devices See http www esda org for additional information on ESD procedures Caution USB Security Key Damage Before installing SafeNet Sentinel security key drivers remove all Sentinel USB keys from the PC If a system driver is installed with a USB key in the port the key may become unusable OmniPlex Neural Data Acquisition System User Guide Document Number OPXMNO001a Document Status Standard Software Version and Issue 1 8 Date April 2013 Copyright 1983 2013 Plexon Inc All rights reserved Printed in the United States of America Plexon Inc Proprietary The information contained herein is the property of Plexon Inc The information is proprietary and restricted solely to assist Plexon Inc customers Neither this document nor the contents may be disclosed copied revealed or used in whole or in part for any other purpose without the prior written permission of Plexon Inc Information is subject to change w
75. age 3 Appendix Appendix B Separation of Spikes and Field Potentials using Digital Filters High sample rate digitization of the wideband signal OmniPlex digitizes neural signals at a sampling rate of 40 kHz 25 microsecond resolution in order to acquire the wideband WB signal with maximum accu racy While classic signal processing theory emphasizes the Nyquist limit which states the the sampling rate need only be twice the frequency of the highest spec tral component of interest this assumes an ideal analog lowpass filter preceding A D conversion and ideal reconstruction of the digitized signal However in practice the highest quality sampling is obtained by using a high sample rate in the A D converter and this is the approach that Plexon neural data acquisition systems have always taken in using a 40 kHz sample rate The fixed analog anti aliasing filter in the DigiAmp is a four pole Bessel with an 8 kHz cutoff so in practice this means that a 40 kHz sample rate yields an oversampling factor of at least four and greater for lower spectral components of the neural signal This results in accurate capture of the time voltage waveform samples which is important for time domain spike sorting algorithms template line band and box sorting which reply on relatively small differences in spike shape to perform unit discrimination In addition the high sample rate preserves the shape of clusters in PCA feature space which 1s importa
76. ain a clean audio signal Most PCs have both front panel and rear panel audio input and output jacks and you can use whichever is more convenient However in rare cases you may find that one or the other provides a noticeably cleaner audio signal than the other and using that output will make working with the test wav file easier 19 1 OmniPlex System Overview and Startup 1 6 Step by Step Starting and Configuring OmniPlex Server 20 OmniPlex Server is the first of the two primary software components of OmniP lex Server is the engine which receives data from hardware devices sends commands to them and contains the topology network of software modules which perform filtering thresholding sorting and other signal processing func tions Once Server has been configured for your hardware which may have already been done by a Plexon Sales Engineer you will probably find that you spend relatively little time interacting with it since the main user interface to OmniPlex is provided by PlexControl which will be described later 1 From the Windows desktop double click the OmniPlex Server shortcut 2 If a system topology configuration diagram similar to the one below is displayed wait for the green progress bar at the bottom of the Server window to finish proceed directly to Step 15 If you do not see a topology diagram continue to Step 3 perform Step 3 through Step 15 for the instructions for using the Topology Wiz
77. al maxima or minima values in the SPKC snapshot The horizontal axis represents amplitude but in terms of standard deviations sigmas on either side of the mean Note that since the default options for SPKC snapshots are to perform an auto threshold after the snapshot is collected and the default auto threshold is placed at 4 sigmas there is a blue line representing the automatically set threshold expressed in terms of sigmas rather than percent In short the basic idea behind using the peak histogram is that for typical signals there will be a large peak in the histogram centered on zero sigmas which corre sponds to the noise in the signal this is because spikes represent a relatively small percentage of the total duration of the SPKC signal so noise samples will OmniPlex Neural Data Acquisition System Version 1 8 tend to be predominant in the distribution By setting the threshold at or beyond the point where the shoulder of this distribution has its first clear discontinuity we reduce the chance that noise will be incorrectly detected as spikes Outside of the central noise peak significant peaks in the histogram such as the very prominent one centered at approximately 8 sigmas in the example usually represent spikes You can see how the section of the histogram between approxi mately 3 sigmas and 5 sigmas is probably the sum of the tails of the central noise distribution and the distribution that is centered at 8
78. anges to the thresholding parameters before proceeding to set up spike sorting If in doubt as to a good waveform length you should make the waveform length no longer than necessary to capture the main features of the spike shape as seen in the main spike window Long waveforms gt 1000 microseconds should be avoided in most cases TIP Waveform length and pre threshold cannot be changed during recording Since you must first stop data acquisition note that this also means that the waveform length and pre post threshold intervals cannot be changed during a recording or while online client programs are read ing live data from OmniPlex Dead time Some thresholding algorithms such as the one in Plexon s Offline Sorter have the concept of dead time which 1s an interval of time after each spike detection during which a thresholding algorithm ignores subsequent threshold crossings Currently OmniPlex does not support a nonzero dead time That is on the next sample point after the end of an extracted spike the thresholder starts scanning the continuous spike signal for the next threshold crossing If the next threshold crossing occurs within the next few samples after the end of the previous spike it is possible that the pre threshold interval of the second spike will overlap the last few points of post threshold interval of the first spike If this causes problems 93 3 Spike Detection either in spike sorting or in your data
79. ard to configure your system eer oa Wait ark FH he l H cha e F n maaga E mmo a Ce amieta sig Pei oll a Le Sra pea ea dia tiran IETS OmniPlex Neural Data Acquisition System Version 1 8 3 4 You can use Server s Topology Wizard to specify the basic configuration of your system to OmniPlex To do so click on the Topology Wizard button in the toolbar rpi OmniPlex Server opxDm G1 b4wb 32ai pxs Topology Wizard Trodality Single electrode 0 Stereotrode E Tetrode T o Stereotrode Mixed single stereotrode Mixed single tetrode Tetrode Mixed single stereo tetrode 0 Pass through M Auxiliary AT card Referencing split O Spike referenced Pass thru voltage divider T oe DigiAmp HST Gain Additional Device Clients G1 Global filters 620 CinePlex interface 21 1 OmniPlex System Overview and Startup 5 In the A D Device section click on either the DigiAmp256 button if you have a big DigiAmp or the DigiAmp64 button if you have a Mini DigiAmp The numbers 256 and 64 refer to the maximum capacity of the two types of DigiAmps not necessarily to the number of channels present in your system A D Device 6 In the Channel Counts section enter the total number of actual channels in your DigiAmp in Total A D Chans A Mini DigiAmp has from 16 to 64 channels with 16 channels per board a big DigiAmp ha
80. are saved in a file with the extension pxs It will display an automatically generated and appropriate name for example opxDm G1 64wb 32a1 pxs Version 1 8 23 1 OmniPlex System Overview and Startup 24 Save in L p Recent Places Libraries L Computer Network PlexonData Name _ opxD G1 256wb 32a1 0001 pxs _ opxD G1 256wbtet 32al pxs _ opxD G1 256wb 32a1 pxs _ opxA 64wb 32ai 2 pxs _ opxA 64wb strobedDI pxs _ opxA 64wb pxs __ opxDm G1 64wb 32ai pxs _ opx4 lowbtet pxs _ opxD G1 256whtet pxs _ opxD G1 256wb 32ai20kHz pxs _ opxD G1 256wb 32ai5kHz pxs _ opx cpx 32ch 31lwb 1direct pxs 4 1 File name Save as type opxDm G 1 b4wb 32ai pas OmniPlex Server Files pxs ka t em Date modified 1 14 2013 4 56 PM 12 20 2012 4 31 PM 12 20 2012 1 57 PM 12 19 2012 7 08 PM 12 19 2012 2 02 PM 12 19 2012 2 02 PM 12 7 2012 6 24 PM 12 5 2012 3 38 PM 12 5 2012 4 35 PM 11 30 2012 2 44 PM 11 30 2012 12 28 11 29 2012 2 29 PM Click Save to accept the default filename and save the pxs file 11 Server will display a message box OmniPlexServer Type PAS File F PXS File PXS File PAS File PAS File PAS File PAS File PAS File PAS File PAS File PAS File PAS File A Please close and restart Server to make the new topology take effect OmniPlex Neural Data Acquisition System 12 Click OK 13 Close Server 2X
81. as from zero you can adjust thresholds manually as described in the next section OmniPlex Neural Data Acquisition System 3 4 Step by Step Adjusting Thresholds Manually There are several different ways that you can manually set or adjust the threshold on a channel e changing the numeric value of the threshold in the properties spreadsheet e changing the numeric value of the threshold in the per channel properties view e dragging the blue threshold line in the SPKC view e dragging the blue threshold line in the single channel spike view e dragging the blue threshold line in the SPKC snapshot peak histogram view Each of these methods will be described below 3 4 1 Changing the value of the threshold in the properties spreadsheet 1 1 Click on the threshold cell for the channel you wish to adjust An edit cursor appears in the cell and up down arrow controls are displayed i300 tne rere remo wm Unis i pye 2 Click the up down arrows to adjust the threshold in increments of 1 or directly edit the numeric value TIP 9 Double clicking to edit numerical value ay If you double click on the numeric value everything but the minus sign if present will be selected and you can type in a new value which will replace the old value 3 To set several successive channels to the same threshold value set the first lowest numbered channel to the desired value
82. ata Acquisition System 185 F Additional Features and Procedures 7 1 Step by Step Saving and Loading PlexControl Settings 1 At any time you can save the settings of all parameters in PlexControl gain thresholds sorting parameters etc to a settings file so that you can restore them later To do this simply click the Save button in the toolbar z PlexControl PlexControll Save As Ji PlexonData 02 em T Mame Date modified Type tn y Unspecified 453 Recent Places _ increasing thresholds 256 pxc 3 12 2013 5 00 PM PXC File _ test256 24 pxc 3 6 2013 6 53 PM PXC File _ def008 pxc 2 28 2013 3 45 PM PXC File _ def007 pxc 2 28 2013 3 45PM PXC File _ def006 pxc 2 26 2013 3 44 PM OPAC File _ def005 pxc 2 28 2013 3 44 PM PXC File _ def004 px 2 28 2013 3 37 PM OPAC File _ def003 pxc 2 28 2013 3 37 PM PXC File _ def002 pxc 2 28 2013 3 31 PMs PAC File _ def001 pxc 2 28 2013 3 31 PM PXC File od 24 prec 2 28 2013 12 57 PM PAC File 4 File name QuickStart Demo pac Save as type PlexControl Files pec Note PlexControl settings files have the extension pxc 2 To load a previously saved pxc file you can use either the Open or Open Most Recently Saved buttons in the toolbar PlexControl PlexControll 7 PlexControl PlexControll CF 186 OmniPlex Neural Data Acquisition System Note that you must stop data acquisition before loading a pxc file and
83. begin the snapshot collection SPEC Continuous i P RED as Ae nt Mag 2 00 a ARAA TOLE los R pm Start Forward Snapshot Collection All Channels om 5 rman T mem dE A N i EE W Continuous 75 3 Spike Detection 6 76 While the snapshot is being collected by default for 10 seconds the Start Forward Snapshot button changes to the Stop Snapshot Collection button a stop sign Do not click the button or the snapshot will be aborted E Cote Z Sy EH Mag 20 gt AATIE Stop Snapshot Collection All Channels ff a TIT IN TT ied WE Continuous SPEC Continuous Ex 2PKC Channel 1 Peak Histogram Also note that while the snapshot is being collected the status bar at the bot tom of the main PlexControl window indicates that continuous snapshot col lection is in progress r AAG Firing Rates Collecting Continuous Snapshot Drops 0 OmniPlex Neural Data Acquisition System 7 Once the collection has completed the status bar shows that analysis of the continuous snapshot Is in progress in this case the analysis consists of the auto thresholding 15 00 mi l Activity fA Firing Rates E Analyzing Continuous Snapshot Drops 8 When the status bar no longer shows Analyzing Continuous Snapshot the auto threshold operation is complete To view the newly set threshold values select the Properties Spreadsheet tab under the multichan
84. bering for continuous channels c sccceseeees 123 o Ef OmniPlex Neural Data Acquisition System 115 5 Recording 5 1 Overview 9 1 2 116 Once you have configured OmniPlex for suitable gain thresholds and spike sort ing parameters you will eventually want to record your data OmniPlex can record data from any or all of its sources to a recording file in either or both of two Plexon file formats PLX format PLX format is an industry standard recording format originated by Plexon in the 1990s It is supported by many applications including Plexon s Offline Sorter NeuroExplorer and used by hundreds if not thousands of custom Matlab scripts and application programs written by users An enormous amount of neurophysio logical data has been recorded by hundreds of labs around the world in PLX for mat PLX recording is supported for legacy use for those cases where an application does not yet support reading PL2 files PL2 format PL2 is Plexon s next generation file format It can contain all the same informa tion as a PLX file including the exact same sample values but it is an extensible format that supports the OmniPlex concept of sources and allows for new types of data to easily be added In addition PL2 addresses certain performance prob lems that PLX can exhibit when working with large amounts of continuous data for example when recording wideband WB or continuous spike SPKC chan nels In such
85. ble Automatically save pxs when recording ends Global Options Automatically load the last used pxs file on startup Automatically save pxs when recording ends same name as plx or pl Show verbose log messages Datapools DO NOT MODIFY 16384 Main 2048 Private Click OK In PlexControl select Global Options from the Configure menu me PlexControl PlexControll Auto Configure All Sources Cancel Auto Confioure Version 1 8 189 F Additional Features and Procedures 190 5 Select the Recording Files tab and enable Auto save pxc Global Options Recording Files Recording Control Data Directory D PlexonData When Start Recording is Pressed File Name generation Open Data File Dialog Prefix dat Begin Recording Immediately Date None File Types to Record E Specify next sequence number pk File Onby 6 pk File and pl File i a pl File Only Next sequence number 1000 et When Recording Ends Auto save pec same name as ple or pl2 Now each time that you record a plx file the current settings in Server and PlexControl will automatically be saved as XXX pxs and XXX pxc where XXX is the name of the plx file In this scheme for each plx file you record PlexControl will create three files with the same name but the extensions plx pxc and pxs If you later wish to run another experiment using the same set tings as a pre
86. cedure L Desktop Window Ma OmniFlex Sereer Ag ph Intemet Explorer Intemet Explorer NT Kemmel amp Syitem Windows Explorer Hast Process for Win Application Web Serv Sysbem Web Server Du Stereo Vision Coniral Client Serwer Runtime Windawes Task blana AdFendet Intemet Explorer Intemet Explorer Local Security Author Hait Foces for Win Windows Wordpad amp COM Surrogate Hack Process for Win Blew ontral Aplicatia Host Frooess for YWAN Host Process Por Win Windows Media Player Hart Procecs for Win Services and Controll Acalray InstallShield Update Client Server RUA Men E ooo CPU Usage 100 Meoimum Frequency status Running Running Running Funning Running Running Running Running Rumning Running Running Running Rumning Running Running Running Runnireg Terminal Running Running Running Running Running Running Running Running Running Burning Rum ning Running Running Running Running Running Running Running Threads 9 7 19 23 30 5 39 g4 1933 33 ka L w oo hu D i H he Lo m Search Handles ci a overage CFU 0 24 O35 D13 T10 a0 O06 006 003 a03 003 103 O02 102 O00 0 00 TOG 000 PR ooo 250 gan ooo 0 00 000 O00 O80 060 0 00 0 00 060 000 200 00 060 0 00 2 00 mo ee oo a e E m e e e E E EE a oo CO Oo E a a amp CPU Total 60 Seconds Serioze CPU Usage
87. ch this helpful consolidation is not possible e g one that is not downstream from the DigiAmp when you want to change the gain you will need to explicitly select a source for which the desired properties can be set by clicking on a view that contains that source Properties for upstream and downstream sources In the larger multichannel Properties Spreadsheet described later you will see that the same helpful consolidation and display of cer tain properties for upstream and downstream sources is performed You can also select sources channels and units by using the Previous Next Source Channel Unit arrows in the toolbar qaa ynn As you repeatedly click the Next Source button right arrow S you will see the Properties view step through all of the sources in the topology Similarly the Previous Next Channel buttons will step through the channels within the 39 1 OmniPlex System Overview and Startup 40 current source Selecting a source or channel never changes any properties of that source or channel it only highlights that source channel in the displays and causes its properties to be displayed If you do not see WB in the bar just below Properties this is probably because you previously clicked on a view that is displaying a different source To cause the Properties view to show the WB properties simply click on the WB tab in the lower right window so that it is the currently selected source
88. chan nel at the time when 500 spikes have been collected on that channel depend ing on the firing rates some channels will complete their snapshot collection before others A snapshot consisting of 10 seconds of spikes on each of 64 channels depending on the firing rates some channels will have more spikes in their snapshot than others Snapshots are useful purposes such as determining the statistics of a continuous signal for use in auto thresholding or for capturing a set of spikes for use in man ual or automatic spike sorting When you are manually defining units for spike sorting as described later you can define the units either directly on the live animated data or on a static snapshot which you use is a matter of preference and of the dynamics of the incoming data You can capture a fresh snapshot at any time and the snapshots for different sources e g SPKC versus SPK are independent for the most part 69 3 Spike Detection 70 TIP Forward and backward snapshots For performance reasons OmniPlex only allows a forward snapshot to be taken of continuous sources You can think of a forward snap shot as a command to start collecting continuous data for the snap shot starting now and going forward for the duration of the snapshot e g for the next 10 seconds On the other hand a spike source SPK can have either a forward snapshot or a backward snap shot A backward snapshot is in effect a comman
89. cording 122 14 15 16 recording As recording starts the Start Recording cursor is disabled and the Pause and Stop Recording buttons are enabled me PlexControl PlexControll File View Display Configure Data Winga thts Help LD oe bh amp 2 ANT Tasks a ki In addition the file size and time indicators in the status bar appear in green ram Snapshot ied Continuous mt Activity Al Firing Rates Frames 1 This indicates the recording status recording versus paused filename cur rent file size and elapsed time If you click the Pause button while recording the status bar changes its display apshot Ried Continuous hed Continuous BG Activity W Firing Rates Frames 1 Drops 0 Note that the first time figure now shows the total elapsed recording time while the second figure shows the total elapsed clock time since the start of the recording whether paused or recording If you now click the Pause button again recording resumes The Frames count in the status bar indicates how many separate frames segments of data have been recorded in the file so far r 13 00 m NUDUS ited Continuous Bul Activity A Firing Rates OmniPlex Neural Data Acquisition System 5 2 1 Version 1 8 17 When you wish to complete the recording and close the recording file click the Stop Recording button in the toolbar PlexControl PlexControll File View D
90. ctangle being dragged by a normal arrow cursor instead of dragging the tab you can cancel this by hitting the ESC key and then releasing the mouse button 56 OmniPlex Neural Data Acquisition System Once you have adjusted the size of the views to your liking the three most common viewing adjustments that you will make for continuous data are changing the magnification vertical scaling the sweep rate and the number of channels displayed in a view 2 3 1 Changing the magnification Version 1 8 In OmniPlex magnification refers to the vertical scaling of the contents of a view usually either continuous signals or the waveforms of detected spikes It does not affect the data itself only your view of it You can change the magnifica tion by either typing a new magnification factor into the Mag value in the tool bar by clicking on the up down arrows to the right of the magnification value or by clicking on the MAG 1 button to restore the magnification to 1 0 SPEC Continuous lt Be Ae SEE BBY Mag 1 00 PX AT View Magnification Factor WIRE SPEC Continuous LA Fee SD ope Ae SRT BT Mag 2 00 2 R amp tT e LES 1s T am a SPEC Continuous P PRE GD IS Ac OFT PBT Mag 1 00 SRST LE Gs 5 1 0 S TT LL et eset Magnification 1m iT If you double click within one channel s display area within the view which expands it to fill the entire vie
91. d to use the last N seconds or N spikes of old data as the snapshot A backward snap shot is useful in that you see the data that will be captured for the snapshot then capture it in comparison when you start a forward snapshot you have yet to see the data that will be collected for the snapshot Also backward snapshot can be taken instantly whereas you must wait for a forward snapshot to be collected Forward and backward snapshots only differ in how the data is collected once the snapshot has been taken by either method there is no difference in the way it is used TIP Collecting a snapshot for an individual channel You can also collect snapshots for individual channels one at a time by collecting a snapshot in a view where only a single channel is dis played as opposed to in a multichannel view Details of this will not be discussed here Usually you will want to take a snapshot of all the channels in a source at the same time The most common use of the continuous snapshot is to automatically set the thresholds that are used for spike detection as described in the following sec tions Using snapshots for spike sorting will be described in a later section OmniPlex Neural Data Acquisition System 3 3 Step by Step Using a Continuous Snapshot to Set Thresholds Automatically 1 If it is not already visible click the SPKC Continuous tab to display the continuous spike signal If only one channel is displayed double c
92. des Rolling and Erase Waveform Display Options E S z Columns 1 Zoom with Chain Arrange Channels in Riow Major Order Show Channel Number Labels Allow Toggling to Show Snapshot When Zoomed Magnification F show Threshold 17 Show Sort Range Adjust Automatically F Show Slice Positions Use Same for all Channels Show Time Voltage Grid E Chain Control Drawing Waveforms Drawas Lines Points Thickness 1 Interpolate main display current channel Update Mode for Live Data Fade Fade Rate Slow Fast Roling Fade and Rolling Modes showing most recent 500 waveforms E Erase Every 10 secs H Erase Erase Mode Standalone Master Slave Appendix Page 18 OmniPlex Neural Data Acquisition System Version 1 8 In Rolling mode the most recent 500 waveforms the same number of waveforms as in snapshot are displayed older waveforms suddenly disappear as opposed to fading out This mode gives every one of the recent waveforms equal visual weight In Erase mode incoming waveforms are drawn on top of each other with no fad ing or rolling until the specified erase time elapses at which time the window is erased and the process starts over from scratch When using Erase mode be aware that while very old waveforms may not be erased from the screen only the most recent 500 spikes are available for interactive operations such as waveform crossing Just as with the other two modes In other
93. device must remain within a limited range of AIGND 11V absolute max This will typically be the case when the signal source is an instru ment that is powered from a wall outlet using a three prong plug but may not be the case for instruments with special isolated outputs and will not be the case for instruments that are battery powered and not connected to ground in any way In order to record signals from such floating instruments it is necessary to pro vide them with a ground reference to the auxiliary I O panel To accomplish this each D sub connector has a jumper block associated with it that allows you to select one of two configurations SENSE default or GND When the jumper is put in the GND position the AISENSE input and connector pins 20 35 for that group of channels become connected to AIGND One of these AIGND pins can then be connected to the floating instrument to ground it Removable 3 3 kQ pull down resistor packs were added to the analog inputs in Revision A of the AuxAI breakout panel In the absence of these pre Revision Appendix Page 50 OmniPlex Neural Data Acquisition System A when a signal was connected to one analog input and adjacent analog inputs were left floating the applied signal typically also appeared on the floating chan nels This is a normal consequence of the multiplexed analog to digital converter in the auxiliary I O card The multiplexer has a small amount of capacitance and during the
94. double click on the zoomed in single channel it will revert back to the multi channel view Before proceeding make sure the view is zoomed in on channel 1 as shown above TIP Understanding zoom and magnification For historical reasons the OmniPlex term for this display mode where only a single channel expands to fill an entire view is zoom Later we will describe magnification which is the OmniPlex term for viewing a display at varying degrees of enlargement for exam ple 1 5 times larger 33 1 OmniPlex System Overview and Startup 34 2 If the wideband signal looks like this where it exceeds the allowable maximum amplitude in either the positive and or negative direction WE Channel 1 Continuous POO R Nl i WBC fa WB Channel 1 Continuous Continuous Fl Peak Histogram Snapshot Peak Histogram Snapshot sd ied W Continuous This is referred to as clipping This situation occurs either when the analog gain is set too high or in an artificial situation when using PC audio as a test signal where the audio output can produce such a high amplitude signal that the voltage divider built into the HTU or noseboard is not enough to reduce it to a reasonable level You should only rarely encounter a situation in an actual experiment where using a unity gain headstage G1 with the lowest DigiAmp gain setting of 50 still results in a clipped wideband signal If you see clipping as
95. ds the latter will be discussed later in this User Guide Automatic unit finding cannot be used with line or box sorting OmniPlex Neural Data Acquisition System 6 8 Step by Step 2D Polygon Sorting In the same way that line sorting uses the technique of waveform crossing to per form live sorting of spike waveforms 2D polygon sorting uses 2D PCA contours to perform sorting of the projections of spikes in PCA feature space Since you already know how to draw PCA contours in live and snapshot modes you know almost all the steps involved in 2D polygon sorting The main difference is that the contours you draw will be used directly as the actual unit definitions You can define units for polygon sorting in either live or snapshot mode for the examples we will use live mode 1 Stop data acquisition change the sorting mode to 2D Polygon and restart data acquisition SPK Source 6 On Device Basic Sorting Channel Type Spike Channels 64 Channel Grouping Single Enabled Record Enabled Fi sampling Freq 40000 Gain 250 Waveform Length a00 FPre Threshold 200 Sort Start 0 Sort End 800 sort Method 2D Polygon Channel 1 on SPK 50 Template Name Line Enabled Box Record Enabled Band Threshold 2D Polygon x 2 Set gain and thresholds if not already set appropriately and collect a spike snapshot 3 Perform steps 1 through 5 from the section Step by Step Defining Units for Template Sorting using PCA Contour Drawing
96. e As Remove Device 200 Lowpass cutoff freq Hz Filter type Downsampled rate Hz Filter parameters in detail The three parameters which are available for the spike and FP separator filters are e Cutoff frequency defaults to 200 Hz for the FP lowpass and 300 Hz for the spike highpass e Number of poles also known as filter order defaults to four poles for both filters e Filter type Bessel Butterworth or Elliptic In addition the downsampling rate can be specified for the FP separator note that this must be a frequency which divides evenly into 40 kHz e g 1 2 4 5 kHz The spike separator includes an optional lowpass filter which will be dis cussed later Appendix Page 6 OmniPlex Neural Data Acquisition System The number of poles affects the steepness of the filter cutoff You might think that the steeper the better but using very high order filters can cause problems due to frequency dependent group delay of field potentials and spike waveform shape changes However Plexon s FPAlign offline utility 1s available for remov ing phase shift and group delay induced by the FP filters see the FPAlign docu mentation for more information In general it is recommended that you not go beyond the four pole default settings unless you find that they are inadequate for removing spikes from your FP signal or low frequency content is leaking into the SPKC signal The Filter Type setting defaults to B
97. e PCA projection TIP Understanding snapshot mode vs Pause Don t confuse snapshot mode with pausing the live display using the Pause button in the main toolbar You must collect a spike snapshot which is a sample of the live data whereas pause mode simply freezes the live displays but does not collect a snapshot You might wonder why you would want to work with the snapshot since it con sists of old data This is true but the trade off is that it can be easier to define units with respect to a fixed set of data that 1s not constantly changing and redrawing from second to second In many cases spike shapes are quite stable over fairly long periods of time so the old data issue is not a significant prob lem Also you can take a new snapshot which will overwrite the previous snap shot at a later time if you wish OmniPlex Neural Data Acquisition System 6 6 Step by Step Defining Units using Spike Snapshots 1 Click Show Snapshot in any of the spike or PCA views to toggle all the spike and PCA views into snapshot mode The spike views display the spikes in the most recently collected snapshot the PCA views show the PCA projection of the spikes in the snapshot CE NAP Se ox pe View Dkpley Configure Cyto Window fut Hep i Ml 8 OB t uwani oare AN el ce a ete stow aver AB marca ANK i SPE Channel Wietomns Snapshot p IBA Mag 170 5 3 Syvten 2 s E S Crest Autom bad stort t Properties 0x
98. e chain Note that you will usually not want to enable Chain Control for a view displaying wideband WB data This is because the wideband and FP signals are usually of a larger amplitude than the spikes and so the spike views will typically use a higher magnification value than wideband or FP views You can use Chain Control and Use Same Magnification for all Channels in com bination for example if Chain Control is enabled and Use Same Magnification is 65 2 PlexControl User Interface disabled changing the magnification of channel 23 in the SPKC view will affect only the magnification of channel 23 in the two SPK views and vice versa TIP Understanding the source associated with the threshold ing device The observant reader will have noticed that the source associated with the thresholding device is not sent to the Main Datapool This 1s because it consists of unsorted spikes and the only use for those spikes is to serve as the input for the sorting device You can think of the source associated with the thresholding device as an internal source which can be safely ignored 66 OmniPlex Neural Data Acquisition System Plexon Inc Chapter 3 Spike Detection 3 1 Spike Detection by TITS SIOIIG siasssscesecavcancesnisscareqeaasnsnsxisensvaanneneasasarebacasinensvasneenseirensi 68 3 2 OMNIPEx Concepis Snaps hols ri a 69 3 3 Step by Step Using a Continuous Snapshot to Set Thresholds Automatically 71 3 4
99. e generation Open Data File Dialog Prefix dat Begin Recording Immediately Date File Types to Record E Specify nest sequence number Next sequence number 1000 phe File Only E pk File and pl File pl File Only When Recording Ends Auto save pec same name as ple or pl 120 OmniPlex Neural Data Acquisition System 9 You can also use the Data Directory field to set the folder to which files will be recorded Global Options When Start Recording is Pressed File Name generation Open Data File Dialog Prefix dat Begin Recording Date None hal 10 Click OK to save your changes Note that you do not have to set these options each time that you record a file and PlexControl will retain these settings each time you run it 11 When you are ready to begin the recording click on Start Recording in the main toolbar a PlexControl PlexControll _ eee gt SPE Cha Start Recording 12 The Start Recording Data dialog appears Start Recording Data Data File Options Data Directory O PlexonData plx Data File Name QuickStartDemo1oplx pl Data File Name File 1 pl2 13 Specify the name of the PLX and or PL2 files to record You can also enter a block of comment text which will be recorded in the file header you can use this for brief descriptive notes or archival information Click OK to start Version 1 8 121 5 Re
100. e of largest peak same side as threshold setting is recommended as shown above because typically you will set the threshold for a channel on the side where the larger amplitude peaks occur You must stop data acquisition before changing the thresholding mode Note that there is one other change which you will probably wish to make when using aligned extraction Due to the peak rather than the threshold crossing being used as the timestamp of spikes the ratio of pre threshold to post threshold time tends to be different when aligned extraction is used in other words a longer pre threshold time is appropriate As a typical example the default OmniPlex settings are a waveform length of 800 microseconds and a pre threshold time of 200 microseconds when aligned extraction is enabled it is suggested that the pre threshold time be increased to 300 microseconds Appendix Page 36 OmniPlex Neural Data Acquisition System Version 1 8 SPK Source 6 On Device Basic Sorting Channel Type Spike Channels d Channel Grouping Enabled Record Enabled Sampling Freq Gain Waveform Length Om start d Sort End 800 Sort Method 2D Polygon However the correct values for waveform length and pre threshold will be some what dependent upon the type and shape of action potentials that you are record ing You should ensure that the waveform length and pre threshold are long enough to capture the features of the spike without includi
101. eboard directly into the headstage connectors Be careful not to bend or twist the headstage connector pins when inserting or removing the noseboard press or pull the noseboard straight in and out not at an angle Each noseboard has four 32 channel connectors on it and can plug into either one or two 64 channel DigiAmp boards Version 1 8 17 1 OmniPlex System Overview and Startup 5b Connect a 1 8 stereo audio cable from the 1 8 line output jack on the front or back of the PC to the 1 8 input jack at the end of the noseboard If you have more than 128 channels you will need a second 64 channel noseboard and a splitter cable with a 1 8 stereo jack on one end and two stereo 1 8 plugs on the other end which will plug into the two noseboards 5c Set the Even Ch and Odd Ch jumpers on the noseboard s to the lowest position 50x Set the Ref jumper s to their highest position GND 18 OmniPlex Neural Data Acquisition System Version 1 8 Note You do not need to turn on the HST PWR switch when using the noseboards 6 Do not play any audio on the PC yet but open the Windows volume control or audio mixer and make sure that Line Out and Headphone out some PCs will only have one or the other output option are enabled not muted and set the volume to about half of maximum amp Volume Mixer Headphones High Definition Audio Device Applications A E Headphones System Sounds TIP Obt
102. eceeeeeeeeeeeeeseaeeeseeeessaeeees 42 Appendix J PlexControl Keyboard ShortCuts cccccccsssseeeceeeeeesseeeeeeseeeeeeeeeesaaaees 47 Appendix K Hardware PinoutsS and COnnections ccccccseeeeeeeeeeeeeeeeeeeeeeeeeeeeeens 48 o E OmniPlex Neural Data Acquisition System Appendix Page 1 Appendix Appendix A Signal Amplitudes and Gain Using the proper gain value is important since a too low gain will result in the signal being digitized with too few bits out of a maximum of 16 bits being used to represent the signal On the other hand a too high gain will cause some or all of the signal to exceed the input range of the A D converter and to be clipped resulting in the tops and bottoms of field potential waveforms to be flattened and spikes to be distorted or even lost entirely While very occasional clipping may be acceptable for example clipping of undesired stimulation or motion artifacts which greatly exceed the amplitude of the neural signal in general you should be careful not to set the gain any higher than necessary since clipping causes more damage to the digitized signal than digitizing it at a slightly lower than ideal res olution A common mistake with new users is to set the gain higher than necessary because the spikes look too small when the gain is kept at a safe value which avoids clipping the wideband signal This is partly because the amplitude of spikes is typically much smaller than
103. eform length to capture long complex action potentials or to decrease the length to avoid capturing an unwanted noise tail when the spikes are shorter 1 To change the thresholding spike detection parameters you must first stop data acquisition either from the main toolbar or the Tasks view a Plextontrol PlexControll File View Display Configure Doses of 2 Once data acquisition has stopped click in the Properties view at the left to change the Waveform Length and Pre Threshold a SPK Source 7 On Device Basic Sorting Channel Type Spike Channels 64 Channel Grouping Single Enabled Record Enabled a Sampling Freq 40000 Gain on Waveform Length 800 Pre Threshold 200 Sort End 800 Sort Method Template OmniPlex Neural Data Acquisition System 3 5 1 Version 1 8 The post threshold length is not editable as it is always the difference between the waveform length and the pre threshold time 800 200 600 microseconds in this example 3 To make the new settings take effect start data acquisition again PlexControl PlexControll File View Display Configs Window Run An lar r S F O Load the pxc file that was last used Note that changing the waveform length will invalidate a number of the spike sorting parameters for example sorting templates and PCA projections depend on the waveform length as described later so you will usually make any ch
104. elow the spike band The spike lowpass filter is intended for use in reducing high frequency noise The analog anti aliasing filter in the DigiAmp preceding the A D conversion stage 1s a four pole Bessel with a cutoff of 8 kHz if the spike lowpass filter 1s used its cutoff should be less than 8 kHz For exam ple a cutoff of 6 kHz will to some extent emulate versions of the Plexon MAP system which employed a 6 kHz analog filter before A D conversion The combi nation of the standard spike highpass filter plus the spike lowpass filter results in what is in effect a bandpass characteristic although you are not constrained to use the same filter type or number of poles for the highpass and lowpass filters The spike lowpass filter should only be used when necessary because excessive lowpass filtering of the wideband signal can result in spikes that are unnecessar ily smoothed off blurring the differences between the waveform shapes from different units and making spike sorting more difficult To see this effect you can try enabling the lowpass filter and setting a very low cutoff e g 2 kHz to get an idea of the potential issues If you believe your wideband signal has excessive Appendix Page 7 Appendix high frequency noise it is recommended that you use the least amount of lowpass filtering that is necessary to remove the noise starting with the default settings and only lowering the cutoff frequency and or increasing the filt
105. em Version 1 8 Much of the User Guide is applicable to both systems in particular digital filter ing thresholding and spike sorting are identical in both functionality and user interface The main difference from an operational point of view is that OmniPlex A has per channel analog gain control and corresponding software functionality for automatically setting gains whereas OmniPlex D has three global gain steps which are mainly intended for headstage gain matching and therefore gain tends to be more of a set and forget with the newer system 1 OmniPlex System Overview and Startup 1 3 Using the User Guide The sections containing step by step instructions are designed to get you started as easily as possible guiding you through typical OmniPlex tasks Therefore you will change very few of the default OmniPlex settings and options such as filter cutoffs sorting methods etc Once you are comfortable with the basics of using OmniPlex you can refer to the Appendix sections to learn about additional options and features that will allow you to use the full capabilities of the system and configure it for your particular experiments You should work through all the numbered steps in the Step by Step sections to acquire a basic proficiency in using OmniPlex Sections marked as OmniPlex Concepts cover background material that you will find useful in understanding the why behind the how to of each section of
106. en described so far using template or line sorting to sort spikes using their time voltage values 1 e the raw sample values OmniPlex also has support for working with spikes in feature space By feature space we mean a low dimensional coordinate system into which raw spike data is projected in a way that emphasizes some useful property The fea ture space approach treats each spike waveform as a single point in a high dimen sional space e g a 32D space for a 32 point 800 microsecond spike where the coordinate in the first dimension 1s the amplitude at the first sample point the coordinate in the second dimension 1s the amplitude at the second point and so on Working directly in such a high dimensional space is generally difficult and computationally intractable and so what is called dimensionality reduction is applied The idea here is that we want to project each point in the high D space into the low D feature space where we can view it and work with it more effi ciently For the purposes of spike sorting we would like the projection to cause spikes of similar shape which originated from the same neuron that is a unit to form clusters of points in the low D feature space A standard feature space 1 e projection method that is used for spike data 1s principal components analysis or PCA A full treatment of PCA is beyond the scope of this User Guide but it is a linear projection whose key property in terms of spike sorting 1s
107. ent Latency RASPUTIN Emulation Options Channel Mapping Server Emulation Enabling Server Emulation will allow RASPUTIN online dients access to the data Enabled MMF Size 64 MB Only send continuous data with sampling rate less than or equal to 40000 Save the pxs file shut down and restart OmniPlex start data acquisition then run any client programs as usual Client considerations for lowest latency operation Version 1 8 Note that Minimize client latency can result in over 2000 Server synchroniza tion events per second being sent to all client programs in order to update clients rapidly Client programs must be designed to handle this high an update rate For example a client which redraws its entire user interface or complex graphical displays on every update will probably use excessive CPU and quickly fall behind the incoming data stream Typically clients will need to perform only the necessary low latency processing such as controlling a neural prosthesis stimu Appendix Page 43 Appendix lator etc on each update but perform UI and display updates at a lower rate e g 10 60 Hz possibly on a separate thread Consult the Plexon Client SDK docu mentation for more information on writing real time clients Performance issues in lowest latency operation In addition enabling Use lowest latency in the DigiAmp options will increase the CPU usage of OmniPlex although it will still remain with
108. er to the main spike window SPK Channel 1 clusters Ar Mn E 2S S f Unit b Fit Tol 0 031 J Parzen Mult 0 7 ee ES Increasing the template fit tolerance has the effect in the PCA display of expanding the area of the clusters which consists of sorted spikes while decreasing the tolerance has the effect of shrinking the sorted area Since there is not a one to one correspondence between the results of a tem plate sort and the results of testing PCA points for containment in a 2D con tour you may notice that a few points around the edges of a PCA cluster remain unsorted While this can be considered a form of beneficial outlier rejection if you wish you can increase the template fit tolerance slightly to in effect expand the area of the cluster that will be sorted so that the template sorting more accurately corresponds to the contour your drew However increasing the tolerance too much can result in spikes in nearby clusters being incorrectly sorted as in this example where the green unit s tolerance is too large and green spikes are appearing well outside the desired cluster OmniPlex Neural Data Acquisition System PPARs GD pea cA ort PS Unit b Fit Tol 0 116 9 Note that if you wish you can define another new unit on the same channel by waveform crossing instead of PCA if you do so you can then use the PCA window to monitor the results of the sorting in PCA space adjust the fit tolerance etc
109. er order with cau tion When you save the pxs topology file in Server the current settings of the spike and FP separators are also saved in the file Appendix Page 8 OmniPlex Neural Data Acquisition System Appendix C PlexControl Spike Display Modes PlexControl s user interface provides a number of display modes and options which are designed to make it easier to view the incoming spikes define units and adjust sorting parameters These include the Show Filter Show All Show Current Unit and Fade Rolling Erase modes Spike Show Filter The Spike Show Filter is not a filter in the sense of signal processing it is an option which filters which types of spikes are displayed in PlexControl It does not affect the actual sorting or recording of data To see the available Show modes click the down arrow in the Show Control in the main toolbar in St gt em i mp Show Al e Naveforms _ ray Selected Unit Sel Unit Unsorted Version 1 8 Appendix Page 9 Appendix The Show options affect the main spike window and the multichannel spike win dow but not the Units window The default 1s to display All spikes We will leave the All Valid setting for later Choose the Sorted setting to display only spikes that are sorted 1 e that match one of the templates atyp orgaan Se a a op Show Sorted A SPK Channel 1 Waveforms 2M SPK Waveforms St 4 Bet rE GD A Mag 1 70 2 ort
110. erent ways in which you can modify the results of the automatic unit finding process You can adjust template fit tolerances for any of the found units just as you would for templates that were created manually However this assumes that the automatic unit finding located an appropriate number of units based on its default settings which was the case in the above example where it found the same three units that we would have defined manually However depending on your data you may decide that the automatic procedure was too sensitive e g unnecessarily split one cluster into two or more units or was too coarse i e inappropriately merged two or more separate clusters into a single sorted unit To address these issues the automatic unit finding algorithm provides what is in effect a unit finding sensitivity control called the Parzen Multiplier which is a parameter of the underlying valley seeking algorithm SPR Channel 1 Clusters Snapshot a EE 2 PCA lt SRT G A E w amp Unit c Fit Tol 0 040 Unlike the fit tolerance which is a unit definition parameter that can be adjusted retroactively i e after a unit template has been defined the value of 165 6 Additional Sorting Methods 166 the Parzen Multiplier is used the next time that automatic unit finding is per formed In other words if you wish to change the value of the Parzen Multi plier you must then perform another round of automatic uni
111. erties spreadsheet for Other events Name PLX chan When a port is configured for mode 3 the value of the 16 bit strobed word itself is only read when the strobe becomes active and changes on those 16 input pins are ignored at all other times Ports A and B can be independently configured for mode 1 or mode 3 in any combination The only caveat is the following If both ports are configured for mode 3 there is still only one strobed event channel to represent the strobed events from both ports This is handled by using the most significant bit bit 16 to indicate which port the strobed even originated from If the strobed event is from port A the high bit will be 0 if from port B the high bit will be 1 This is done by OmniPlex only when it sees that both ports are in mode 3 and means that the signal sent into the 16th bit on the front panel connector will be ignored over written in this case Analysis of the strobed event words in other applications Matlab scripts etc must use the value of the high bit to determine which port each strobed word is from Digital event rasters ticks can be viewed in the Activity view in PlexControl See the section PlexControl Activity Display on page 7 198 for more informa tion When you save the pxs topology file in Server the current settings of the DI card are also saved in the file See Appendix K Hardware Pinouts and Connections for details on the physical pin assig
112. essel for both filters for the following rea sons Bessel filters induce the least amount of frequency dependent time shift group delay so that the time domain relationship between spikes and field potentials 1s preserved Also for spikes Bessels cause the least change to the shape of spike waveforms by comparison Butterworth filters cause more over shoot and Elliptic also known as Cauer filters cause even more shape distor tion Bessels are therefore the most benign filters to use for spike FP separation However the other two filter types have advantages in some situations Butter worths have a maximally flat amplitude characteristic in the passband so if the relative amplitude or power of different FP spectral components is of primary interest you may wish to use a Butterworth filter for the FP lowpass filter Also note that for the same number of poles and cutoff frequency Butterworth filters have a somewhat sharper frequency cutoff characteristic than Bessels Elliptic filters have the steepest cutoff behavior at the expense of more severe group delay variation and spike shape alteration You should only use an Elliptic filter when it 1s difficult to achieve adequate spike FP separation using the other filter types Spike lowpass filter Version 1 8 The Spike Separator also has an optional lowpass filter This 1s not the same as the lowpass filter which is used for FP separation which is used with a cutoff fre quency b
113. ex Neural Data Acquisition System 47 2 PlexControl User Interface 2 1 Overview 48 In Step 1 of Step by Step Setting the Wideband Gain you learned that double clicking on a channel in the WB Continuous view toggles the view between showing multiple channels and showing a larger view of just one channel In order to view the other continuous signals which we just discussed SPKC and FP it will be helpful to learn a few more things about the PlexControl user inter face Although the examples will focus on continuous signals most of this infor mation also applies to the other views in PlexControl such as the ones displaying detected spike waveforms After starting data acquisition and setting the wideband gain to a reasonable value as already described your PlexControl user interface should look something like this the spikes may look somewhat larger or smaller this 1s not a problem as long as they aren t clipping in which case you should reduce the wideband gain 2 Pee diacak Pee Pee Pee Pe F Ly a a ae J al ee r z 3 f PAF BRA SA a i EA i mni mane T i Cau ema BA T a oe ee ee eee fe If not select Create View Layout for Sources from the View menu or from the Tasks view at the upper left of the main window as described in step 2 of Start ing PlexControl In the default view layout PlexControl shows the following items in its views you will already be familiar with
114. f America Telephone 1 214 369 4957 Fax 1 214 369 1775 www plexon com Copyright 1983 2013 Plexon Inc All Rights Reserved Plexon Inc Proprietary The information contained herein is the property of Plexon Inc The information is proprietary and restricted solely to assist Plexon Inc customers Neither this document nor the contents may be disclosed copied revealed or used in whole or in part for any other purpose without the prior written permission of Plexon Inc This document must be returned upon request of Plexon Inc Information is subject to change without notice Plexon Inc reserves the right to make changes in equipment design or components as progress in engineering or manufacturing may warrant Document Number OPXMNOO001a Document Status Standard Software Version and Issue 1 8 Date April 2013 r LEXON
115. f data will begin unpause e When the RSTART line sees a false level by default a falling edge but this is also configurable recording of data will pause but the file will remain open for additional recording when RSTART goes true again e Clicking the Stop Recording toolbar button will finalize the recording and close the file Here are the corresponding settings that should be used Start Recording From GUI Only After Occurence s of an Event Source 11 CinePlex Data Channel Any Value 1 After U J0 10 Stop Recording From GUI Only E Ater Oecurence s of an Event Source 11 GinePlex Data Channel Any Value 1 After Stopping Allow Restart Recording to a New File Pause Recording 0 From GUI On Mter 1 Occurence s of an Event Source 10 Other events Channel RISTOP Value 1 Aft er 0 0 0 Resume Recording From GUI Onl Afer 1 Occurence s of an Event Source 10 Other events Channel RSTART Value 1 Note every Resume Recording starts a Frame In the file each frame of recorded data will be bracketed by Start and Stop events event channels 258 and 259 respectively 196 OmniPlex Neural Data Acquisition System 4 Here is a variation where instead of using level transitions on RSTART to pause and resume recording we use two separate single bit event chan
116. figure Fast updating requires restart use with caution on slower machines Allow saving pec during data acquisition use with caution at high channel counts E Only report drops during recording Always show live view not snapshot while autosorting entire source This will not affect any previously drawn contours only ones that you draw after enabling the option Click OK and note how subsequently drawn contours are replaced with ellipses as you finish drawing each one OmniPlex Neural Data Acquisition System Version 1 8 j Pa A ORT Be 4 aha ot Li ef E el E Parzen Mult 1 0 ga SPK Waveforms P SPK Channel 1 Clusters 30 3D Clusters Fey Properties SpreadSheet You can move and rotate these contours in the same way as previously described for the non elliptical contours Note that a heuristic procedure not a standard fitting procedure is used for the cleanup of hand drawn contours which gives an excellent fit in typical cases and a reasonable result even in pathological cases such as this one 177 6 Additional Sorting Methods SPK Channel 1 Clusters Snapshot IX SE l i Pca cA OFT AEB SE SPK Waveforms Sn B SPK Channel 1 Clus 3D 3D Clusters Properties SpreadSheet 178 OmniPlex Neural Data Acquisition System SPR Channel 1 Clusters Snapshot ww AX ZE SPK Waveforms Sn SPK Crane 1 Clus 30 3D Clusters Pro
117. from the right button menu Rec WB Rec SpkCont Set All Selected Channels Like Topmost Selected Channel Set All Higher Numbered Channels Like Selected Channel Select All Set Values for All Channels 5 Il Fi 6 Atthis point you could begin recording and by default the data would be recorded in PLX format However it is useful to be aware of some of the Version 1 8 119 5 Recording recording options that are available To view the main recording options select Global Options from the Configure menu PlexControl PlexControll File View Display a Configure ce le tel SP Gory ident Reset All Options to Defaults Auto Configure All Sources om Create View Cancel Auto Contfigure Sio Autormatical p 7 When the Global Options dialog is displayed click the Recording Files tab Global Options Saving and Restoring E Automatically Load pxc File on Startup unless Ctrl is held down when PlexCo Last Used pxc file Default pec file 8 In the Recording Files options page the File Types to Record section controls whether recordings are written in PLX format PL2 format or both formats in parallel You will usually want to choose one or the other format but the parallel recording option may be useful if you want to compare the two files e g for sizes and load times Global Options Data Directory D PlexonData When Start Recording is Pressed File Nam
118. g parameters in effect for that channel and outputs the result still on channel SPK001 which is sent to the Main Datapool 10 OmniPlex Neural Data Acquisition System For this example the same description would apply in parallel to the remaining 63 neural channels e g WB002 WB064 In other words the WB source con sists of 64 channels WB001 WB064 and similarly for the other sources Non neural sources such as digital input and auxiliary analog input sources send their data directly to the Main Datapool rather than through a chain of processing devices at least in the current version of OmniPlex Later you will see that the multi window tabbed user interface in PlexControl has windows or tabs within windows that display each of the sources Here s a preview JEn Mas Si Aai rag lage EA ay INRE AA Her wR n umuuj an oe eT nm aka A barad Frun TORA iAP Erria TR TITE Mag 1g Ee mg ee ee A Pe Pa Pah Pt Pa Pra Poe ba o aa SS 4 a i je pa a ir ere ae Fo aaia 4 Peet i a ri F ba F r k 6 Se r E i i a i i a 2r z ai F yA a ier k i y g i F im hf EE i CrN Bina Frs A aj ies a Pelt Pre Pa aiii p SeS k i A F nahr hT a Pa ii a a oa i Ti Lee fasted AP n AY pm nt Pe pan os F aa my ah F an ath gpw A F ie AAAA AAA AYA DAL WAN Rhyl yA th Praga VAIN AY NAAN ot ne y AAAA Ani If all this discussion about topologies devices and sources seems i
119. g the ESC key and then releasing the mouse button 51 2 PlexControl User Interface 52 3 Pa SPK Waveforms Fag Clust WE Continuous JS mh A Similar instructions apply for adjusting the width of a view in this case a vertical splitter dragging cursor will appear when you hover over the splitter bar between adjacent views and you can drag the splitter left or right B T Gsen Ea Geen r E Gen ken Geen ksen Ei a pe Geen Gsen Gen mag ana Remember if you ever have a problem with the window layout you can always do a Create View Layout for Sources to restore everything to the default layout OmniPlex Neural Data Acquisition System 2 3 Step by Step Using the View Toolbars and Options In addition to the main set of toolbars located near the top of the PlexControl main window several of the views have their own toolbars for accessing func tionality specific to each view These toolbars are hidden by default but can be easily toggled on and off For example in the upper right corner of a view displaying continuous signals 1 click the down arrow to display the toolbar WB Continuous Can Os 55 10s k z hii E E A E EA hh ha L i a 15 00 mv 15 00 mV Tt tt TT 15 00 mV TIP Double click to return to multichannel display When a view has the focus indicated by its title bar displaying in orange you can press the T key on the keyboard to toggle i
120. gital events if your digital sig nals are very noisy or have ringing on the edges this can produce redundant digi tal events If you suspect this is happening examine your signals on a scope to verify that they are not noisy and that they have clean edge transitions and make sure that proper grounding 1s used It is always a good idea to make a test record ing to verify correct connectivity and reliable acquisition of digital events before recording actual experimental data Auxiliary analog input card Version 1 8 See Appendix F Auxiliary Analog Input Aux AI for general information on using the AuxAI card with the OmniPlex software The AuxAI card provides 32 analog inputs which are by default sampled at a rate of 1 kHz per channel The 32 analog inputs AI 32 are divided into two 16 chan nel groups AI 16 amp AI 17 32 Access to these inputs is provided through two 37 pin D sub connectors as shown below Alternately AI 8 can be accessed through eight BNC connectors located in the center of the panel Care should be taken to only connect AI 8 in one location either on the 37 pin connector or on the BNC connector but not both Appendix Page 49 Appendix AIGND or SENSEI 20 AIGND or SENSEI 21 AIGND or SENSEI 22 AIGND or SENSEI 23 AIGND or SENSEI 24 AIGND or SENSEI 25 AIGND or SENSEI 26 AIGND or SENSEI 27 AIGND or SENSEI 28 AIGND or SENSEI 29 AIGND or SENSEI 30 AIGND or SENSEI
121. h 1s displaying a particular source for example an SPK channel within the multichannel spike view causes that source and channel to be selected and its properties to be displayed in the properties view at the left side of the window Also when you select a channel in any of the main sources WB SPKC SPK or FP the corresponding channel in all the other multichannel source views is iden tified with a colored rectangle For example selecting SPKO14 in the multichan nel spike view will cause channels WB014 SPKCO014 and FP014 to be highlighted as the current channel within each of their respective multichannel views However selecting a channel within a source which does not originate from the DigiAmp such as digital event DI channels and Auxiliary Analog Input AI channels does not affect the current channel within other sources Besides single clicking on a specific channel in any multichannel view to select it you can select a channel by double clicking on that channel s row in the prop erties spreadsheet The currently selected channel s row number is prefixed with gt gt in the spreadsheet You can rearrange the views and nest them within each other which causes them to appear as a row of tabs to customize the interface slightly or totally reconfig ure it See Appendix D Advanced User Interface Features for more details When first learning to use OmniPlex it is recommended that you not make major changes to the la
122. h the main spike window and the multichannel spike window Appendix Page 14 OmniPlex Neural Data Acquisition System Show All Show Current Unit When there are several units defined on the same channel by default their tem plate waveforms are all displayed on top of each other in unit editing mode gt SPK Channel 1 Waveforms IX i l Ei Est A Mag 1 70 Arj OFT a f cL o all You can change this with the Show All Show Current Unit button in the toolbar Version 1 8 Appendix Page 15 Appendix L K Channel Waveforms v A xX SPK Waveforms lAl et eee A Mag 1 70 jorr pag i aH RR E gt Unit d Fit Tol 0 038 Show Current Unit causes only the template for the currently selected unit to be displayed SPK Channel 1 Waveforms IX 4 Mag 1 70 A5 ont pBt E A A E Unit a Fit Tol 0 031 J Ao oa Appendix Page 16 OmniPlex Neural Data Acquisition System Fade Rolling Erase You may have noticed that in the main spike window after a few seconds spikes don t suddenly disappear rather they slowly fade away This is referred to as Fade mode and is the default display mode for the main spike window Version 1 8 Appendix Page 17 Appendix It is intended to reduce the visual clutter of old spikes and to make it more obvious which action potentials are the most recent ones The Options dialog allows you to select between Fade mode and two other mo
123. heet 174 OmniPlex Neural Data Acquisition System 6 You can rotate the contour by holding down the Shift key while dragging the handle E cor ch wa 1 Ch ct EHA Bet Bet GO Pca c4 aT PB OA Bi Parzen Mult 1 0 2 Ae H BE SPK Waveforms H SPK Channel 1 Clusters 3D Clusters FE Properties SpreadSheet The sorting parameters are updated i e sent to Server as soon as you release the mouse button Version 1 8 175 6 Additional Sorting Methods 176 6 8 1 Cleanup of hand drawn PCA contours There is an option which automatically cleans up your hand drawn contours by converting them to ellipses since clusters are often elliptical in shape this is a reasonable assumption To enable this feature display the Global Option dialog from the Configure menu and select the option Global Options oA Saving and Restoring E Automatically Load pxc File on Startup unless Ctd is held down when PlexControl is started Last Used pxc file Default poor file Persist View Layout and Per View Options to from poc File Disable Auto Gain Threshold PCA and Sot After Loading a pac File E Automatically begin Spike Snapshot collection on start of data acquisition E Adjust Threshold and Unit Templates with Gain Changes E Re collect Spike Snapshots and Re un Selected Analyses After Changes Gang together settings for channels within the same stereotrode tetrade Show status dialog while performing Auto Con
124. hen appear on un connected channels as described above Both analog input D sub connectors also provide access to power 5V and DGND that can be used to power external devices The total combined current drawn from the 5V terminals should be kept under 1 A Revision A auxiliary I O panels incorporate resettable fuses that will cut off the power 1f too much cur rent is drawn from the 5V terminals The most likely scenario of this happening would be if the power and ground pins were accidentally shorted The resettable fuses also called positive temperature coefficient devices or PTCs will reset after the overload condition has been removed and the device has cooled down AuxAl digital outputs Version 1 8 In addition to the 32 analog inputs the AuxAI card also provides up to 32 digital outputs depending on the model of AuxAI card installed Two 26 pin HDDsub connectors provide access to the 32 digital outputs DO 32 These digital outputs can be controlled using the PlexDO utility included with the C C and Matlab client development kits available from the Plexon website In the PlexDO utility DO 32 are referred to as bits 32 In future releases of OmniPlex the digital outputs may be used to provide addi tional functionality Appendix Page 51 Appendix Pin 1 Connector labeled DIGITAL OUT 16 Pin Function 1 DO1 Sl CO N l oO A j PO NO o_o D o1 O N
125. hot as a frozen segment of the SPKC data rather it displays the peak his togram for the snapshot data which is considerably more useful 1 Click the SPKC Continuous tab if you have not yet collected a snapshot for that channel you will see something like this i SPKC Channell Peak Histogram Snapshot _ Red WE Channel SPKC Channel 1 EH SPKC Channel 1 EA 2 Display the toolbar if it is not already visible and click the Start Forward Snapshot Collection button note that since we are only viewing one channel only that channel s snapshot will be collected le as 4 lt a Start Forward Snapshot Collection Channel 1 S WB Channel 1 8 SPKC Channel 1 EN SPKC Channel 1 S Continuous MM Activity Bl Firing Rates Version 1 8 87 3 Spike Detection 88 3 A progress bar is displayed as the continuous snapshot is being collected SPKC Channel 1 Peak Histogram Snapshot xXx EERS Sa WE Channel 1 R SPKC Channel 1 EN SPKC Channel 1 A Continuous Mj Activity fi Firing Rates t 534 387 Sec V 217 mV Collecting Continuous Snapshot Drops 0 4 When collection is complete the peak histogram for the channel is displayed SPKC Channel 1 Peak Histogram Snapshot xX EFTER Sl WE Channel 1 SPKC Channel 1 EI SPKC Channel 1 E Continuous Activity R Firing Rates The peak histogram represents the distribution of peak loc
126. icate that you can adjust the threshold Click and drag to move the threshold to the desired position When setting thresholds using this or any other manual method avoid setting the threshold down in the noise as in this example A Fal ao Se Ae SPT A Mag 2 25 SE GS ST 0 0s 0 58 1 0s 84 OmniPlex Neural Data Acquisition System In addition to the problems described in the Concepts section on thresholding if the threshold is very close to zero you can potentially overload the system with the high number of noise spikes that are generated On the other hand setting a threshold value that is unnecessarily large 1 e too conservative may cause low amplitude spikes to be missed 7 Bt Eme ai amp SS Td wW j ri m m aS Ls a La The raster tick display along the top edge of the view gives immediate visual feedback of the effect of your threshold changes on the detection of spikes The tick marks indicate the times of detected spikes In the threshold too large example it is clear that many obvious spikes are not being detected TIP The drop indicator If the Drop indicator at the right end of the status bar shows a non zero value and the indicator is red this shows that data has been dropped and is usually a sign of excessive load on the system such as an extreme number of noise spikes or interference from a CPU intensive application running on the same machine as OmniPle
127. iew Options i Tasks wa Global Options Reset All Options to Defaults ag 1 J0 System P SR Auto Configure All Sources Create View er ae ree for Sources i 2 Automaticall Collect New Snapshot for Source Configure Al Collect New Snapshot for Channel Properties Take Snapshot for Source 5 AA oee sic s Take Snapshot for Channel Channel Type S Rename Channels Channels Auto Sort current Source ans Groupir 5 Auto Sort current Channel Enable i Record Enabled x a jan ope Hi i 7 TIP Auto Sort grayed out If the Auto Sort menu item is grayed out it is probably because the SPK source is not currently selected 168 OmniPlex Neural Data Acquisition System Version 1 8 5 As the automatic unit finding proceeds you can see which channels have been processed by watching the multichannel spike or PCA views Si 7 Bt pa A Mag 1 00 gt Zi Ont PBT _ a a enh pe PRENN o _ a a e ai a wa i ew n NN pios oag ai O AN en ee ai a Soe a oo Se oe fe 2 my File fe smh Fe fem OPK Waveforms SPK Clusters 3D 3D Clusters Properties SpreadSheet 6 For performance reasons it is recommended that you view the live data not the spike snapshot while a multichannel auto sort unit finding is in progress In fact if you have the snapshot displayed and begin a multichannel auto sort PlexControl will toggle the views back into live mode to avoid this problem However once the auto sort has com
128. if not please contact Plexon support plexon com for installation assistance before attempting to operate the system Appendix K Hardware Pinouts and Connections contains information on pinouts and cabling which may be useful when connecting OmniPlex to external devices and systems such as a behavioral control system It is also assumed that you are familiar with basic concepts of neural electrophys iology such as spikes action potentials and field potentials OmniPlex D versus OmniPlex A This User Guide is for users of Plexon s latest version of OmniPlex which uses the Plexon DigiAmp or Mini DigiAmp This system is referred to as OmniPlex D as opposed to the earlier pre DigiAmp version OmniPlex A You will sometimes hear these versions called the digital system OmniPlex D and the analog system OmniPlex A which is somewhat misleading since the main difference is whether the analog to digital A D conversion is done in the same box as the analog preamplification and signal conditioning versus in a sep arate card in the OmniPlex chassis In other words the link from the Plexon blue box to the OmniPlex chassis is digital in OmniPlex D and analog in OmniPlex A The digital link used in DigiAmp systems provides better signal isolation and noise rejection and allows the use of a single link cable as opposed to the multiple analog ribbon cables used in OmniPlex A systems OmniPlex Neural Data Acquisition Syst
129. il WE L 3 s mn a a i a Seca Att A At ad AR Ae AeA AA TT Tau TPP PTET PR a MAYET T EN iy Se esas ee on BL ip Le kee 4 m Terim apy ET Daea PI Jn l ere r Tera koa C r Pyr kr i a rs alr Fi ins rd Bried a r a ra byi Pre Tamimi T Ser im b F LE i r Te ra Thana 11 8 err d Hera ALi keal rd Erzeni Paak ed Traki E id dares SEL Ed Mira ee ie ares iu P Tte ke r FO rg Nel TY ee ee 2 Be Sle cy Se ie HY ee Tl p U i E Fir aim by Parr i Version 1 8 Appendix Page 27 Appendix Appendix E DigiAmp Analog Highpass Filter and Referencing Besides the DigiAmp gain which is controlled from PlexControl there are two other user accessible analog parameters which are set in the DigiAmp device options in Server Edit Device i Device Options 2 3 Show Device Characteristics Add New Source To Device Remove Device Digi Amp Device Settings Highpass Filter 0 05 Hz Referencing Ch 1 16 Ch 17 32 Ch 33 48 Ch 45 64 RefA RefA RefA RefA Ore ORB ORM Ref F Use lowest latency caution increases CPU load M Enable timestamp checking cs Highpass filter The Highpass Filter options determine the frequency of the analog highpass low cut filter which blocks DC offsets and very low frequency artifacts The high pass filter precedes the analog gain and A D conversion stages so the cutoff fre q
130. in the available resources on a properly configured PC provided by Plexon However the mar gin of horsepower available to other applications running on the same machine will be reduced and the chances for conflict with other applications which have latency demands or run at elevated priority may be greater When you configure OmniPlex for lowest latency operation it is highly recommended that you per form several dry run tests in the intended usage scenario to verify that OmniP lex and any other applications do not drop data or exhibit degraded responsiveness The Windows Task Manager can be useful in monitoring the CPU usage to run Task Manager right click on the Windows taskbar and select Start Task Manager Toolbars Cascade windows Show windows stacked Show windows side by side Show the desktop Start Task Manager NS Lock the taskbar Properties Appendix Page 44 OmniPlex Neural Data Acquisition System Version 1 8 Jm Windows Task Manager File Options View Help Applications Processes Services Performance Networking Users CPL Usage CPU Usage History Memory Physical Memory Usage History Physical Memory MB System Total Handles Cached Threads Available Processes Free Up Time 0 03 30 17 Commit GB 5 11 Kernel Memory MB Paged Nonpaged PP Resource Monitor Processes 80 CPU Usage 0 Physical
131. indicate that the snapshot has been collected 98 mexcontvol Recarmeil E fie View Degiy Configure Dita Window Pun Help pe Re eee ee Boek is eo hg s hoai ag i Totis 9 ORK SPKChameil Waeetoons 9X i SPK Waeetorns 3x 3 Sitem a ki Create View Layout for uos KA atkcally Configure f source Rg tat Pe p Dat SS SPK Sore Snapshet le 9 Moving the cursor outside of the Spike Snapshot Progress view will cause it to collapse back into the tab at the bottom left of the window 10 Note that with real data some channels will complete their snapshots quickly but others may take much longer depending on the per channel firing rates In such cases you may wish to pin the view so that it remains visible without having to pop it up from its tab each time To do so click on the pushpin in its upper right corner Spe b Spe See Tee See See ore on mj mT m ma ny i 138 OmniPlex Neural Data Acquisition System 11 The Spike Snapshot Progress View then attaches itself to the right side of the multichannel window St Bt D A Mag 1 00 AE ont BEE Version 1 8 19 6 Additional Sorting Methods 12 When the required number of spikes has been collected 500 spikes by default for each SPK channel the No PCA for that channel is replaced by a display of PCA clusters SPK Clusters IX PAra EA PE SA SPK Waveforms BA SPK Cl
132. is the reverse of the startup sequence When the Server application is closed 1 e you exit to Windows all data acquisi tion is stopped and the power to the DigiAmp is turned off The blue link cable between the PSL card in the chassis and the DigiAmp can then be safely unplugged You should never plug or unplug the blue link cable while Server is open even when data acquisition is stopped You can verify the DigiAmp power status via the row of three green LEDs on the PSL card in the chassis if all three LEDs are on power to the DigiAmp is on 1f only the leftmost LED is on power to the DigiAmp is off and the cable can be plugged or unplugged The headstages can only be powered when the PSL power to the DigiAmp is on as indicated by the three green LEDs Of course the HST PWR toggle switch on the DigiAmp must also be on to enable the headstage power You will find that if you shut down PlexControl without first stopping data acqui sition data acquisition continues to run in Server which is expected If you now re open PlexControl it will automatically reconnect to Server while data acquisi tion is running and continue displaying incoming data as it did before you shut it down However this has the potential to cause occasional problems particularly at high channel counts Therefore it is not recommended that you make a habit of leaving Server running without PlexControl attached to it As a general rule when you are done using Ple
133. isplay Configure Data Window Run Help gt eed PO HANE LELE ECS ort og Tasks be 10x SPK Stop Recording IMPORTANT It is strongly recommended that you make a short test recording and examine it in Nex Matlab Offline Sorter or whatever the intended destination for the subsequent use or analysis of your data might be before proceeding to make important recordings in an actual experiment This will help reveal any problems in terms of which sources were recorded signal quality proper triggering on digital event inputs etc Large amounts of time and effort can be wasted if you make a long recording or a series of recordings before discovering that some setting was not correct that an input cable was bad etc TIP Avoid changing OmniPlex settings while recording If at all possible avoid making changes to OmniPlex settings while a recording is in progress unless you are aware of the potential conse quences in the recorded data For example if you have defined units a b and c on a channel and in the middle of a recording you delete unit b unit c is by default renamed to unit b and any analysis of the channel will have to account for this Likewise changing thresholds fit tolerances and other parameters during a recording may create issues for subsequent analysis of the data On the other hand there are cases where the input signals drift during a long recording and adjusting parameters in PlexContro
134. ited for use with auto matic sorting e g band sorting As with any toolbox of techniques each user will find that they have preferences as to which methods work best for them their working methods and their data First we will describe the simplest and probably most widely used sorting method template sorting and the simplest unit definition method waveform crossing Once you are familiar with this you will understand a number of tech niques which are applicable to the other methods which you can then learn at your convenience Version 1 8 97 4 Basic Spike Sorting 4 2 Step by Step Unit Definition using Template Sorting and Wave form Crossing 1 As described in previous sections start data acquisition set an appropriate gain and collect an SPKC snapshot so that suitable thresholds are set on all channels and spikes are appearing in the multichannel spike window w TIP Af Set the sorting mode before starting data acquisition Before starting data acquisition make sure that OmniPlex is set to the correct sorting mode as shown in the image below Properties 1O xX SPK Source 6 On Device Basic Sorting Channel Type Spike Channels 64 Channel Grouping Single Enabled Sampling Freq 40000 Gain 250 Waveform Length 800 Pre Threshold 200 Sort Start 0 Ma me p KOL Enabled F Record Enabled a 98 OmniPlex Neural Data Acquisition System 2 In the main spike window display its toolba
135. ithout notice Plexon Inc reserves the right to make changes in equipment design or components as progress in engineering or manufacturing may warrant PLEXON the five line symbol CinePlex DigiAmp MiniDigi Offline Sorter OmniPlex PlexBright PlexStim and Radiant are registered and unregistered trademarks of Plexon Inc Dallas Texas USA Other product and company names men tioned are trademarks or registered trademarks of their respective owners iv OmniPlex Plexon Inc Version 1 8 Plexon Inc V Publication History April 2013 This is the first publication of the User Guide for Version 1 8 of the OmniPlex System It replaces the OmniPlex Quick Start Guide published previously OmniPlex Neural Data Acquisition System vi OmniPlex Neural Data Acquisition System Plexon Inc Version 1 8 Plexon Inc Contents Publication History Chapter 1 OmniPlex System Overview and Startup Overview 2 Components 3 OmniPlex D versus OmniPlexA 4 Using the User Guide 6 OmniPlex Concepts Devices and Sources 7 Step by Step Power up and Connections 12 Step by Step Starting and Configuring OmniPlex Server 20 Step by Step Starting PlexControl 26 Step by Step Starting Data Acquisition 28 Step by Step Setting the Wideband Gain 32 Setting the Wideband Gain with a Live Neural Signal 43 OmniPlex Concepts Separating the Wideband Signal into Field Potentials and Spikes Chapter 2 PlexControl User Interface
136. ition System input range than 10 Vpp a voltage divider can be inserted between the external device and the AI inputs See Appendix K Hardware Pinouts and Connections for details on connecting to the Aux AI breakout panel Continuous data from the Aux AI card is an independent source in the Server topology and data for the AI source 1s written directly to the Main Datapool without any signal processing The only device option for the Aux AI card is the per channel sampling rate Edit Device Edit Device Options Show Device ae a Add New Source To Device Remove Device 5 OB 0 000 __ _ H G o o Aux Analog Input Device Settings samping rate 1 Note that you must stop data acquisition before changing the sampling rate AI channels are shown in their own tab in PlexControl labeled AI Continu 29 ous Version 1 8 Appendix Page 31 Appendix A Fat op Spe Ae ORT PET Mag 1 00 Z So T he Pm Le oe T 3750 00 mW SNA 3750 00 mv 3750 00 mi 3750 00 mv 3750 00 mi 3750 00 mv 3750 00 mW SNA 3790 00 mi The sweep rate magnification and number of channels can be adjusted as with the other continuous views but none of the gain control or thresholding function ality is applicable However you can use the Properties Spreadsheet with the AI source selected to enable and di
137. kes unless the overall activity on the channel was very low Note that the Short ISI bar does not affect the sorting in any way it is simply a monitoring tool to alert you to potential sorting problems Spike display modes PlexControl provides several spike display modes and options which can be very useful when adding units adjusting sorting parameters and monitoring the results of spike sorting See Appendix C PlexControl Spike Display Modes for more information Deleting a unit 1 To delete a unit select it by clicking on it in the Units window Cn rL n IR L Pipe PoE i n n n Unsaon 2 To delete the selected unit click the Delete Unit button in the toolbar 111 4 Basic Spike Sorting Alternatively you can right click in the Units window to display a menu and select Remove Selected Unit Remove Selected Unit Remove All Units Show Options Show Snapshot Options The selected unit is deleted and any units which followed it in alphabetical order are renamed accordingly For example if you have units a b c and d and delete unit c unit d will be renamed to unit c TIP Removing units by setting tolerance to minimum If you need to delete a unit but for some reason want to avoid the automatic reassignment of unit names set the undesired unit s fit tol erance to the minimum value instead of deleting it In most cases this will effectively remove that unit fro
138. l during a recording is necessary to track a unit or compensate for other changes TIP Disable channels before starting the recording For performance reasons PlexControl does not allow you to change the record enable checkboxes during a recording so make sure the enables are set as desired before starting to record PLX channel numbering for continuous channels Within OmniPlex channels are source relative for example in a 64 channel sys tems the WB channels are numbered 64 the SPKC channels are numbered 64 123 5 Recording 124 etc However for historical reasons all the continuous channels in a PLX record ing file are numbered in a single continuous range Therefore when a PLX file is recorded the continuous channels in each source in OmniPlex are automatically mapped into this single linear range of channels In the Properties Spreadsheet the PLX chan column shows the PLX channel which the channels of each source will be recorded as for example Properties SpreadSheet for SPKC O nere PKCO1 oPRKCOZ PKCOS oPRKCO4 SPKCOS oPRKCO6 oPRKCO SPKCOS oPRKCOG SPKC10 oPKC11 You can use the previous next source buttons in the main toolbar to quickly step through the sources to see what PLX channel ranges each will be assigned to each one using the Properties Spreadsheet OmniPlex Neural Data Acquisition System Plexon Inc Chapter 6 Additional Sorting Methods
139. late sorting Note that the crossing line does not disappear when you finish drawing the line gt SPK MAG opt peg 128 OmniPlex Neural Data Acquisition System Version 1 8 5 Also note that if you move the cursor tip over either end of the line it changes to a line edit cursor to indicate that you can move either end of the line We can see that there are some spikes that are incorrectly being sorted into unit a because one crossing line is sometimes not an adequate sorting criteria To add another crossing line for the same unit click the Add Line button in the toolbar SPK Channel 1 Waveforms aga b This is a case where the Selected Unit mode for the Show filter see Appendix C PlexControl Spike Display Modes is particularly useful as it makes the addition of more lines to tighten up the sorting criteria easier Here is an example after a total of four lines have been added with the Show filter set to Selected Unit 129 6 Additional Sorting Methods SPK Channel 1 Waveforms AX SPK Waveforms SZ E BE D cA Mag 1 70 HE ore aAA SS SN 7 You can also use the Delete Line command to delete the most recently added line gt SPE Channel 1 Waveforms EZ BE RE D cA Mag 1 70 P OFT p AIG ss Remove Line You can add as many lines per unit definition as you like although in practice you should find that no more than three or four lines are
140. ld 15 000 Also note that it reminds you that the WB source is on attached to the Mini DigiAmp device i e it refers to this part of the topology diagram in Server as described in the previous section OmniPlex Concepts Devices and Sources Version 1 8 37 1 OmniPlex System Overview and Startup 38 Plexon Mini es 3 WE DigiAmp Y 4 Paris 64 Chs 64 Chs The upper section of the Properties view displays the properties that are com mon to all the channels in that source while the lower section displays per channel properties The Properties window is context dependent it displays the properties of the most recently selected source and the most recently selected channel within that source For example if you clicked on channel 27 in the multichannel spike window the Properties view would display the prop erties for source SPK channel 27 If the properties for the WB source are displayed skip to Step 6 If some other source s properties are displayed i e not WB continue to Step 5 Double click to return to multichannel display Remember that if a multichannel continuous display or any multi channel display is zoomed that is only displaying a single channel you can double click it to return to a multichannel display where you can select individual channels by single clicking within that chan nel s rectangle Observant readers will note that there are some properties listed for the
141. lexControl User Interface 62 2 3 4 Pausing the displays 2 3 9 A feature related to changing the sweep speed but which applies to all views not just continuous views is Display Pause which freezes the all graphical displays To pause the display click on the Display Pause button in the main OmniPlex toolbar at the top of the main window Help OS PP St Gy oi NS SEO U eX Chas Da All animated views will be paused until you click the button again Note that this has no effect on the acquisition processing or recording of data which will con tinue as before It is simply a handy way to freeze data views so that you can inspect them in a static state Do not confuse this with snapshots which are described later Pausing the display does not take a snapshot and displaying a snapshot does not freeze displays other than the one which 1s displaying the snapshot Continuous view options There are a number of display options associated with each view Each view s options which can be set independently are accessed by clicking the Options button in its toolbar SPEC Channel 1 Continuous A 3 Ao PRE Mag 1 50 IAR GLE Tic a T ptions RRS A TIT ee ee ee ee T M AIEEE ATE E any khaa TEE The other OPT button accesses snapshot options which will be described later When you click the Options button the View Options dialog is displayed OmniPlex Neural Data Acquisition System Con
142. lick anywhere within the display area to return to multichannel display mode You do not need to display every channel as long as two or more channels are displayed you are in multichannel mode and snapshot collection and analysis will be applied to all channels even the ones that are not visible onscreen gt SPEC Continuous P pa Ag OT PET Mag 2 00 TIR A T 0s E 25 I AAA AT TT ETAT el SPEC Continuous Ge Baal SPKC Channel 1 Peak Histograrr SPEC Continuous 71 Version 1 8 3 Spike Detection 2 72 Click on the Snapshot Options button in the toolbar not the Options button to its left SPEC Continuous LA Pa Gop pe Ae Shr PET Mag 2 00 2 F R TIE wo A Fa Snapshot Options MT Tn ir D Py The Snapshot Options for the SPKC view are displayed You can see that the default length of a snapshot of continuous data is 10 seconds and that the first time that you collect a SPKC snapshot the snapshot will be used to automatically set the thresholds for the SPKC source Continuous Snapshot Options Collection Auto Gain Auto Threshold Sources SOUrCe SPEC Snapshot Buffer Buffer Size seconds When anew Snapshot first becomes available for a channel Perform Auto Gain v Perform Auto Threshalding _ OmniPlex Neural Data Acquisition System Version 1 8 TIP Increase snapshot length with caution Increasing the length of the sna
143. m as the equivalent threshold in sigmas and vice versa TIP Be careful when adjusting thresholds in the main spike window Be careful when adjusting thresholds in the main spike window since you are only viewing the detected spikes not the continuous spike SPKC signal which is what spike detection is actually per formed on For example if you set the threshold very far away from zero you will not see any spikes at all in the main spike window although of course the SPKC signal is still present and can be viewed in the SPKC Continuous view Similarly even if you have an appropriate threshold value set if the firing rate on the channel is low you may only occasionally see spikes making it difficult to judge the effect of adjusting the threshold In such cases you should use the SPKC Continuous view and or the SPKC peak histogram to set the threshold as previously described 91 3 Spike Detection 3 5 Step by Step Changing the Spike Extraction Parameters 92 By default when OmniPlex detects a threshold crossing in the SPKC data stream it extracts an 800 microsecond segment and outputs it to the corresponding chan nel on the SPK source The 800 microsecond waveform segment consists by default of a 200 microsecond pre threshold interval and a 600 microsecond post threshold interval with the timestamp for the spike defined as the time of thresh old crossing You can change these values for example to increase the wav
144. m the sorting process 3 If you wish to delete all the units on a channel select Remove All Units from the right button menu or use the Remove All Units button in the toolbar SPK Channel 1 Units BO Be m ort pst i lacna Remove All Units 4 2 7 Replacing an existing unit Replacing a unit is similar to adding a new unit except that the new unit will replace the unit that was selected at the time you clicked the Replace Unit button 112 OmniPlex Neural Data Acquisition System 7 BED A Mag 1 70 gt TP ont BB gt Unit b Fit Tol 0 039 Replace the Selected Unit For example if you have units a b c and d and unit b 1s selected clicking Replace Selected Unit will then overwrite the unit definition for unit b The pro cedure is otherwise identical to that previously described for adding a new unit Note that this is not the same as selecting an existing unit and changing its sorting parameters such as template tolerance or editing its points the Replace Units command completely overwrites the old unit with the new one Version 1 8 113 4 Basic Spike Sorting 114 OmniPlex Neural Data Acquisition System Plexon Inc Chapter 5 Recording Be TE ewes eninge see eared cee AE ET 116 dic UE ae TON ira EEEE 116 APL 900k taeda cision erecentiak ema 116 idle eC poi iat renratiteeasn ear eee eteiaten 117 5 2 Step Dy Step Recording isdirtercemicnnenineenns einen 118 5 2 1 PLX channel num
145. n the display window for the channel in the WB Continu ous view OmniPlex Neural Data Acquisition System 1 10 Setting the Wideband Gain with a Live Neural Signal Version 1 8 When you are working with a live neural signal rather than a test signal from a PC the gain setting process is usually simpler that the procedure described above Now that you know how to adjust the gain and monitor the wideband sig nal for clipping these two guidelines should cover most situations e If using a unity gain headstage G1 set the DigiAmp gain to 1000 1f clip ping of the wideband signal occurs reduce the gain as necessary until 1t occu pies no more than 1 2 to 2 3 of the maximum amplitude range e If using a gain of 20 headstage G20 set the DigiAmp gain to 50 1f the wideband signal occupies a very small portion of the maximum amplitude range carefully increase the DigiAmp gain until the signal occupies no more than 1 2 to 2 3 of the maximum amplitude range Remember that unlike the test signal with a live neural signal you will often have different signal amplitudes on different channels In such cases make sure to keep the gain low enough to prevent clipping on the channel with the highest amplitude signals Chapter 2 PlexControl User Interface describes how to change the number of channels that are displayed at one time and other viewing parameters 43 1 OmniPlex System Overview and Startup 1 11 OmniPlex Concepts Separating
146. nal where the FP component is a simple low fre quency 5 Hz sine wave Real FPs would be more complex low frequency signals Highpass filtering with a cutoff of approximately 200 300 Hz yields the con tinuous spike signal SPKC source sampled at the same 40 kHz rate as the original wideband signal ad oe T a Poe i al WE Channel 1 Co wel SPEC Channel C iid FP Continuous Pi Informally you can think of removing the field potentials as flattening the base line of the wideband signal without this flattening it would be impossible to detect spikes by comparing the continuous signal amplitude against a fixed volt age threshold OmniPlex allows you to configure the characteristics of the spike and FP separa tor filters and the downsampling but for these examples you will use the default settings See Appendix B Separation of Spikes and Field Potentials using Digital Version 1 8 45 1 OmniPlex System Overview and Startup Filters for details on how to change the default settings and some of the tradeoffs involved 46 OmniPlex Neural Data Acquisition System Plexon Inc Chapter 2 PlexControl User Interface Ph re Fe ERE AE IEEE EAN AEE PE A EN EEE O E EEN E 48 2 2 Step By Step Resizing Windows using the Splitter Bars cccceessseeeeeeeeeeeeeeeeeeees 50 2 3 Step by Step Using the View Toolbars and Options ccccseeeceeceeeceeeeeseeeeeeeeeeeeens 53 l OmniPl
147. nces for Template and Band Units 9 Set to a constant value of 0 1 Setto 1 times the standard deviation of waveforms Fit Tolerances for 2D Ellipses 2 times the standard deviation of feature points Adjust the initial fit tolerance as desired and click OK to accept your changes 4 2 4 The Short ISI Indicator In cases where too loose sorting parameters are causing too many spikes to be sorted into a given unit one possible indication of the problem 1s that the firing rate of the spikes for that unit is too high in other words it s unlikely that one neuron could have produced that many action potentials per second In the Units window the Short ISI Indicator is a red bar and associated value for the percent age of spikes that have an inter spike interval ISI less than the refractory period 1 e recovery interval of a single neuron 108 OmniPlex Neural Data Acquisition System Version 1 8 SPK Channel Units _ In effect the Short ISI Indicator is a warning that the current sorting parameters are resulting in sorted spikes that do not correspond to a physiologically plausible scenario By default OmniPlex assumes that the minimum refractory period for a unit is one millisecond 1 e a 1 kHz maximum firing rate You can change this default typically to reduce it by displaying the toolbar for the Units window and clicking the Options button gt SPK Channel 1 Units EG 4 Bi ets lrc rrt U o
148. ndix Appendix F Auxiliary Analog Input Aux Al The Auxiliary Analog Input AuxAI device is a 32 channel A D card in the OmniPlex chassis which is provided for direct acquisition of non neural low fre quency signals such as those output by position or orientation sensors By direct we mean that OmniPlex provides no preamplification or other analog signal conditioning for these inputs Sampling rates of up to 5 kHz per channel or 20 kHz per channel for the fast version of the Aux AI card are supported but the default rate is 1 kHz the same rate that is used for digitizing field potentials Note that the 32 inputs are sampled in multiplexed fashion within each sampling period unlike the simultaneous sampling implemented in the DigiAmp However the same master clock from the TIM card is used to drive both devices as well as the digital input DI card insuring synchronized sampling across all devices Easy access to the 32 input channels is provided via a BNC D sub breakout panel located immediately to the right of the Aux AI card in the chassis y A q 09 42 A 02 A ry Nj l MADE IN TEXAS BY TEXANS The input range of the Aux AI channels is a fixed 5V with 16 bit resolution Even for an input signal with an amplitude of only 0 5V the signal will still be digitized to better than 12 bits of resolution For applications requiring a greater Appendix Page 30 OmniPlex Neural Data Acquis
149. needed in most cases 130 OmniPlex Neural Data Acquisition System Version 1 8 TIP Using the sorting lines Line sorting is quite effective in terms of being able to very closely specify the desired shape of the bundle of waveforms that constitute a unit You will sometimes hear this referred to as making the spike jump through hoops However keep in mind that some parts of spikes in particular the tail tend to have more amplitude variance than the region around the peaks As a general rule the sorting lines should be tighter to the bundle in the more well defined part of the spike and looser if used at all in the tail and other higher variance regions 8 You can continue to define more units on the same channel using the Add Unit button again TIP Lines per unit versus units per channel Novice users sometime confuse adding lines with adding units remember that you can have multiple units per channel and multiple lines per unit On a given channel unit a could have three lines unit b only one line unit c two lines etc While editing a particular unit you can only modify the lines used to define that unit Note OmniPlex requires that all the channels on a spike source use the same sorting method In practice this means that all the spike channels in the system must use the same sorting method 131 6 Additional Sorting Methods 6 2 OmniPlex Concepts PCA While you can use OmniPlex as has be
150. nel spike window SPE J SPEC Continuous iF Fe D lT eg lE Bed Mag 1 00 mi EA A hE 41 iho Eo Us 10s 158 The Properties Spreadsheet shows properties for the channels of the currently selected source in this case the SPKC continuous spike source The Thresh old column shows the threshold values that were just set by the auto threshold ing of the SPKC snapshot Properties spreadsheet for SPKC m PLX chan Enabled Threshold gt gt SPKCOO1 SPKCOOZ i 10 697 ee ee ee E os ee are aa Reiter meinen ee e a s E T T eee eee ee eee ee neiulince mind aun e TE ns E nn ee ee eee A E o ee ee eee ere ao ee ee Eo ao a ee Eo nno a a a A E ao Version 1 8 77 3 Spike Detection 78 The threshold value in percent is relative to the maximum amplitude that can be digitized without clipping For example if the SPKC view has a range of 5 mV to 5 mV and the threshold is 10 then 5 mV 0 10 0 5 mV or 500 microvolts Remember that as mentioned previously the amplitude scale bar at the right end of the continuous displays indicates the values for 75 and 75 of the actual minimum and maximum displayable amplitude values In other words if the scale bar extends from 3 75 mV to 3 75 mV the actual voltage limits before clipping are 5 mV to 5 mV In addition to or as an alternative to using auto thresholding to set the thresholds on all channels at a given number of sigm
151. nels to pause and unpause Stat Recording Pause Recording From GUI Only From GUI Only After Occurence s of an Event After 1 Occurence s of an Event Source 11 CinePlex Data Source 9 Single bit events Channel Any Channel 8 EVTO8 Value 1 Value 1 After U J0 J0 After 0 J0 z JU Stop Recording Resume Recording From GUI Onty From GUI Only Ater Occurence s of an Event After 1 Occurence s of an Event Source 11 CinePlex Data Source 9 Single bit events Channel Any Channel 16 EVT16 Value 1 Value 1 After O J0 z j Afer O J0 M Immediately Pause after Starting Recording Note every Resume Recording starts a Frame fi After Stopping Allow Restart Recording to a New File When you use digital events to pause and resume the effect is exactly as if you had clicked on the Pause button in the toolbar to pause and resume recording 5 When you click the Stop button in the toolbar the recording is ended and the file closed regardless of whether the state of the recording is currently paused or not Note that when you use event triggered recording there is a small amount of delay between when the RSTART RSTOP occurs and when recording actu ally starts and stops This delay is typically around 100 ms but can be longer in some cases to be safe you should allow at least one second between an RSTOP and the next RSTA
152. ng parameters and for the actual spike sorting OmniPlex spike sorting methods The following spike sorting methods which will be described later are currently supported by OmniPlex e Template sorting e Line sorting e Band sorting e Box sorting e 2D polygon sorting The first four sorting methods operate directly on the set of waveforms samples 1 e the raw detected spike while polygon sorting operates on a projection of the waveform into a two dimensional feature space These are the algorithms that run in the sorting device in Server sorting incoming spikes in real time and writing them to the Main Datapool OmniPlex unit definition methods OmniPlex supports three methods for manually defining units given a set of spikes These are the techniques that are available in PlexControl for your use the unit definitions that are created are sent to the sorting device in Server to per form the actual sorting e Waveform crossing OmniPlex Neural Data Acquisition System e 2D PCA cluster circling e 3D PCA cluster circling Any of the unit definition methods can be used to define units for any of the sort ing methods with the exception of the line and box sorting methods Line sorting and box sorting are different in that the unit definition method and the sorting method are identical for each method in these two sorting methods you graphi cally specify the sorting parameters directly on the waveforms as opposed to
153. ng unwanted noise and artifacts at the head or tail of the spike Appendix Page 37 Appendix Appendix H Enhanced PCA Feature Space In addition to the standard PCA principal components analysis feature space OmniPlex supports an improved version of PCA which was developed by Plexon specifically for spike sorting applications called Enhanced PCA Standard PCA determines a projection in which the first component is in the direction of maxi mum variance in the original data the second component is in the direction of second greatest variance and so on Enhanced PCA uses not only variance but separability of the data in calculating the projection For example if there is a sample position where a group of spikes has a large amount of amplitude vari ance but it 1s basically noise without any structure within the distribution of amplitudes at that sample time Enhanced PCA will de emphasize that compo nent of the data in the resulting projection In contrast samples where there is a high degree of separability even though the amplitude variance may not be large are emphasized in the projection In many cases the net result of Enhanced PCA is to make the feature space clus ters more compact and distinct However the degree of improvement is data dependent and so you should compare standard PCA and Enhanced PCA to determine which is optimal for your application Here is an example of standard PCA top versus Enhanced PCA bottom
154. nit 104 Changing the default for the initial fit tolerance 107 The Short ISI Indicator 108 Spike display modes 111 Deletinga unit 111 Replacing an existing unit 112 Chapter 5 Recording 115 Overview 116 PLX format 116 PL2 format 116 What to record 117 Step by Step Recording 118 PLX channel numbering for continuous channels 123 Chapter 6 Additional Sorting Methods 125 Step by Step Line Sorting 126 OmniPlex Concepts PCA 132 Step by Step Taking a Spike Snapshot and Viewing PCA Clusters 135 Step by Step Defining Units for Template Sorting using PCA Contour Drawing 149 OmniPlex Concepts Snapshot Mode versus Live Display 154 Step by Step Defining Units using Spike Snapshots 157 Step by Step Automatic Sorting Automatic Unit Finding 163 Automatic unit finding on all channels 166 Step by Step 2D Polygon Sorting 171 Cleanup of hand drawn PCA contours 176 Ellipse overlap handling 180 Automatic unit finding with 2D polygon sorting 181 Defining units by line crossing with 2D polygon sorting 183 Chapter 7 Additional Features and Procedures 185 Step by Step Saving and Loading PlexControl Settings 186 Version 1 8 Plexon Inc OmniPlex Neural Data Acquisition System Step by Step Automatically Maintaining Compatible Sets of PXS and PXC Files 188 Digital Inout Card Configuration 191 Digital input modes 192 RSTART and RSTOP events 194 Step by Step Event Triggered Recording 195 PlexControl Activity Display 198 Starting and Shutting Do
155. nments for digital input channels strobe bits and the RSTART line Version 1 8 193 F Additional Features and Procedures 7 3 2 RSTART and RSTOP events Port A has one additional input which is not present on port B which is the RSTART line RSTART is different from the other DI inputs in that it generates events on both the leading and trailing edges of input pulses Leading edges pro duce RSTART events while trailing edges produce RSTOP events These are used for so called level triggered recording in PlexControl where they start and stop recording so pulses on RSTART are in fact typically seconds minutes or even hours in duration See the section below Step by Step Event Triggered Recording for more information 194 OmniPlex Neural Data Acquisition System 7 4 Step by Step Event Triggered Recording In addition to manually starting stopping pausing and resuming recording you can configure PlexControl to perform any or all of these actions when it sees a user specified digital event 1 To configure the event triggered recording options display the Global Options dialog from the Configure menu PlexControl PlexControll Ble View Display Configure Data Window Run Help View Options Global Options P Reset All Options to Defaults APKC Auto Contigure All Sources Cancel Auto Configure 2 General Feature Space Snapshots Control Restrictions
156. nt for automatic unit finding operations which work in the feature space Spike FP separation The digitized wideband signal is typically separated into field potentials FPs and a continuous spike signal SPKC using OmniPlex s digital filters with the separation parameters determined by the user according to his or her needs there is no universally applicable definition of the upper frequency limit of a field potential or the lower frequency limit of spikes Depending on the experiment and type of neural signals being acquired it is often preferable to set the filter cut off frequencies for spikes and FPs independently as opposed to attempting to split the spectral content of the wideband signal at a single frequency Also the class of filter for example Butterworth versus Bessel and the steepness of the fil ter number of poles may be different for the lowpass FP filter and the highpass spike filter OmniPlex provides default filter settings that are based on typical usage scenarios but allows these settings to be easily customized One consideration is that the cutoff of the FP lowpass filter must be appropriate for the downsampling which is performed on the lowpass filtered signal For example for the default FP downsampling rate of 1 kHz there should be no significant spectral content above 500 kHz after lowpass filtering so the lowpass filter cutoff frequency should be well below this frequency otherwise aliasing will re
157. ntimidating all that you really need to remember is the above list of sources especially the first five or six which will quickly become familiar as you learn to use OmniP lex Version 1 8 11 1 OmniPlex System Overview and Startup 1 5 Step by Step Power up and Connections If you already have a running system with all the cables connected and a head stage tester unit HTU connected to the audio output of the PC you can skip this section and go directly to the section Starting and Configuring OmniPlex Server 1 Unless you know that the OmniPlex hardware and the PC have already been powered up in the correct order chassis first then PC perform steps 1a 1d da If itis on shut down the PC close Windows and fully power down not just Sleep or Hibernate 1b If it is on turn off the power to the chassis rocker switch on rear panel of chassis AC 100 240V 50 60 Hz OSS ENCL 3U CPC 8 300 2774 00 ee ii di 1c Turn the chassis power on You should see a green Power LED light up at the left end of the front panel 12 OmniPlex Neural Data Acquisition System Version 1 8 1d Restart the PC Allow Windows to boot up normally You should see green LEDs light up on the leftmost card in the chassis link card If you do not see the link card light up possibly the black link cable to the PC is not connected in this case connect the cable and repeat the procedure from Step 1a TIMI CONT
158. ontrol c ccccccsscescescncsseececssesesescceccccesseseenccessseeteesesess 26 1 8 Step by Step Starting Data ACQUISION ecard geredecedbncicecterdescssduetieerccesian eee 28 1 9 Step by Step Setting the Wideband Gain cccccccccccseseeeeeesseeeeseeeeeesaeeeeeseeeeeesaaes 32 1 10 Setting the Wideband Gain with a Live Neural Signal ccccccssseeeeeeeeeeeeeeeeeeeeaeeees 43 1 11 OmniPlex Concepts Separating the Wideband Signal into Field Potentials and Spikes44 a OmniPlex Neural Data Acquisition System 1 1 OmniPlex System Overview and Startup 1 1 Overview OmniPlex is a modular high performance system for the acquisition time stamping recording and visualization of neural signals associated non neural signals and hardware digital events It supports up to 256 channels of low noise wideband signal acquisition at a sampling rate of 40 kHz per channel The contin uously digitized wideband data is the input to a set of software processing mod ules which support flexible user configurable separation of spikes and field potentials spike detection and alignment and state of the art spike sorting algo rithms Visualization of signals spikes and events along with control of all processing and recording parameters is provided by PlexControl a customizable software application which is the main user interface to the OmniPlex system Experimen tal data acquired by OmniPlex can also be sent in real
159. pendix Page 41 Appendix Appendix I Lowest Latency Operation For applications such as brain machine interface BMI experiments closed loop stimulation etc it is important to operate OmniPlex with the lowest possible latency By latency we mean the total time for data acquisition signal processing spike sorting and delivery of sorted spikes to external programs such as clients and Matlab scripts When configured and used as described an OmniPlex system using the DigiAmp or Mini DigiAmp is capable of an average end to end latency of approximately one millisecond 1 In the DigiAmp device settings make sure that Use lowest latency is enabled Edit Device ene Device Options i a a E a aS a Show Device Characteristics _ Add New Source To Device E Remove Device Digi Amp Device Settings Highpass Filter 0 05 Hz 0 5Hz Referencing Ch 1 16 Ch 17 32 Ch 33 48 Ch 49 64 RefA RefA RefA RefA Enable timestamp checking OK Appendix Page 42 OmniPlex Neural Data Acquisition System 2 4 In Server select RASPUTIN Emulation Options from the Configure menu rpi OmniPlex Server opxDm G1 64wb 32ai pxs Data Window Run Help Add a Device Add a Source Edit Device Options View Options Ctrl C Global Options Reset All Options to Defaults In the options dialog select the Server Emulation page and enable Minimize Cli
160. perties SpreadSheet Version 1 8 179 6 Additional Sorting Methods 6 8 2 Ellipse overlap handling In cases where a spike s PCA projection falls within the overlap of two or more contours the 2D distance from the spike s projection to the center of each over lapping ellipse is used as a tie breaker This has the beneficial effect of allowing a small cluster that falls within the outskirts of a larger cluster to be sorted more correctly The following is not a realistic example but gives some idea of how this works ee ee ee Tamsin Bt ell Bet Gee ab pea c4 ORT Bet A A BS Parzen Mult 0 7 4 SE SPK Waveforms 6 SPK Channel 1 Clusters 3D 3D Clusters Properties SpreadSheet Spikes within the green ellipse also fall within the large yellow ellipse but most are sorted into the green unit since they are closer to its center 180 OmniPlex Neural Data Acquisition System 6 8 3 Version 1 8 Automatic unit finding with 2D polygon sorting You can also perform automatic unit finding while in 2D polygon sorting mode The main difference relative to template sorting is that the unit finding creates unit definitions consisting of ellipses that are fit to the clouds of sorted PCA points SPK Channel 1 Clusters Snapshot Te F E amp Parzen Mult 0 4 gt pay Channel 1 Snapshot E SPK Waveforms Snap A SPK Channel 1 Clusters 303D Clusters Properties SpreadSheet
161. pleted you can switch back and forth between live and snapshot modes as usual TIP Monitor auto sorting If you select the highest numbered SPK channel in the multichannel display e g channel 64 in the example above you can watch the main spike window to see when sorted spikes start to appear as an easily visible indicator of when auto sorting has finished on all chan nels TIP Allow auto sort to complete Do not start another auto sort while an auto sort is already in prog ress in general allow an auto sort to complete before adding delet ing or replacing units 169 6 Additional Sorting Methods 170 Remember that automatic unit finding is just another tool for creating unit defini tions and the unit definitions that it produces can be used as is or augmented manually For example you may wish to set the Parzen Multiplier to only find large obvious clusters then manually inspect the results and manually add units corresponding to smaller or less distinct clusters that are not as easily found auto matically You might decide to delete or manually replace some of the automati cally found units but leave the majority of them as 1s Such approaches can give the best of both worlds automatic and manual while saving considerable time compared to defining every unit on every channel manually In addition to template sorting automatic unit finding can produce unit defini tions for the band and 2D polygon sorting metho
162. present on port A pin 23 Pin 23 is ground on port B On both ports pin 22 is the strobe bit used only when the port 1s configured for mode 3 If configured in Server as high true a voltage level of approximately OV will be a logic 0 and a level of approximately 5V will be a logic 1 If configured as low true then OV is a logic 1 and 5V is a logic 0 Pin 19 g Pin Function Data 1 Data 2 Data 3 Data 6 Data 7 Data 8 Data 9 Data 10 Data 11 Data 12 Data 13 Data 14 Data 15 J h h NO A Ol Appendix Page 48 OmniPlex Neural Data Acquisition System 2 S 6 T 8 9 0 2 3 4 5 6 The Data pins inputs will float high 1 e will be pulled up to a constant 5V if they are not connected This should not be a problem for mode 1 since only edge transitions are detected but in mode 3 floating inputs will appear as 1 true bits in the strobed word value 1f the port is set for high true logic It is recommended that you ground all unused inputs to avoid such problems Note that transitions edges on the digital input lines are detected by the DI hard ware at a rate of 20 MHz but since the timestamp resolution of digital events in OmniPlex is 40 kHz events that are sent into the DI card at a rate higher than 40 kHz will result in multiple digital events with the same 40 kHz timestamp Even if you do not intentionally input high frequency di
163. pshot above the default length of 10 seconds should be done with caution since this will also increase the amount of time require to process the snapshot TIP Auto Threshold option and button If you disable the Perform Auto Thresholding option snapshots can still be collected but you will have to use the Auto Threshold button in the toolbar to perform an auto threshold using the most recently collected snapshot SPEC Continuous A Pat DAA 221 P Mag 100 gt F A amp tT e b Oe Tie ee Perform Auto Thresholding on the Current Snapshot All Channels E WB Continuous 8 SPKC Continuous EN Peak Histogram Snapshot 8 Continuous f 73 3 Spike Detection 74 4 If you select the Auto Threshold tab you will see the default settings that will be used for auto thresholding Continuous Snapshot Options On Source Set the threshold at 4 Threshold Sign Positive Negative The sign of the mean signal As you will see below when a continuous snapshot is collected OmniPlex uses it to derive per channel histograms of the peaks in the continuous signal The auto threshold procedure sets the threshold at a certain number of stan dard deviations sigmas from the mean of this distribution Click OK or Can cel to dismiss the Snapshot Options dialog OmniPlex Neural Data Acquisition System Version 1 8 5 Click the Start Forward Snapshot button in the toolbar to
164. pshot before the PCA can be calcu lated Version 1 8 141 6 Additional Sorting Methods TIP Calculating PCA for backwards snapshots If you collect a backwards snapshot which collects the previous 500 spikes on each channel instantly as opposed to starting collection of incoming spikes until the next 500 are collected you must then click the PCA button to calculate the PCA for the backwards snapshot 14 Double click on channel 1 in the multichannel PCA display to zoom it to single channel mode SPK Clusters l Ret D l A Ont By oe ee ck SPK Waveforms P SPK Channel 1 Clusters 303D Clusters Properties SpreadSheet 15 Depending on your monitor and your preferences you may wish to use a larger point size for the PCA dots You can also switch to Rolling or Erase 142 OmniPlex Neural Data Acquisition System modes just as with the main spike windows If you wish to change the display settings click on the Options button in the toolbar SPK Channel 1 Clusters i St A Bi BE SD rca ow Ort Pas Version 1 8 143 6 Additional Sorting Methods 16 Inthe Options dialog you can change the Point Size and Update Mode as desired 2D Cluster View Options Channel Grid Rows J Columns 8 E Zoom with Chain F Arrange Channels in Row Major Order Show Channel Number Labels Allow Toggling to Show Snapshot Drawing Waveform Points Point Size When Zoomed Update Mode for Live
165. r by clicking on the down arrow at the upper right corner of the window SPK Channel 1 Waveforms 3 Make sure that the incoming spikes are displayed at a large enough size that you can see them clearly use the Magnification control in the toolbar to increase the magnification if necessary SPE Channel 1 Waveforms At 4 BB Be ff Mag 1 70 k opt Aoa n View Magnification Factor Version 1 8 99 4 Basic Spike Sorting 4 After adjusting the magnification click on the Edit Units button p po CETA at ot a 4 a cA Mag 1 70 TE ony ped Edit Units This enters unit editing mode in which you can add delete and modify units on the currently selected channel The unit editing toolbar is displayed below the main spike toolbar gt SPE Channel 1 Waveforms EHA St Bet A Mag 1 70 gt Zi r PEF EN FS amp Define a unit Bs e Note how the Edit Units button remains highlighted in the main spike toolbar to indicate that you are in unit editing mode If you click on the Edit Units but ton again you will exit from unit editing mode and the unit editing toolbar will disappear But for now remain in unit editing mode TIP Click to select a current channel While in unit editing mode or at any other time you can click on any channel in the multichannel spike window to select it as the current channel In other words you don t have to jump in and out of unit editing
166. r the gain of 1000 is too high when using a G1 headstage However once you have selected an appropriate gain value you should not need to adjust the gain again during an experiment unless the signal amplitude increases so much that clipping of the wideband signal occurs in which case you should reduce the DigiAmp gain to prevent distortion of the sig nal Note that the gain value applies to all the channels in the DigiAmp See Appendix A Signal Amplitudes and Gain for additional information on gain clipping and related issues For the purposes of this User Guide the situation is slightly different than it would be in an actual experiment since we are using an audio file being played through a noseboard voltage divider as our test signal What you will do next depends on the amplitude of the wideband test signal coming from the PC s audio output as shown in the WB Continuous view 1 First to get a better look at the signal double click in the WB Continuous view inside of the first row labeled 1 at the left WEB Continuous Uo kaiih e e hia ei ee k This will expand that channel s display so that it occupies the entire WB Con tinuous view note that the view s title bar now shows WB Channel 1 Contin uous instead of the previous WB Continuous OmniPlex Neural Data Acquisition System Version 1 8 ied WB Channel 1 Continuous Peak Histogram Snapshot Sid Continuous If you now
167. rks which can merge together into a horizontal bar when the firing rate is high can potentially obscure the very tops of signal peaks but if this is the case you are risking clipping the wideband signal and should reduce the gain as described below In a way the row of spike ticks serves as a danger zone into which continuous signals should rarely if ever cross into If the wideband signal is now displayed at a suitable amplitude in PlexControl you can proceed to Step 5 If you increase the output level from the PC s Line Out to its maximum but the wideband signal displayed in PlexControl is still too low in amplitude then you will need to increase the DigiAmp gain as described in Step 4 4 To change the DigiAmp gain which is the analog gain applied to all channels of the wideband signal before A D conversion digitization first verify that the Properties view a view containing a spreadsheet like grid at the left side of the PlexControl window shows the properties for source WB depending on your topology the source number may be different source numbers can generally be ignored Properties n 0x WB Source 3 ert Plexon Mini DigiAmp Channel Type Analog Channels 64 Channel Grouping Single Enabled Record Enabled Fi Sampling Freq 40000 Gain a0 Waveform Length a00 Pre Threshold 200 Sort Start 0 Sort End 800 sort Method Template Channel 1 on WE Source 3 Name WEOL Enabled El Record Enabled E Thresho
168. s r Geraro asai oa Put eea l ET Se i i Hihera ge Hema miga l rrm ec Eq e e Fimen kini l O PPa a l acia EF Dapa A ase i it hee The green rectangles correspond to devices that output analog signals e g elec trodes headstages light blue rectangles correspond to devices that output con tinuously digitized sample data e g DigiAmp digital filters auxiliary analog input card red rectangles correspond to devices that output digital event data e g digital input card CinePlex interface keyboard event detector and the remaining rectangles correspond to devices that have unique functions thresh olding device for spike detection sorting device for spike sorting Each device in the topology the larger rectangular boxes has associated with it one or more sources the smaller square boxes to the right of each device where a source is defined as a contiguous range of channels output by a hardware 1 OmniPlex System Overview and Startup or software device The topology diagram provides an excellent high level view of what processing is applied in what order and what source types are associated with which devices The Main Datapool can be thought of as a continuously updated buffer area which is the destination of all the input and processing chains and from which the acquired and processed data of all different types is made available
169. s here a group of waveforms are crossed to add a third unit SPR Channel 1 Waveforms Snapshot Si A BBE ARE GD A Mag 1 70 gt 5 err pe aa Version 1 8 183 6 Additional Sorting Methods SPK Channel 1 Clusters Snapshot ee E Bet Rat GO Poa lt A ORT BF AAA Parzen Mult 0 4 amp la Waveforms Sn R SPK Channel 1 Clus 3D Clusters Properties SpreadSheet As with automatic unit finding in polygon sorting an ellipse is fitted to the cloud of points corresponding to the group of waveforms with the tightness of fit con trolled by the ellipse fit tolerance previously described 184 OmniPlex Neural Data Acquisition System Plexon Inc Chapter 7 Additional Features and Procedures 7 1 Step by Step Saving and Loading PlexControl SettingS ccceeeeeeeeeeeeeeeeeteeeeees 186 7 2 Step by Step Automatically Maintaining Compatible Sets of PXS and PXC Files 188 Ta DIGI input Card CoON OUIAOT corsssccsrermtieperioneainameesa emma 191 7 4 Step by Step Event Triggered Recording c ccccccsesecessseeseereesesenseseneeeeeeessenees 195 FoF GONI rOn DRP oaa 198 7 6 Starting and Shutting Down Server and PlexControl ccccccsecceeeseeesseseeeseeeessaeees 202 F Troubleshooting Stanup FroDIEMIS nee ne aiaia 203 7 8 Step by Step Resetting All OmniPlex Options to Defaults cccceeeeeeeeeeeeeeeeeeeeees 204 I OmniPlex Neural D
170. s 64 to 256 channels with 64 channels per board If you are unsure of the number of channels contact Plexon for assistance When you enter a channel count in Total A D Chans the corresponding number is automatically entered in the Single electrode field Channel Counts 64 Total A D chans 54 Single electrode 0 Stereotrode 0 Tetrode 0 Pass through 7 In the Channel Counts section make sure the Auxiliary Al Card option is checked if you have an AuxAl card in your chassis if you are unsure 22 OmniPlex Neural Data Acquisition System compare your chassis cards to those shown in the photo or contact Plexon for assistance Channel Counts 64 Total A D chans 54 Single electrode 0 Stereotrode 0 Tetrode 32 Pass through W Auxiliary Al card 8 Leave all other Topology Wizard settings at their default values However for future reference note that there is an option which indicates whether you are using a unity gain G1 or gain of 20 G20 headstage DigiAmp HST Gain Gi G20 For the purposes of the User Guide we will use the G1 option but in actual use make sure that your topology includes the correct headstage gain set ting 9 Click OK Wait for Server to generate a new topology diagram and to go through the DigiAmp initialization sequence as indicated by the green progress bar at the bottom of the window 10 Server will display a Save As dialog asking you for the name for your new topology topologies
171. sable recording of individual channels ar al i E Ae ian re _ _ io oe ee one A e e a AE ed A a Pe ooo AN3 a E E ne _ a SS A e ae ooe ee A Pj Pj P e ee l TEN Appendix Page 32 OmniPlex Neural Data Acquisition System TIP AuxAl sampling rate If you attempt to load a pxc file which was saved with a different AuxAI sampling rate than the rate currently in effect in Server the sampling rate loaded from the pxc will override the Server rate Version 1 8 Appendix Page 33 Appendix Appendix G More on Thresholding Aligned Extraction By default OmniPlex uses a standard thresholding spike extraction algorithm which defines the time at which the spike waveform crosses exceeds the thresh old as its timestamp While this is a classic method of thresholding it has some drawbacks First t means that as the threshold is raised or lowered the threshold hits the spike at different points on a rising or falling edge potentially resulting in the timestamp changing by one two or more sample positions Another mani festation of the same effect is that spikes of different amplitudes will have slight timestamp offsets relative to each other While the size of these timestamp errors or jitter is too small to cause problems in most spike train analyses it does have a significant effect on spike sorting it causes smearing of clusters in feature space The basic problem
172. shown above with the test signal since the DigiAmp defaults to its lowest gain of 50 you must reduce the volume level of the PC s Line Out using the Windows volume control or audio mixer A Volume Mixer Headphones High Definition Audio Device Applications E Headphones System Sounds OmniPlex Neural Data Acquisition System When reducing the test signal level using the PC s volume control try to set it to a level such that the largest peaks of the wideband signal occupy about 1 2 to 2 3 the vertical range as shown in the WB Continuous view WB Channel 1 Continuous F l Eoee EE a IUO OUUM s Eg Ti ERA T TTT BBE W8 Channel 1 Continuous EA Peak Histogram Snapshot ff Continuous The goal is to prevent the wideband signal from clipping the A D converters that is exceeding their allowed maximum input range See Appendix A Sig nal Amplitudes and Gain for more detailed information on this topic Note that maximum positive voltage limit before clipping is the bottom of the gray row of tick marks which merge together into a horizontal bar when they are very close to each other just below the time labels while the greatest negative voltage limit is the bottom edge of the view For now you can ignore the tick marks as well as the thin blue horizontal line these will be explained later You can skip Step 3 and Step 4 since they cover the opposite case where the signal amplitude is too small
173. sult The highpass filter used to extract the continuous spike signal SPKC must remove low frequency non spike signals whether they be legitimate field poten tials or low frequency artifacts such as motion artifacts stimulation artifacts power line hum etc Low frequency content leaking into the SPKC can result in a Appendix Page 4 OmniPlex Neural Data Acquisition System wandering baseline which will adversely affect spike detection since the thresholding operation assumes that there 1s no significant low frequency content Setting filter parameters in Server You can access the parameters for each filter which applies to all channels in the respective sources SPKC or FP in the Server topology diagram To do so first stop data acquisition go to the Server window and right click on either the Spike Separator or FP Separator device in the topology Select Edit Device Options to display the options dialog For example for the Spike Separator device Edit Device Edit Device Options Shoa Dene eee ee ree Add New Source To Device Remove Device 300 Highpass cutoff freq Hz siter ype E Lowpass filter 6000 Lowpass cutoff freq Hz Number of poles Bessel Filter type Version 1 8 Appendix Page 5 Appendix And for the FP Separator device l l O m Edit Device Edit Device Options Show Device Characteristics For Add New Source To Device ee e
174. t Bt rT rid The Options dialog for the Units window is displayed You can set the value of the minimum ISI as well as the scaling of the red warning bar 109 4 Basic Spike Sorting Units View Options Display Sources Channel Grid Size Rows J 3 Columns 1 Zoom with Chain Allow Toggling to Show Snapshot Update Mode for Live Data Erase every 10 SECS Erase Mode Standalone Master Slave Minimum Units to Show 3 J Show Unsorted Inter Spike Interval Minimum Refractory Period 1000 Percentage of Short ISI for Maximum Bar Height 10 Cancel When multiple units are defined on a channel each is shown in the Units window with its name and Short ISI bar SPK Channel 1 Units Assuming that you have set a reasonable value for the Minimum Refractory Period in the Options dialog the two most common reasons for a high percentage of Short ISI spikes are 110 OmniPlex Neural Data Acquisition System 4 2 5 4 2 6 Version 1 8 e The threshold is set too low and is resulting in a significant number of noise spikes which are being detected at a firing rate higher than would be possible for an actual neuron e Two or more units are being incorrectly sorted into a single unit as an extreme example of this if you drew a waveform crossing line across all the waveforms on a channel resulting in all spikes being sorted into unit a you would very likely see a high percentage of Short ISI spi
175. t finding whose results i e unit definitions will then overwrite the previous ones As a general guideline to find more clusters reduce the Parzen Multiplier value to find fewer clusters increase the Parzen Multiplier However auto matic unit finding which is in essence an unsupervised classification problem is a complex task especially when dealing with noisy data and you will some times find counter intuitive results when you change the Parzen Multiplier Fortunately the default value of 0 7 works well with many types of spike data 6 7 1 Automatic unit finding on all channels 1 OmniPlex can also perform automatic unit finding on all spike channels instead of one at a time To do this it is recommended that you first unzoom the PCA display i e return to a multichannel PCA view by double clicking in the view if it is Zoomed This is so that you can see the progress of the automatic unit finding as it works through all the spike channels You can view either the multichannel spike or multichannel PCA views according to your preference Also make sure that you have collected a spike snapshot If you already have units defined on some or all channels you may wish to remove them before starting the automatic unit finding This is optional since the unit finder will delete any existing units on each channel it processes but it makes it easier to view the channel by channel progress of the unit finding if OmniPlex Neural
176. that those sample positions which have high variance across a given set of spikes are given greater weight in calculating the projection The motivation behind this is that samples where there is more amplitude spread within a group of spikes are more likely to have separation between the amplitude values corresponding to different units The PCA projection of a 32 point spike results in a 32D point in PCA space how ever PCA orders the coordinates in order of decreasing variance so that the first few coordinates contain most of the variance and the higher order coordinates represent mainly noise and can be discarded By taking the first two or three PCA coordinates and dropping the others we obtain a projection into 2D or 3D PCA feature space and achieve the desired dimensionality reduction Here is an exam ple of spikes and their corresponding 2D PCA projections where each point in the PCA display corresponds to one spike in the main spike window 132 OmniPlex Neural Data Acquisition System SPK Channel 1 Waveforms A X i SPK Channel 1 Clusters SS A BY FRE GD A Mag 1 70 5 SF ont pet I EE Be D pra Ont Bae al ee K Channel 1 AME L a d E SPK Waveforms P SPK Channel 1 3030 Clusters Prope And similarly the 3D projections SPK Channel 1 Waveforms OX i SPK Channel 1 3D Clusters R Z BS BE aD cH Mag 1 70 S Lp 2 u ais a fe z Bi Channel 1 grid 4 00 mV
177. the amplitude of the field potentials upon which they are superimposed In other words wideband amplitude field potential amplitude spike amplitude where a typical case might be something like wideband amplitude 2 2 mv pp field potential amplitude 2 0 mv pp spike amplitude 200 uv pp But there is no need to use analog gain as a substitute for visual magnification since OmniPlex provides highly accurate low noise A D conversion of even low level signal components such as small spikes and a set of software magnifi cation tools to allow you to view spikes at a comfortable size In fact if you crank up the gain while looking only at spikes you may not even be aware that you are causing clipping of the wideband signal The maximum allowable signal level at the recording electrode before amplifica tion 1S 10 V pp total gain For example if you are using a unity gain G1 headstage and a DigiAmp gain setting of 1000 10 V pp 1000 10 mV pp 1 e 5 mV Voltages exceeding this value will cause clipping at the A D converter unless you reduce the DigiAmp gain In summary Always view the wideband signal when setting gain and avoid set ting the DigiAmp gain so high that it causes clipping of the wideband signal on Appendix Page 2 OmniPlex Neural Data Acquisition System any channel then use magnification to visually enlarge the spikes in the displays as necessary Version 1 8 Appendix P
178. the same digital signal processing functionality as OmniPlex If the SPKC source is recorded then this issue is avoided Digital events keyboard events and CinePlex events are always recorded there are no enable disable checkboxes for these sources Version 1 8 117 5 Recording 5 2 Step by Step Recording 1 Before recording a file select the sources and channels which you wish to record Click on the Properties Spreadsheet tab to view the record enable options E SPK Ta ns Pa SPK ip E Clusters 3D SPK Channel 1 3D Clusters H Properties SpreadSheet for 2 If any of the sources WB SPKC SPK or FP are currently selected you will see the record enable columns for all the others as shown above If some other source is selected and you do not see the above Rec columns use the previous next source buttons in the main toolbar to step through the available sources until the desired Rec columns are displayed SP le 1 70 a ie Or ee 3 Check the appropriate boxes to indicate which channels of which sources you wish to record Remember that you can select multiple channels within a column and set them all to the same setting as the topmost row as described 118 OmniPlex Neural Data Acquisition System previously For example to enable recording for all WB channels enable WB recording for the top channel then click on the Rec WB column header oo 4 Select Set All Channels Like Topmost Selected Channel
179. tinuous View Options Channel Grid Size Rows of Columns 1 E Zoom with Chain Show Channel Number Labels E Allow Toggling to Show Snapshot Show Tick Marks for Associated Sorting Source Spikes Sweep Mode 9 Standalone Master Show Time Scale Show Voltage Scale Show Threshold when zoomed slave Magnification Use Same Magnification for all Channels E Chain Control Some of the options should be self explanatory or are advanced options and will not be described here Two that will be described are Use Same Magnification for All Channels and Chain Control 2 3 6 Use Same Magnification for all Channels By default changing the magnification value in a view s toolbar affects all the channels in a view However by unchecking Use Same Magnification for all Channels each channel can have its own magnification value which can be use ful when the signal amplitude varies widely from channel to channel When this option is unchecked you must select a channel by clicking on it before adjusting its magnification In this example only channel 5 which is selected has had its magnification increased to 2 0 while the other channels remain at their default magnification of 1 0 Version 1 8 63 PlexControl User Interface 2 3 7 A Fae Daal BEE Mag 2 00 HE A T T 1s is gt 25 TIP Changing magnification on the selected channel If you change the magnification value in the toolbar and don t see
180. ts tool bar on and off The view s toolbar is displayed WE Continuous PA Bt BD ae Ac OPT A Mag 1 00 2 FT Ee 105 mE a You can hover the cursor over each of the buttons in the toolbar to see a 2 tooltip description of the button s function A ORT BET Mag 1 00 TE ce oT TT hl Version 1 8 53 2 PlexControl User Interface 3 If you want to hide the toolbar for example to save vertical display space click the down arrow in the upper right corner again WB Continuous SA PRE SS IS Ac OPT BET Mag 1 00 2 F O Tt e a Los J i Lae Te E nE K E E O o A A A A A E 15 00 mW 15 00 mV i TT AN Pa THI 15 00 mil MY 4 Certain of the functions available in the continuous view toolbars are particularly useful in working with the spike continuous data For example since the amplitude of spikes is usually much smaller than the amplitude of the wideband signal you will typically use the magnification feature more often when working with spikes To view the spike continuous SPKC view click on the tab labeled SPKC Continuous AF Pad gt as Ac Oct BB Mag 1 00 gt S amp T LE Peak ied FP Continu ied Al Continui We Continu Peak Histogra S SPKC Conti 54 OmniPlex Neural Data Acquisition System The SPKC Continuous view is displayed Os 55 10s rata rt vette aiiai aii NIU
181. two options that are highlighted determine how spike timestamps are dis played If you turn off Show Per Unit Timelines all the ticks for a given spike channel are displayed interleaved on the same row similar to the display in the small strip at the top of each SPKC channel in its continuous view OmniPlex Neural Data Acquisition System Version 1 8 SPK Activity ee hd W E Co acces LLE I iji Watt i 1 N i SPKC C Wl Ch B FP Cont RRM AL Cont il Il Ml Firing Ra r 201 F Additional Features and Procedures 7 6 Starting and Shutting Down Server and PlexControl There are a few best practices to keep in mind regarding the sequence in which Server and PlexControl are started and shut down The recommended startup sequence is to run Server wait for the initialization sequence to complete indicated by the green progress bar at the bottom of the Server window then start PlexControl then start data acquisition It is possible to first run PlexControl which will then automatically start Server before allow ing you to continue however if this method ever fails you should fall back to the recommended sequence When you are completely finished with the system and want to shut down Omni Plex the recommended sequence is to stop data acquisition from PlexControl then close PlexControl then close Server In other words the shutdown sequence
182. uares error between it and each of the templates for that channel is calculated To match a template the error value for the spike relative to that template must be less than the fit tolerance If a spike is within the fit tolerance of more than one template then the unit whose template yielded the lowest error closest template fit wins If the incoming spike is not within the error tolerance of any of the templates that are defined on its channel it remains unsorted Therefore the definition of each unit consists of the template waveform and the associated fit tolerance Once created the unit definition 1s sent from PlexControl to the sorting device in Server which immediately begins using it to sort incom ing spikes which are then displayed in PlexControl in their unit colors Note You can use the mouse to move individual template points as marked by the small squares However this can be a time consuming process and is gener ally unnecessary TIP Unit and Unit definition Informally you will often see the terms unit and unit definition used interchangeably TIP Add several units using this shortcut Rather than clicking the Add Unit button in the toolbar each time you wish to add a new unit you can simply hold down the CTRL key and draw a crossing line in the main spike window which is interpreted as an Add Unit command An experienced user can quickly add sev eral units using this shortc
183. uency selected here affects the wideband signal and all signals derived from it SPKC FP By default this is set to the lowest frequency 0 05 Hz which Appendix Page 28 OmniPlex Neural Data Acquisition System enables the recording of the lowest frequency field potentials without significant phase shift group delay issues However such a low cutoff can be inconvenient when recording of very low frequencies is not needed in particular if there is DC offset on the input signal you may have to wait several seconds after data acqui sition is started or a headstage is powered on before the baseline settles to zero due to the large time constant of the filter In such cases you may wish to use a cutoff of 0 5 Hz If you are experiencing problems due to high amplitude low fre quency artifacts e g motion artifacts you may wish to try the highest cutoff fre quency of 3 Hz although this may cause phase shift issues with recording of field potentials below 10 Hz However remember that the FPAlign offline utility may be used to remove most of the phase shifts induced by the filters Referencing Version 1 8 The Referencing section controls analog reference selection with individual con trol of each group of 16 channels RefA typically corresponds to a buffered ground while RefB corresponds to a true reference Consult the documentation for the specific headstages which you are using for additional details Appendix Page 29 Appe
184. usters 30 3D Clusters Properties SpreadSheet TIP Taking snapshots You do not have to wait for every channel to finish its snapshot to begin working with the channels that are ready Note You will sometimes see especially with test signals where every channel is nearly identical that the PCA clusters for some channels will appear to be flipped or mirrored vertically and or horizontally compared to other channels This is because the mathematical definition of PCA is invariant to sign changes since PCA is based on variance In other words two PCA displays one of which is the mirror image of the other are mathematically equivalent 140 OmniPlex Neural Data Acquisition System 13 Note that the default for spike snapshot collection is to calculate PCA when the snapshot collection is complete as shown in the spike snapshot options Spike Snapshot Options Source SPK Snapshot Buffer Buffer Size Eli Spikes per Channel End a Forward Snapshot Automatically after collecting a full Snapshot Buffer or after 60 seconds have elapsed Automatically after collecting for 10 seconds Only Manually When a new Snapshot first becomes available for a channel W Calculate PCA Perform Automatic Sorting This is generally the most convenient method however you can also manu ally initiate the PCA calculation using the PCA button in the toolbar However you still must collect a spike sna
185. ut Version 1 8 103 4 Basic Spike Sorting 104 4 2 2 Changing the fit tolerance for a unit Sorted and unsorted units for the current channel are also displayed in the Units window below the main spike window gt Tasks O Xx SPK Channell Waveforms iX GA BE BE a Mag 1 70 o A System R z A A EB Unit a Fit Tol 0 033 i Dania a 7 ay Create View Layout for i Sources AR Automatically Configure All Sources Start Recording Data a Stop Data Acquisition Properties O x SPK Source 6 On Device Basic Sorting Channel Type Spike Channels 64 Channel Grouping Single Enabled Record Enabled Sampling Freq 40000 Gain 250 Waveform Length 800 Pre Threshold 200 Sort Start 0 Sort End B00 Sort Method Template Channel 1 on SFK Source 6 Name SPEOL Enabled F Record Enabled W Threshold 12 093 Unit a Fit Tolerance 0 033 SPK Channel 1 Units This is useful because it reduces the visual clutter and allows you to see what is being sorted into each unit in isolation Within the Units Window the colored highlight rectangle indicates the currently selected unit which 1s analogous to the currently selected source and channel You can click on a unit in the Units Window to select that unit which allows you to perform tasks on it such as changing its fit tolerance or deleting it OmniPlex Neural Data Acquisition System Version 1 8 When
186. vated by a desire to not miss any spikes however in addition to incorrectly detecting noise as spikes this can cause parts of valid spikes to be missed if a noise triggered detection occurs immediately before a valid spike While thresholds can be set manually for each channel as described later the problems just described can largely be avoided by taking a continuous snapshot of the SPKC signal and using PlexCon trol s auto thresholding feature to set the thresholds in a consistent well defined way Auto thresholding is also much faster than setting thresholds manually especially for systems with many channels OmniPlex Neural Data Acquisition System 3 2 OmniPlex Concepts Snapshots Version 1 8 OmniPlex has the ability to take snapshots of continuous data or of detected spike waveforms A snapshot can be thought of as a temporary copy of the incoming data containing either a given number of seconds of continuous data or either a given number of seconds worth of spikes or a given fixed number of spikes Here are some examples of typical snapshots A snapshot consisting of 10 seconds of continuous spike SPKC data for each of 64 channels with the snapshots collected taken in parallel a 10 sec ond snapshot will contain 400 000 samples per channel at a 40 kHz sampling rate A snapshot consisting of 500 spikes on each of 64 channels with the snapshot collection starting at the same time on each channel but ending on each
187. vious session you can load the corresponding pxs and pxc files in Server and PlexControl respectively OmniPlex Neural Data Acquisition System 7 3 Digital Input Card Configuration Version 1 8 The Digital Input DI card in the OmniPlex chassis allows you to input signals from external digital sources such as behavioral systems switches levers etc These digital input signals are detected by the DI card timestamped with a reso lution of 25 microseconds and written to the Main Datapool as channels within one of two DI sources either Single bit events or Other events as described below The DI card has two front panel 26 pin connectors referred to as port A bottom and port B top Each port can be configured to operate in mode 1 or mode 3 and for high true or low true logic To view or modify the DI card settings first stop data acquisition go to the Server window and right click on the Plexon Digital Input device in the topology Select Edit Device Options to display the options dialog o T Edit Device epes sai Edit Device Options eee es Show Device Characteristics Add New Source To Device Remove Device 191 F Additional Features and Procedures Plexon Digital Input Configuration Port A Port B Mode 1 individual events Mode 1 individual events Mode 2 combo 8 8 Mode 2 combo amp 8 Mode 3 strobed word
188. w additional information becomes available At the bottom of the PlexControl main window the status bar continuously displays the time and voltage corresponding to the cursor position as you move the cursor within the view For example you can point to a spike peak to get an approximate 57 58 PlexControl User Interface 2 3 2 measurement of its amplitude Note that the time displayed here is absolute time since data acquisition started Fih a mR Ag ae T OF mit PPL TTD PrP Tur yy yd ia iN aidi ET ial NAIN t 3111 525 sec V 4 44 mV TIP Pause the display for convenient viewing Pausing the display as described later makes it easier to point at spe cific parts of the displayed signal The time voltage readout in the status bar will still track the moving cursor position even if the dis play is paused Note that the amplitude bar at the right end of the continuous displays 1s marked with minimum and maximum values but the top and bottom of the bar are at 75 of the actual minimum and maximum values for the display In the example shown above the actual amplitude range of the display extends beyond the top and bottom of the scale bar all the way to the very top and bottom of the black background area In this case the actual minimum and maximum displayable amplitudes are 10 mV and 10 mV Changing the sweep rate You can change the horizontal sweep scroll rate of the continuous displays
189. wn Server and PlexControl 202 Troubleshooting Startup Problems 203 Step by Step Resetting All OmniPlex Options to Defaults 204 Appendix Appendix A Signal Amplitudes and Gain A 2 Appendix B Separation of Spikes and Field Potentials using Digital Filters A 4 Appendix C PlexControl Spike Display Modes A 9 Appendix D Advanced User Interface Features A 21 Appendix E DigiAmp Analog Highpass Filter and Referencing A 28 Appendix F Auxiliary Analog Input Aux Al A 30 Appendix G More on Thresholding Aligned Extraction A 34 Appendix H Enhanced PCA Feature Space A 38 Appendix Lowest Latency Operation A 42 Appendix J PlexControl Keyboard Shortcuts A 47 Appendix K Hardware Pinouts and Connections A 48 A 1 Version 1 8 x OmniPlex Neural Data Acquisition System Plexon Inc Version 1 8 Plexon Inc Chapter 1 OmniPlex System Overview and Startup 1a ee OE E E A E ese deena wise a aaa 2 Eea e ay 210 U Ree in ane ee EE oS Ae ea Peon AE N T ee ee tare eee ee a po RW cg iy DEEE EE gt EEA tree te ter tee hee a Renn cette een cere ne nce a ee Me Meer Soren ty Rete E PEt On 6 1 4 OmniPlex Concepts Devices and SOUIC S cceceeececeeeeeeeeeeeeneeeeeeeeeaeaeeeeeeeeaeeeeees T 1 5 Step by Step Power up and ConnectionS ssssssrsensssnssrrensnrnnrrsernnnrnenesnreeserneresssnnsnee 12 1 6 Step by Step Starting and Configuring OmniPlex Server ccccceeceesseeeeeeeeeeeeeeaeees 20 1 7 Step by Step Starting PlexC
190. words imagine that you set the erase time to 3600 seconds or one hour and allow the display to accumulate thousands or millions of waveforms in that time then after an hour you do a waveform crossing on a spike that was drawn an hour ago you may see an error message indicating that no waveforms were crossed and this is because those waveforms are not among the 500 most recent incoming spikes When using Erase mode with a long redraw interval note that you can manually erase the display at any time using either Erase from the right button menu for the main spike window or the Erase button in the toolbar Appendix Page 19 Appendix iF Ce m aa o i Show Threshold Show Sort Range Show Slice Positions 7 Show Time Voltage Grid SPK Channel 45 Waveforms ft 4 Bet Pe a 1 70 ele eee ail Erase the Display Some users prefer to use this method so that they have total control over when the display is erased Note that the other spike and continuous displays have their own individual Erase commands The 2D and 3D PCA displays also support Fade Rolling and Erase modes 2D PCA only when in zoomed single channel mode Appendix Page 20 OmniPlex Neural Data Acquisition System Appendix D Advanced User Interface Features The basic features of the OmniPlex user interface are described in the main body of the User Guide The following more advanced features are handy for users who wish
191. x You can reset the Drop indicator to zero using the Reset Drop Count command in the Data menu Drops are brief gaps in the data but are not errors in timestamping See the section on Performance Consid erations for more information Version 1 8 85 3 Spike Detection 86 15 00 mv Ba y PlexControl PlexControll File View Display Configure DOE ce bed a Tasks Stop Data System Create View Layout for So Automatically Configure A b Start Recording Data E Stop Data Acquisition ka Reset Drop Count Start Recording TIP Thresholds at high magnification At very high magnifications and large threshold values e g 15x magnification with a 40 threshold the blue threshold line can dis appear due to it being beyond the top or bottom of the displayed amplitude range 1 e it s off the screen In such cases you may need to set the threshold value numerically using one of the previ ously described methods or temporarily reduce the magnification in order to bring the threshold close enough to zero that it remains visi ble when you restore the high magnification OmniPlex Neural Data Acquisition System 3 4 4 Dragging the threshold line in the SPKC snapshot peak histogram view Although as described previously a snapshot of a channel of continuous data consists of a certain duration of that signal OmniPlex does not display a SPKC snaps
192. xControl you should also shut down Server Abruptly closing PlexControl in the midst of a complex multichannel operation e g auto sorting is not recommended and in some cases can cause a crash In addition if you then restart PlexControl it may be in an inconsistent state If this happens then at a minimum you should stop and restart data acquisition before proceeding 202 OmniPlex Neural Data Acquisition System 7 7 Troubleshooting Startup Problems If you ever encounter a situation where data acquisition fails to start and or you receive any error message from Server the first thing to try before contacting Plexon support support plexon com is to exit from PlexControl and Server check all cables and power and restart OmniPlex If this does not help cycle the power on the chassis never do this while OmniPlex is running then reboot Windows and try again However in most cases where the problem is an unplugged cable wrong type of DigiAmp etc Server will display an error mes sage informing you of the problem Problems involving incorrect or inconsistent application settings can often be solved with the software reset procedure described in the next section Version 1 8 203 F Additional Features and Procedures 7 8 Step by Step Resetting All OmniPlex Options to Defaults If you ever need to reset all PlexControl and Server options to their defaults use the following procedure The one setting that will not be reset
193. yout so that it will be easier to follow the examples shown here However you may want to make some of the views larger or smaller depending on what you are working on and the aspect ratio of your monitor The easiest way to do this is to drag the splitter bar that divides adjacent views making one larger and the other smaller As an example you can enlarge the lower right view which is displaying the continuous sources 49 50 2 PlexControl User Interface 2 2 Step By Step Resizing Windows using the Splitter Bars 1 Move the mouse cursor to the horizontal bar between views and without holding down the mouse button move the mouse up and down across the bar until you see the cursor change from the standard arrow cursor to the splitter dragging cursor hot ied Continuous E Peak Histogram Snapshot ied C OmniPlex Neural Data Acquisition System Version 1 8 Properties SpreadSheet 105 ied Continuous Peak Histogram Snapshot aed Conti When you see the cursor change hold down the left mouse button and drag to move the divider between the two windows as shown below The divider displays as a gray bar while you are dragging it Release the left button when you are done resizing the windows rerties SpreadSheet 108 158 If you accidentally drag the entire window as shown by a large shaded rect angle being dragged by a normal arrow cursor instead of dragging the divider bar you can cancel this by hittin

OmniPlex User Guide.book

Contents

Download Pdf Manuals

Related Search

Related Contents