SpikeTaro Version 1.0 User`s Manual
Contents
1. Setting of parameters for chart display User selects this Graph Properties window will opens 22 26 SpikeTaro Version 1 0 User s Manual Graph Properties Axis Range Y Axis Range Min Axis Titles Title and Line X Axis Title Graph Title ENAKE OOOO Y Axis Title Amplitude MS LII Gothic 8 Line Colo Bick Y Axis Labels A Axis Label Font Setting Line Width MS LII Gothic 8 Y Axis Label Font Setting MS LI Gothic 9 Cancel User can set ranges of X Y axises maximum minimum auto range titles of axises font size type chart title line color and width By click OK button these parameters are reflected 23 26 SpikeTaro Version 1 0 User s Manual 2 9 2 Raster plot 1 Change window size Size of the raster plot can be changed by dragging size grip mark located in right bottom of raster plot window 2 Popup menu Popup menu is appeared when user clicks raster plot area by right button of mouse The functions of menu Save Graphics Properties are the same of above popup menu of time chart except setting parameters of Marker Color and Marker Size e When user clicks Save As Text spike peak time sequence of each cluster will be output Ch 1 Raster Plot Cluster ID Save Graphics Save As Text Properties 24 26 SpikeTaro Version 1 0 User s Manual 2 9 3 Clustering results plot 1 Change window size Size of the clu2. 63 14 64 13 63 13 63 14 13 63 13 63 14 64 13 63 13 63 14 64 Time y Time 1 Time A Time 0 X Cluster ID 10 Sort IP X Cluster ID 12 Sort 5Ue UU3 659e 003 i 595e 003 1 UYe UUS 159 003 9 46e 004 q 5 4 99e UU3 341e 003 405e 003 4 3be UUs 9 JJe UUd 905e 003 2 00 06 13 19 26 32 0 2 00 06 13 19 26 32 13 63 13 63 14 64 13 63 13 63 14 64 13 63 13 63 14 64 13 63 13 63 14 64 Time A Time Time Time Size grip mark 18 26 SpikeTaro Version 1 0 User s Manual After change outer window size Windows Control Tile button is appeared by right mouse button clicking at gray region of outer window When user selects Tile respective time charts are rewritten corresponding with size of outer window Ch 1 Sorting Result Data Cluster ID 1 Sorti jal px Cluster ID 2 Sorti gt lt Cluster ID 3 Sorti M mp p lt Cluster ID 4 Sorti s ia 00 06 13 19 26 32 00 06 13 19 26 32 0 13 13 63 14 64 13 63 13 63 14 64 13 63 13 Cluster ID 6 Sorti OD b Cluster ID 7 Sorti m 3 00 05 13 19 25 32 i 0 2 00 05 13 19 25 32 00 05 13 19 25 32 13 63 13 63 14 64 13 63 13 63 14 64 13 63 13 63 14 64 13 63 13 63 14 64 Time Time i i 2 X 6596 003 159e 003 341e 003 2 00 06 13 19 26 32 0 2 00 06 13 19 26 32 13 63 13 63 14 64 13 63 13 63 14 64 13 63 13 63 14 64 13 63 13 63 14 64 Time Time Time l Time Ch 1 Sorting Result Data Cluster ID 1 Sorting Result Data x Cluster ID 2 Sorting Result Data Cluster ID 3
3. box SpikeTaro outputs sorting result as waveform e Raster Plot To check this box SpikeTaro outputs raster plots of each separated cluster To click OK button in Sorting and Clustering Setting dialog sorting process starts After finishing the process sorting results are shown on your display Sorting Result 1 Cluster information i Sorting Results Summary E E3 channel 1 Detected Spike Count 546 Number of spikes including Cluster 15 Number of spikes including Cluster 57 Humber of spikes including Glusterg 53 Humber of spikes including Glusterd 18 Humber of spikes including Cluster 15 Number of spikes including Cluster 13 Number of spikes including Cluster 60 Number of spikes including Clusters 11 Number of spikes including Cluster 77 Number of spikes including Glusterl 16 Number of spikes including Glusterll 1 Number of spikes including Cluster 15 Ignored Spike Count 241 Cluster Information window This window indicates follows information e Total spike count detected by SpikeTaro e Spike count in each cluster e Detected but ignored spike count By drag lower right side of the window user can change the window size 14 26 SpikeTaro Version 1 0 User s Manual sorting Result2 Waveform of each cluster SpikeTaro outputs waveform of each cluster Title bar in each waveform window shows cluster id which correspond with above Cluster Info
4. chart treatment see section 2 9 Chart treatment 11 26 SpikeTaro Version 1 0 User s Manual 2 5 Sorting By clicking Sorting button in main menu the Sorting and Clustering Setting dialog opens Sorting process is applied to most recently processed FIR filtered data i Sorting and Clustering Setting sorting Parameters lenored Spikes BaseLine Threshold 0003 The clusters which include spike count af Contribution Ratio tr 2 0990 2 Assume the same spike with Spike Height 102 B 24 5 for total spike count are ignored The clusters which include less than E Diference spikes are ignored Output tems A sorting Results Raster Plot Cancel Sorting and Clustering Setting Dialog Sorting and Clustering Setting dialog consists of several parameter groups 1 Sorting Parameters Group e Baseline Threshold Signal selection threshold When signal peak is larger than this threshold the spike data which includes raising phase peak and falling phase is detected as sorted target For example user sets this value to 5 0 red horizontal line against following data three spike waveforms red waveforms are detected as sorted targets 12 26 SpikeTaro Version 1 0 User s Manual FIR Filtered Data ei Ch 1 Filtered Data ace Baseline threshold ensample e Contribution Ratio r 2 SpikeTaro sorts spikes by correlation coefficient between two spike wa
5. Sorting Result Data Cluster ID 4 Sorting Result Data 0663 1313 1963 2614 3264 0663 1313 1963 3264 Time F Time y Cluster ID 6 Sorting Result Data Cluster ID 7 Sorting Result Data Cluster ID 8 Sorting Result Data ES AE uM 10980 TUE 0013 0663 1313 1963 3264 EE Ut 0013 0663 1313 1963 2614 3264 US 0013 0663 1313 1963 2614 3264 Time A i Time a Cluster ID 9 Sorting Result Data 3 Cluster ID 12 Sorting Result Data yugi i bpse UUd d pgpe uus BEL 3o 38534 lt HUA 3 Ewe 28 00 9Joe uud D 264 0663 1313 1963 2614 3264 E 0013 0663 1313 1963 2614 3264 Time Time y i y Time Changing outer window size and rewrite respective time chart 19 26 SpikeTaro Version 1 0 User s Manual 2 Treatment of respective time charts e Changing window size Respective time charts can move freely within the outer window by dragging these title bars Moreover user can change the window size by dragging size grip mark red circle in under figure Gh 1 Sorting Result Data Cluster ID 2 Sorting R olx Cluster ID 3 Sorting R D E Cluster ID 1 Sorting R DH X AAA AA AAA A A AA Cluster ID 7 Sorting Result Data Title bar 116e 002 Gluster ID 5 Sorti 661e 003 E 161e 003 Amplitude 3 39e 003 Gluster ID 9 Sorti 8 29e 003 E SRE 134e 002 0013 20 26 SpikeTaro Version 1 0 User s Manual e Magnification display of chart data User can magnify displayed data in the time char by
6. SpikeTaro Version 1 0 User s Manual Spike Taro ver 1 00 Chinou Jouhou Shisutemu Inc SpikeTaro Version 1 0 User s Manual Manual version 1 0 rev2 O 2010 Chinou Jouhou Shisutemu Inc All rights reserved For SpikeTaro 1 0 1 26 SpikeTaro Version 1 0 User s Manual Contents is Meee CHG Ul Otis MENORES RO ULT D T LT IT TITULI UTERE 3 2 HOW LO SS SO ee aO A A AE AA pltug B usata Baek AE 3 LN Wats SN RE eRe aT BCE A ARR E O AY DONTE RY Be SPL OTE SEPT SOMEONE ETS RY Bear OY DOE 3 MED SSL death a AS ARES sek bis du bS Dd irse Pino a ae hd eS 4 2 3 Ladina phy pito o ed Mo os 4 aed ahs ah II hea ee D D NM C NE A ES ast E E E E E E S E E E N E EEE A E E D DUX WA E TE O A EE E EET E E E E EE E E bis 6 2 MS E A EE O LM ME Ma al 8 VS OE A A ar a a A A A AE e e a r OE A a E A 12 LAE CN NERIS Pa 16 Ded Pitormat IO abour Pikeli Oss arinen qan erSd ES pa AE 17 oa E E EE A II A 17 2 Chia Uo We Ca UMeMG aan do pite encoder bote arca oda dew salvada 17 AE EE EE E E EE E A E E E a 17 A a EI aaa o a Do a a a a is 24 255 octo ls ESTAS Fs IDO A a iaa 20 CCO e US eaat ETT 26 2 26 SpikeTaro Version 1 0 User s Manual 1 Introduction SpikeTaro is a program which has noise filtering function high level analyzing spike sorting and clustering functions for neurophysiological data SpikeTaro s features include e Noise cutoff function by digital filter e Separation of single spike for synthesized signal of multi spik
7. al Data Data Record Count Data Includes Time Column Scale Factor for Y Time Data Column Number 1 Unit s vw Stimulation Recording Rate 2000 00 Stim Data Channel Scale Factor for Y 100 Stim Threshold _ Disable Stimulation Display Stimulation Stim Data Column Number 3 Stim Threshold 000 V Disable Stimulation Display Load Physiological Data Dialog SpikeTaro supports file types of wav and text as input data format 2 3 1 Wav File By selecting wav file in Open data file dialog Wav Data Input group in the Load Physiological Data dialog will be active e SpikeTaro supports only PCM non compression type wav file Following parameters can set in the Load Physiological Data dialog e Data Record Count Input total data channel count in the wav file In case of stimulation channel is included in the wav file the count includes stimulation channel 5 26 SpikeTaro Version 1 0 User s Manual e Scale Factor for Y If necessary input scale factor for physiological data This factor operates on all channels of physiological data except stimulation data e Data Includes Stimulation Record In case of including stimulation record in input data check this check box e Stim Data Cannel Input channel number of stimulation channel Count starts at 1 e Stim Threshold SpikeTaro determines to turn stimulation on off by this threshold e Disable Stimulation Di
8. cute Ward method of conventional clustering method This process is independence on above spike sorting process In this process SpikeTaro uses spike height and spike duration as clustering parameters By clicking Clustering button in main form the Process Parameters dialog is opened again Clustering process is applied to FIR filtered data Sorting and Clustering Setting sorting Parameters Baseline Threshold 0003 Contribution Ratio ir 2 Assume the same spike with spike Height Difference M Clustering Ward Method Number of Cluster Ignored Spikes The clusters which include spike count of X for total spike count are ignored The clusters which include less than spikes are ignored Output tems sorting Results Raster Plot Cancel Sorting and Clustering Setting Dialog 1 Clustering Ward Method e Number of Cluster Set number of cluster separated by Ward method Default is cluster count gotten by previous sorting process 16 26 SpikeTaro Version 1 0 User s Manual By clicking OK button clustering result is displayed Ch 1 Clustering Results Cluster Clusterz Cluster3 Cluster Cluster5 Cluster amp Cluster Cluster amp Cluster8 Cluster10 Cluster Cluster12 a EI ag a un Spike Duration ms Clustering result About the plot treatment see section 2 9 Chart treatment 2 1 Information about Spikelaro By clicking Abou
9. dragging area of the chart Vertical and horizontal scroll bars are appeared in magnified chart To reset scale click circle shaped button located in top or left side of the slide bars Gh 1 Sorting Result Data Cluster ID 1 Sorting R olx Cluster ID 2 Sorting R Cluster ID 3 Sorting R A EE SEALS QQmuUmOxco2 Gluster ID 7 Sorting Result Data 116e 002 Gluster ID 5 Sorti 661e 003 161e 003 Amplitude 339e 003 8 39e 003 1 34e 002 Ch 1 Sorting Result Data Cluster ID 1 Sorting R ollx Cluster ID 2 Sorting R m x Cluster ID 3 Sorting R m x 114e 002 Cluster ID 5 Sorti E 641e 003 Amplitude 1416 003 Cluster ID 9 Sorti 359e 003 HER 21 26 SpikeTaro Version 1 0 User s Manual e Popup menu Popup menu is appeared when user clicks time chart area by right button of mouse Cluster ID 7 Sorting Result Data 116e 002 c MEM Save Graphics E 161e 003 Save as Text Properties 339e 003 basal 839e 003 134e 002 0 Popup menu Popup menu includes Save Graphics Save as Text and Properties buttons e Save Graphics Save displaying chart as graphics file As Saving graphics format Enhanced Meta File emf Bitmap bmp PNG png are available e Save as Text Save displaying chart as text file Tab separated text data and comma separated text data CVS Format are available e Properties
10. e waveform during period of spike duration e Spike Sorting based on comparing with spike waveforms by correlation coefficients e Clustering by conventional clustering method Ward Method e Producing raster plot e Output publication quality graphics 2 How to use Spikelaro 2 1 Start up Important Login Windows system as administrator to use SpikeTaro Click SpikeTaro s shortcut on your desktop of Windows system or SpikeTaro s icon located in Windows Start Menu of Start CJS SpikeTaro 1 0 SpikeTaro will start At first starting time inputting of license file file extension is license is required Please select license file in License CD in License Authentication dialog 3 26 SpikeTaro Version 1 0 User s Manual 2 2 Main menu FIRst of all main menu window is opened SpikeTaro 1 0 C FileOpen K File Open Button Filtering Button Sorting Button Clustering Button About Button Main menu 4 26 SpikeTaro Version 1 0 User s Manual 2 3 Loading physiological data In order to load physiological data to SpikeTaro user clicks File Open button After that Open data file dialog opens By user selecting input file and clicking OK button in Open data file dialog Load Physiological Data dialog which is inputted data parameters opens Load Physiological Data Wav Data Input Text Data Input Physiological Data Time and Physiologic
11. ristic becomes to be sharper However phase delay of filtering data increases Low Cutoff Frequency Hz Input low side of cutoff frequency If you want to use low pass filter input 0 High Pass Filter If you want to use high pass filter check this box High Cutoff Frequency Hz Input high side of cutoff frequency Display button Clicking this button amplitude characteristic corresponding with setting parameters is shown in chart area And phase delay information number of data point and delay time are displayed under the Display button FIR Filter Setting Number of Impulse Responses Low Cutoff Frequency Hz 120 4 Amplitude Characteristics Hight Pass Filter High Cutoff Frequency Hz 1800 2 Ampulitude Gain Display Phase Delay 256 points 128 ma 2000 4000 6000 000 pacar FIR Filter Setting Dialog after setting parameters 9 26 SpikeTaro Version 1 0 User s Manual Supplemental information User can magnify frequency range by dragging chart area FIR Filter Setting Number of Impulse Responses Low Cutoff Frequency Hz f Hight Pass Filter Amplitude Characteristics i e ol High Cutoff Frequency Hz 1800 Display Ampulitude Gain AA a m jtm Phase Delay 256 points 128 me 2000 4000 6000 8000 a eina FIR Filter Setting Number of Impulse Responses 513 w Ampli
12. rmation Gh 1 Sorting Result Data Cluster ID 1 Sorti lolx 4 fUe UU3 dde UUZ 2 r e UUs 5536 005 3le Lul3 Zae bhb fe ut3 71 1 f amp UU 00 06 13 19 26 32 00 06 13 19 26 32 13 63 13 63 14 64 13 63 13 63 14 64 Time Time 0 2 13 63 13 63 14 64 Gluster ID 6 Sorti g3Ue UU 3 30e 003 1 70e 003 B le UUs 711 fe UUe 2 13 63 13 63 14 64 488 003 4 488 003 00 06 13 19 26 32 13 63 13 63 14 64 00 06 13 19 26 32 13 63 13 63 14 64 Time Cluster ID 10 Sort Cluster ID 11 Sort D X 659e 003 159e 003 341e 003 gt 511e U0S 1 UYe UUS 4 PUe 00 3 4 3be 006 y9 gue uus3 2 00 06 13 19 26 32 0 2 13 63 13 63 14 64 13 63 13 63 14 64 13 63 13 63 14 64 Time Time Time Waveform in each cluster About chart treatment see section 2 9 Chart treatment Sorting Result3 Raster plot Cluster ID 7 Sorti BEB Cluster ID 4 Sorti 669e 003 1 69e 003 331e 003 0 2 13 63 13 63 14 64 Cluster ID 8 Sorti aid 00 06 13 19 26 32 13 63 13 63 14 64 Time Cluster ID 12 Sort D X 5 95e 003 9 46e 004 405e 003 905e 003 00 06 13 19 26 32 13 63 13 63 14 64 Time SpikeTaro also outputs raster plot separated by each cluster id Gh 1 Raster Plot ES zm ul E Time s Raster plot About the plot treatment see section 2 9 Chart treatment 15 26 2 6 Clustering SpikeTaro Version 1 0 User s Manual SpikeTaro can exe
13. splay If you don t want to display stimulation marker in charts and raster plot check this check box 2 3 2 Text File By selecting text file in Open data file dialog Text Data Input group in the Load Physiological Data dialog will be active ASCII text type is required for input data SpikeTaro accepts following text format e Tab separated text data e Comma separated text data CVS Format LF and CR LF is available as Linefeed code 6 26 SpikeTaro Version 1 0 User s Manual SpikeTaro requires tabulated data as input data An example is shown as follows Data File Header String Free format Free format time chldata ch n data stimulator 0 0001 2 125 1 325 0 0 0 0002 2 201 1 283 0 0 Column 1 Column 2 Column n 1 Column n 2 Input data format exsample SpikeTaro skips header part of input data In Load Physiological Data dialog set up the following parameters Data Includes Time Column If input data include time column turn on this check box Time Data Column Number Input column number of time count from 1 Unit Choice unit of time s ms ps is available Recording Rate In case of data does not include time column input sampling frequency of input data Scale Factor for Y If necessary input scale factor for physiological data This factor operates on all channels of physiological data except time and stimulation columns Data Includes Stimula
14. stering results plot can be changed by dragging size grip mark located in right bottom of the plot window 2 Change marker size User can change marker size by clicking A or W buttons located in right bottom of the window 3 Popup menu Popup menu is appeared when user clicks the plot area by right button of mouse The functions of menu Save Graphics Properties are the same of previously explained in time chart except setting parameters of Marker Color and Marker Size Ch 1 Glustering Results Save Graphics Properties e gt cn e I e a wn Spike Duration ms 25 26 aat Cluster1 Cluster2 Cluster3 Cluster4 Cluster5 Cluster6 Cluster Cluster8 Cluster9 Cluster10 Cluster11 Cluster12 SpikeTaro Version 1 0 User s Manual 3 Contact us Contact information about SpikeTaro is as follows SpikeTaro customer support TEL 814753217300 PAXS 481 75 321 1305 E mail Spiketaro chino js com We also announce new SpikeTaro information in SpikeTaro home pages Pease visit our home pages SpikeTaro home page URL http www spiketaro com en English http www spiketaro com ja Japanese 26 26
15. t button in main menu SpikeTaro s version number license information and contact information are displayed 2 8 Exit Spikelaro To Exit SpikeTaro Click X button in title bar of the main menu 2 9 Chart treatment 2 9 1 Time charts In this section we explain treatment methods of time charts which are Raw Data chart FIR Filtered Data chart and Sorting Results chart For above charts the treatment methods are common Now we explain the treatment methods using Sorting Results chart 17 26 SpikeTaro Version 1 0 User s Manual 1 Change window size Time chart is displayed by following format that outer window includes respective time charts Size of the outer window can be changed by dragging size grip mark located in right bottom of outer window Ch 1 Sorting Result Data DER Cluster ID 1 Sorti x l m EJ Cluster 1D 4 Sorti ox 4 e us i page uug i 669e 003 D 100 4 6 338 UU3 5 DUe UUd Ti ue uu 3 Se UU 189e 003 ZA AUS UUS aue uu bp fe UU3 331e 003 5 4Ue UUS re ja 1 1 e 0U 0D 05 13 19 25 3 oo 05 13 19 25 32 6 13 63 13 63 14 64 13 63 13 63 14 13 63 13 63 14 64 13 63 13 63 Time j Time Cluster ID 5 Sorti D x Cluster ID 6 Sorti all Cluster ID 8 Sorti O Ix V 3Ue UUs nm E 130e E pIeT 2 48e UU3 6 Ue UUS 3 a e uus 4 480 003 11 fe UU2 1 348 002 4 306 003 00 06 13 19 26 32 0 2 00 06 13 19 26 32 00 06 13 19 26 32 13 63 13
16. tion Record In case of including stimulation record in input data check this check box Stim data Column Number Input column number of stimulation record Stim threshold SpikeTaro determines to turn stimulation on off by this threshold Disable Stimulation Display If you don t want to display stimulation marker in charts and raster plot check this check box 7 26 SpikeTaro Version 1 0 User s Manual After clicking OK button the chart of raw data is displayed Raw Data El EJES EE Ch 1 Raw Data E 2 D re d 1 7e 00 682e 004 9 2 2e 0043 1 938 002 D Raw data chart Above figure is a result of loading sample data including program CD File name SampleData txt Stimulation marker was shown as heavy line under physiological chart About chart treatment see section 2 9 Chart treatment 2 4 Filtering SpikeTaro is implemented FIR finite impulse responses filter which is liner phase digital filter By clicking FIR Filter button at main menu the FIR Filter Setting dialog opens FIR Filter Setting Amplitude Characteristics Low Cutoff Frequency Hz HA Hight Pass Filter High Cutoff Frequency Hz 1800 Display Phase Delay 0 points 0 mz Cancel FIR Filter Setting dialog 8 26 SpikeTaro Version 1 0 User s Manual Number of Impulse Responses Choice number of impulse response In case of choosing lager number frequency cutoff characte
17. tude Characteristics Low Cutott Frequency Hz 120 2 T p T 4 Hight Pass Filter High Cutoff Frequency Hz 1800 2 Ampulitude Gain p T T p T 4 p T T p T 4 p T T p T 4 p T 4 T p p T 4 T p p T 4 T p p T 6 Phase Delay 256 1089 1289 1489 1689 1889 2089 2289 2489 125 me Frequency Hz Cancel Magnification of frequency range A slide bar is appeared in magnified chart To reset scale click circle shaped button located in left side of the slide bar 10 26 SpikeTaro Version 1 0 User s Manual OK button By clicking OK button FIR filter is applied to the input data After finishing filter process SpikeTaro shows FIR filtered result as chart Important information Filtering process executed by improper parameters often lead to incorrect sorting result If spike height changes significantly comparing with before and after filtering process not only noise but also spike frequency elements are probably cut off In such a case user should better readjust cutoff parameters in FIR Filter Setting dialog FIR Filtered Data Ea fx aaa ES Ch 1 FIR Filtered Data 91 002 19 7e 002 8 fe8e 003 n D Z a E E 9158 0004 1 O3e 002 42 058 002 0 FIR filtered data About
18. veforms This is a threshold which two spike waveforms belong in the same spike group we call cluster below To increase this value the judge level that two spikes belong in the same cluster becomes severer e Assume the Same Spike with Spike Height Difference 9 Sometimes spike height changes during recording even though the spike evokes from the same origin for example bursting vs non bursting condition changing recording condition depending on time etc This parameter indicates tolerating percentage of spike height thought that spikes evoked from the same origin 2 Ignored Spikes Group e The clusters which include spike count of X for total spike count are ignored e The clusters which include less than X spikes are ignored Above two parameters indicate setting condition that clusters of sorting results are ignored Now if sorting process output a lot of clusters and in each cluster includes few spikes user can ignore such the clusters using those parameters For example e Input data includes 1000 spikes e After sorting 20 clusters were created 13 26 SpikeTaro Version 1 0 User s Manual e In those 20 clusters 5 clusters include over 150 spikes e Remaining 15 clusters include less or equal tol0 spikes In above situation this parameter set value at 1 or 10 SpikeTaro ignores the 15 clusters which include less or equal to 10 spikes 3 Output Items Group e Sorting Results To check this
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