User Manual - BioMed Central
Contents
1. http www mathworks com matlabcentral fileexchan e 1 5590 fillnans ihowat gmail com http www mathworks com matlabcentral fileexchange 12180 moisy fast u psud fr fileseries rename renumber files recursive directories all files Blair Greenan colorbarf m http www mathworks com matlabcentral fileexchange 1135 greenanb Omar dfo mpo gc ca Carlos Adrian Vargas Aguilera nubeobscura O hotma il com cm and cb utiliti http www mathworks com matlabcentral fileexchange 24371 es Folder colormap and colorbar utilities sep 20092. Flashlight Movie Export electrograms Figure size Ka 20 0 220 starttimeAwindow sec 1 3 9 10 11 12 13 14 18 19 20 21 22 27 28 29 33 34 35 36 37 38 39 41 42 43 44 45 46 47 49 50 51 52 53 54 55 56 57 58 59 60 61 Select channels using buttons a GEMS ATs marked File Edit View Insert Tools Desktop Window Help Other Functions Display control d Users ryasO02 BackedUpDirectory GEMS GEMS_v1 O exampleFiles ExampleFile_markeddata_pigl0exp2_OT0300 mat Global y axes _ Plot clustered waves Plot wave numbers C Dont Plot Markers View ALL markers Remove current plots Process controls Save Markers Add Points Delete Points Type channel numbers to detele their markers C Manual Cluster Wave orphans Y Choose Markers Type channel numbers to detele their markers using amplitude limits Amplitude bounds Lower Upper Remove Markers Maps Activation Maps Amplitude Maps Velocity Maps Interval Maps Downstroke width Maps Plot x y t Flashlight Movie Export electrograms Figure size ER 20 0 220 starttime Awindow sec GEMS ATs marked DER Ki File Edit View Insert Tools Desktop Window Help Other Functions d Users ryas002 BackedUpDirectory GEMS GEMS v1 OtexampleFilestExampleFile markeddata pig10exp2 OTo300 mat Global y axes Display control Plot clustered wave C Dont Plot Markers 2033 uv Wiew AL
3. Parameter file ExampleFile piglOexp2 OTol100 defaultParameters mat this can be read in the Set parameters or Read in parameter box Electrode configuration file ExampleFile elecConfig pig10 txt this can be read into the Read in the electrode config file box Marked file ExampleFile markeddata pigl0exp2 0T0300 mat this can be read into the Read in the analysed mat file box Once user presses Done GEMS will launch the AT figure containing marked data If user opens analysed file then you can skip to Section 11 MN GEMS v1 3 Startup File Edit View Insert Tools Desktop Window Help Read in the main batitt mat file 44J Readin the analyzed mat file G GEMS GEMS v1 3 exampleFiles Examplel yy Set parameters or Read in parameter ES d Ni Set Parameters defaultParams m Read inthe electrode confia file G GEMS GEMS _v1 3 exampleFiles Examplel yy F wl Show channels 1 10 Process entire file all channels all time Figure 7 Select files a GEMS R0 6 File Edit View Insert Tools Desktop Window Help DataScro Pre screen Ch1 E Wfask GEMS paper Paper pig14exp1_0T0200_Elec mat CHA Pre screen M Dispaly controls Loose axis Filtering controls Remove Baseline Methods None 2 23071 uv Level 12 Window 10 Filter Methods None M Limits 1 60 Poly Order 9 Window 5039 uv 5781 uv 15780 uv ch7 Filter Electro
4. 0 0748192 sik 0 C 0 C 0 0 0 04045 0 C 0 01 0 C 0 d 0 Figure 2 Unemap txt file containing raw recorded data b A txt file from SmoothMap with the following format the first entry is the total number of header rows second entry is the number of electrodes third entry 1s the total number of rows of entry fourth entry is the frequency in Hz the following 6 rows are just 1s as shown in Figure 3 The data is listed is so that each row represents data for all electrodes per time t Figure 3 SmoothMap txt file containing raw recorded data c A simple txt file with the same format as the SmoothMap Go file format as shown in Figure 3 with no headers 4 2 Electrode configuration file A txt file usually referred to as electrode configuration or matrix file The file contains the list of electrodes and their orientation as shown in Figure 4 This file can be generated manually or using GEMS outlined further in Section 7 The first line of the file is a default setup line just set it as shown in Figure 4 The first entry of the second line 1s the total number of channels recorded from 160 in Figure 4 The second entry of the second line is the number of columns 8 in Figure 4 The third entry of the second line is the number of rows 20 Figure 4 The final entry of the second line is the inter electrode spacing in mm 7 62 mm in Figure 4 Third
5. 248s 246s 2445 242s 240s 238s Figure 19 Activation maps Use the next previous buttons under each plot to move through the different wave numbers events You can use the next waves and previous waves buttons to increment decrement all figures Also you can use the wave number list box to manually select which wave number you want to look at in each plot You can globalise the scale of all the three figures by checking the Use global scale checkbox all figures will have a unified scale You can display the electrodes onto the maps by clicking on the Display electrode numbers checkbox Page 27 of 48 7 8 10 11 You can display the conduction blocks by selecting the Display conduction blocks checkbox Conduction blocks will be displayed as grey patches You can switch between contours and patch plots using the Plot contours checkbox If the checkbox is selected for the AT maps and interval maps you can set the spacing between the contours and the calibration colormap value For time if you want to force the contour plot colormap to colorcode according to this amount of time otherwise leave blank to let matlab draw the contours as it pleases For the other maps you can set the number of contour lines You can save the data uninterpolated into text files by pressing the Save data to txt file buttons under each plot OR you can save all the data for all the waves into a txt file by pressing the Save A
6. 2011 User Manual GEMS Gastrointestinal Electrical Mapping Suite Auckland UniServices Limited and Jonathan C Erickson Developers Jonathan C Erickson Rita Yassi Nira Paskaranandavadivel Contact us gems academic gmail com Website https sites google com site gimappingsuite Table of Contents Ll Sot e EE 1 2 System requirements cccccseccseccseccseccseeceececceucceusceuscesscessceueceseceseceseceseceeeteeeseenseenes 1 2 1 BAN E 1 2 2 SO a op Oh a au atau ap li 1 AN Lsi oi Aa mm NM MM A 1 3 1 Div e ET 1 3 2 Pena A op Oi Ga o en A a A a 2 A Fiesreg iredior I Sia A mal aata kaia saama EE IE 2 4 1 Raw recorded data file srera ciron er a a E T 2 4 2 Electrode CON SUT a ees 4 MEE CEM ef eg e mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmamrrcrrrmrmmmrmrcrrm 5 s kinoga E 7 6 1 SE RET 2 i A 7 6 2 Jen SOUCO au E al S 7 7 Electrodeconiiguraton bh VUE 10 S Delault parameters sota E AE 12 9 Main GEMS figure CONTO Since ciao 14 10 EE 16 11 AUTO MAIN mmmmmmmmmmmmmmmmmmmmmmm mmmmmrmrmmmmmmmmmmmmmmmmmmmmmmmmmmmi 18 12 POS OSS le aa a aasa 23 13 Time Amplitude Velocity Interval Downstroke width maps 27 14 Has ugi le EE 29 15 Statistical ANALYSIS sisi 31 16 SAV Se 5 NR ERREUR 32 17 To re load analysed data ets 32 18 BEI Qu OO ER 33 19 Elei ge Ee ln 34 20 For developers open source only 38 21 Back end MOM atl ON raa mm maat m a al 40 211 lsterl ALSO FIA EE 40 21 2 FEVT GCC CU nn d
7. Christopher wavelet_matlab http atoc colorado edu research wavelets Torrence Folder chrisOrsinc com Gilbert P Compo _ compo colorado edu o m Peder Axensten waltbar m http jupiter ethz ch kausb perplith files waitbar m peder axensten se II a ett Eis 8 Toby Driscoll unplot m http www mathworks com matlabcentral fileexchange 283 1 driscoll udel edu o Chris Cannell uigetfile2 m http www mathworks com matlabcentral fileexchange 9254 ccannell O vt edu uigetdir2 m uigetfile2 http www mathworks com matlabcentral fileexchange 9521 uigetdir2 http www mathworks com matlabcentral fileexchange 7772 suplabel Evan Brooks scrollfigdemo m evan brooks wpafb _ af mil Ohad Gal ohad gal amat com progressbar m Steve Hoelzer _ shoelzer gmail com Sergei Koptenko local ext mod E Folder Jan Simon fSGolayFilt m John Iversen freezeColors m iversen C nsi edu http www mathworks com matlabcentral fileexchange 5253 scrolling figure demo content scrollfigdemo m http www mathworks com matlabcentral fileexchange 3607 progressbar http www mathworks co uk matlabcentral fileexchange 3170 local min max nearest neighbour htt www mathworks com matlabcentral fileexchang e 5661 unfreezeColors m freezecolors unfreezecolors http www mathworks com matlabcentral fileexchange 7943
8. 18 objects O bytes d My Computer Figure 1 Extracted GEMS folders 4 Files required for GEMS The only file needed for GEMS to work is a file that contains the raw recorded data Other files can also be read into GEMS which contain extra information 4 1 Rawrecorded datafile There are 3 types of files that can be important into GEMS 1 2 A bdf file usually obtained from the Biosemi system A mat file with the following format any file containing stored variables named ElecData resamp and fs can be used ElecData 1s an Nsigs x Nsamps data matrix data in rows resamp is a Boolean 0 1 specifying whether or not the data has been is to be resampled prior to loading fs is a scalar specified the original sampling frequency txt files a A txt file from Unemap with the following format first line starting with the word time followed by the number of channels or electrodes The first column contains the times in seconds the potentials for each time and electrode are saved in the remaining columns as shown in Figure 2 ime 1 2 2 00000000 1 07479 0 159529 4 00000000 1 13595 0 180106 6 00000000 1 11128 0 154438 5 00000000 1 09522 10 00000000 12 00000000 14 00000000 16 00000000 15 00000000 20 00000000 22 00000000 24 00000000 26 00000000 28 00000000 30 00000000 32 00000000 34 00000000 36 00000000 38 00000000 40 00000000 42 00000000 44 00000000 4600000000 48 00000000 50
9. JUpaateDisplay 5 Vl elacit V Ma DS Clbk OM 2 VeloctyMapecClbk w2 VaveReconstruct abclabel abs amp mpDeriv add TO Apoint 3 jada Ti Apt ladjustbarbase at centroid amp signal amplitude calcTimecluster v2 append armapsdb iarsiufilt artfdet audgmenthaqueue augmenteaueue axissquidpas bharweb baseline_removal_mediantilt baseline removal medianfilt batchDetect baylycurvetit bdf2ascii bdfParam_clbk bdidateyyvorkspace lkotplav bdtviewerhlexCompileScript icalcStats E Path Total number of functions 490 dX Isers ryas nzi ackedllpDirectory GEMS w EMS wi EEN Total number of lines 43356 Figure 22 Function call tree 21 Back end information 21 1Clustering algorithm This algorithm 1s used to group detected ATs from different channels or cluster them under the same event number The algorithm basically implements a region erowing clustering algorithm The criterion for membership in a cluster is that the activation time under investigation must not defer more than DTMAX user parameter than the estimated time The estimated time is computed as the mean of the ATs for the first few points After the regions becomes large enough also a user parameter N BAYLY the estimated time is computed by using the points already in the cluster to generate the coefficients for a Bayly surface f x y a x 2 b y 2 c x y d x e y f the
10. a OR you can manually type the channel numbers in the channel listbox at the bottom of the AT marked figure A figure will pop up with buttons The Select channels using buttons will turn red to indicate that you are post processing The green buttons on the Channels Map figure Figure 16 refer to the channels that were auto marked If user has discarded any channels in the pre screening stage the buttons of these discarded channels will be shown here in grey and they will be locked File Edit View Insert Tools Desktop Window Help igure 1 Channels map post processing You can select the channels either freely horizontally or vertically in the Selection Type list box green circle in Figure 16 If you select vertical or horizontal you can specify how many channels to select from the Number of Channels to select list box red circle in Figure 16 As you select the channels to view the plot will change on the ATs marked figure You can then delete false markers or add more markers using the Delete Points and Add Points buttons dark blue circle in Figure 14 When you click the Add Points button the button will change to Adding Points in red Figure 17 a To add markers point where you want to add the marker with the mouse and use the left mouse click Use the right mouse click to mark the last point you want to add and that will automatically finish the adding process If you are in the c
11. but short enough to avoid grouping two independent ATS into a single event Recommended value 6 s for gastric In GEMS this parameter can be found under the Parameters Figure Detection parameters refractory Nedge edge detector kernel width Integer number of samples in edge detection kernel Helps identify deflection direction Should be set to match the time scale of active waveform s main deflection Therefore when choosing Nedge be mindful of the sampling frequency A value of 1s 2 30 samples for 30 Hz sampling works well for gastric slow wave In GEMS this parameter can be found under the Parameters Figure Detection parameters Nedge 22 References JC Erickson G O Grady P Du C Obioha W Qiao WO Richards LA Bradshaw AJ Pullan and LK Cheng Falling edge variable threshold FEVT method for the automated detection of gastric slow wave events in high resolution serosal electrode recordings Ann Biomed Eng 38 4 1511 1529 2009 JC Erickson C Obioha A Goodale LA Bradshaw and WO Richards Detection of Small Bowel Frequencies from Noninvasive Biomagnetic Measurements IEEE Trans Biomed Eng 56 9 2181 2189 2009 S Mukhopadhyay and GC Ray A new interpretation of nonlinear energy operator and its efficacy in spike detection JEEE Trans Biomed Eng 43 2 180 187 1998 http ieeexplore ieee org ielx5 10 14396 00661266 pdf arnumber 66 1266 JC Erickson G O Grady P Du J
12. 00000000 52 00000000 54 00000000 56 00000000 58 00000000 60 00000000 a 4 3 6 7 8 9 ll AN koks aa Gi Ho 0 95501 0 93989 0 0159975 1 03746 0 832639 0 00199575 1 1369 0 781821 0 0312959 1 21388 0 853866 0 0496652 1 26633 1 0235 0 063171 1 32653 1 21191 0 0750356 0 131208 1 0472 0 0943966 1 00008 0 0516211 0 949082 0 008727 19 0 797723 0 0824068 0 650121 0 168763 1 39014 1 68351 0 0968432 0 585999 0 205905 1 38369 1 82843 0 0961844 0 559394 0 221617 1 3643 1 87884 0 0897977 0 516607 0 242808 1 31605 1 99629 0 0758389 0 429183 0 300994 1 31305 2 1664 0 0718164 0 428969 0 288155 1 2449 2 1421 0 0562132 0 440615 0 273251 1 20124 2 09423 0 0458262 0 503196 0 217784 1 09705 1 92161 0 0200037 0 540529 0 168116 0 987188 0 653668 0 0601639 0 797626 0 785326 0 00736415 0 847687 0 923239 0 07951 0 898081 1 04907 0 141513 0 975353 0 976389 1 12401 0 172818 1 04432 0 844226 1 11181 0 152578 1 14699 0 780125 1 10904 0 141171 1 20097 0 838392 1 05698 0 0936149 1 28637 1 00497 0 0657841 0 979175 0 0397615 0 961727 0 0164411 0 806966 0 0782322 0 651324 0 168068 1 40475 1 68494 0 102045 0 616013 0 188889 1 39188 1 77196 0 0980636 0 120135 1 37917 1 38196 0 0858727 1 39393 1 51487 0 0939782 1 73657 0 000857842 1 41673 0 0427223 1 28421 0 0349196 1 12534 0 0264826 0 0100206 0 00457327 0 0334209 0 0459153 1 33
13. 300 sec or to max allowable Rewind decrements time 60 sec or to min allowable O sec FastRewind decrements time 300 sec or to min allowable 0 sec Playback params controls the parameters when Play 1s set to on Increment is the amount by which the time is advanced before displaying next chunk of data in sec Default is 60 sec Pausetime is the amount of time to wait before trying to display the next data chunk in sec Default 1s 2 sec 11 The More Actions menu light blue circle in Figure 12 The relevant options are a Set Parameters bring up the parameter figure b Read analyzed data read a mat file which contains analysed data c User Manual a call to this user manual ono oe 10 Pre screen 1 To eliminate bad channels from being considered for marking click on the Pre screen button on the GEMS figure pink circle in Figure 12 2 A figure will pop up On the left hand side you can select multiple channels to view at one time red circle in Figure 13 You can achieve that by clicking on a channel number e g channel 50 hold down the shift key and select another channel number e g channel 80 you should see all the channels between 50 and 80 are selected If you want to select scattered channels then hold down the ctrl key while clicking on channel numbers 3 The channels will be displayed in the GEMS figure If you are happy with the channel 1 e good channel then clic
14. 9 9 6 9 9 9 9 9 9 9 5 9 8 99 9 9 6 amp amp 9 9 9 9 99 5 9 8 9 9 9 9 6 amp amp 9 9 9 S 99 9 9 9 9 9 9 9 9 9 9 9 9 9 8 5 9 99990 9 5 6 9 9 9 8 5 9 9999009 9 6 9 9 9 9 9 9 9 9 5 9 9 99 9 9 Figure 10 Electrode Configuration 8 Default parameters To set the default parameters More Actions Set Parameters red circle in Figure 8 The parameters will be displayed in a figure as shown in Figure 11 Parameters are grouped into different sections and they can be accessed using the buttons on the top of the figure highlighted in red circle After you change the parameters click on the Change Parameters button to update the parameters otherwise nothing will be updated The Change Parameters button updates the parameters for the current file you are using in GEMS if you exit GEMS and re launch it it will not go back to these parameters unless you have saved the parameters to a file and read that file back in next step explains how to save the parameters to a file To save the list of parameters to a mat file click on Save Parameters Make sure you save the parameters at the end before you exit so it will keep the latest parameters If you save the parameters to a file and then later on change something in the figure and forget to save it next time you read the set of parameters they will not be the latest 1 e pressing the Change Parameters 1s n
15. GEMS Manual Color Selection Sele File Edit View Insert Tools Desktop Window Help a Number of colors Colors Waves xe b Figure 20 Flashlight movie 15 Statistical analysis 1 6 ya EN Group Map File Edit View To calculate the mean and STD for group of electrodes select Other Functions Statistical Analysis from the ATs marked figure A new figure will pop up as shown in Figure 21 In Figure 21 the electrode configuration is shown in a form of buttons To group electrodes user can click on the desired buttons and then enter a group name in the Group Name edit box then press the Group button green circle in Figure 21 If user presses the Group button without entering a group name an automated group name will be generated The created groups will be displayed in the Group List listbox To calculate the average and std AT amplitude and velocity for the created groups user can select single or multiple groups by holding the shift of ctrl button while selecting from the Group List listbox and the desired wave numbers from the Waves listbox blue circle Figure 21 To calculate the average and std interval for the created groups user can select single or multiple groups by holding the shift of ctrl button while selecting from the Group List listbox and the desired wave numbers from the Waves listbox in the Interval section To save the created groups to
16. baseline drift user can select a baseline removal method from the Remove Baseline Methods list red circle in Figure 12 To apply the baseline drift removal and the filtering user must click on Filter to see any changes in the viewed signals NOTE some baseline removal methods will require the appropriate toolboxes 1 e DWT requires wavelet toolbox The drop down menu Filter blue circle in Figure 12 allows the user to select the filter method The boxes just below it allows you to set the filter limits associated with the filtering methods note the boxes will lock unlock depending on the filtering method chosen For all filter types except CWT Stopband Limits indicates the filter s passband For CWT Stopband Limits indicates the stopband frequencies For the WT filters you can enter multiple Limits e g 0 20 40 60 with CWT Passband passes all frequencies in the range of 0 20 and 40 60 cpm blocking the 20 40 cpm band You can NOT use this feature when the filter type is butterworth The current filter types are butterworth 2 order butterworth filter Filter limits specify b DWT dwt denoising filter typically not used CWT Passband cwt denoising filter mother wavelet is morlet the limits entered in CWT stopband cwt denoising filter mother wavelet is morlet specify stopband CWT has the advantage of an effectively infinitely sharp passband but is quite slow For 20 channels of 1800 s
17. in the AT figure and save it to a tif file User can set the size of the figure to export by setting the value green box If you want to generate electrogram figure with no markers select the Don t Plot Markers checkbox To unify the scale of all the y axes displayed in the AT figure check the Global y axes check box on the AT marked figure Figure 14 a Other Functions menu bar a Export Unclustered Data to txt File exports the activation times amplitude and width of the downward stroke to txt file of the unclustered marked activation times b Export Markers to txt File SmoothMap exports the markers to txt file which can be read into SmoothMap 1 J k l Export Markers to mat File exports the markers to mat file which can be read into GEMS This is the same as pressing the Save Markers button Cluster Waves REGROUPS forces GEMS to recluster the current marked ATs Orient Electrodes changes the orientation of the electrodes This will open another GUI figure window which allows you to orient the electrodes as desired This effects the display only of latter figures to be generated For example if you want to see on your computer screen the gastric slow wave propagating as if you were looking down at the test subject head at top you can choose the appropriate options rotate flip horz flip vert to accomplish this This also typically requires knowledge of how the electrode was orien
18. line should be empty Fourth line onwards contains the electrode configuration electrode numbers used in the experiment Figure 4 An example of electrode configuration file 5 GEMS architecture Data analysis in GEMS 1s divided into three stages pre processing processing and post processing as shown in Figure 5 In the pre processing stage the raw recorded data input is converted to a file that is visualized and filtered in MATLAB Channel electrode selection controls allow the user to discard electrodes with no reliable recorded data e g due to poor contact of the electrode with the GI tract or a technical fault The output of the pre processing stage is the filtered data which becomes the input for the processing stage Using the in built algorithms activation times can be automatically detected and the marked events can be partitioned and grouped clustered into a series of wave fronts The output of the processing stage is marked clustered events which becomes the input for the final post processing stage In this stage pseudo colored contour maps can be produced to show the propagation and distribution of activation times amplitudes and velocity fields In addition propagation movies can be produced to allow animated visualization of the spread of electrical activity At each stage the user can interact with the program perform processing steps and tune multiple parameters to their needs via t
19. 351 1 21568 0 0784937 1 37529 1 37161 0 0843062 1 39964 1 51298 0 0948919 Jr gr 0 149172 0 186858 0 215207 0 237376 0 257378 0 265959 0 264009 0 253311 0 232362 0 221577 0 197511 0 181354 0 142965 0 241025 0 274295 0 268074 18 1 83425 0 202355 0 272889 0 109288 0 0481075 0 0706 0 0935275 0 127455 0 152018 0 189889 0 210696 0 260039 0 273367 0 275368 19 20 1 93201 2 09367 2 23064 2 34353 2 48516 2 83148 2 86189 2 85806 2 8211 2 90178 2 78789 2 7089 2 49868 2 26861 0 253118 0 151636 1 85541 0 168375 1 84591 0 184011 1 94849 0 237476 2 11142 0 284153 2 20174 0 313913 2 38057 2 84541 ao 23290 21 22 23 24 25 26 271 0 232817 0 280168 0 321178 0 359582 0 397027 0 27465 2 61444 0 430274 2 73951 0 442154 0 0245979 0 03842 16 0 0659412 0 448643 0 455793 0 446237 0 426965 0 617954 0 517243 0 339105 0 260805 0 225971 0 197661 0 165955 0 149904 0 42634 0 174811 0 393578 0 250334 0 36972 0 296663 0 308742 1 85941 0 408725 0 486594 0 67121 0 661282 0 645604 1 88207 0 214788 0 363778 2 50572 0 401523 2 60137 0 427477 2 74317 0 444838 0 458948 0 456937 0 206025 0027451 0 0190 0 5843 0 502435 0 327165 0 282592 0 170107 0 17863 D C 0 0745424 0 00244289 0 05970 0 0
20. GEMS as shown in Figure 6 MATLAB 7 8 0 R2009a File Edit Debug Desktop Window Help a GI a H O ry Current Directory d Users ryasOO2 MATLAB Shortcuts al Howto Add 2 What s New v a eoa x I Command Window LENA Command History gt Workspace A E mer Lem d HO del M Wb Stack gt gt addpath genpath d Users ryas002 BackedUpDirectory GEMS GEMS 20100205 fe gt gt GENS d clc Value i a z amp 4 02 10 12 47 amp Name Current Di addpath genpath d 1 Users GIPro toaparams ah toaparams toaCell toapararms ah r for i 1 5 Aisp adhajadfh end HS 5 02 10 11 38 addpath genpath d Users GEMS clear ele addpath genpath d Users gems DUE elear mole addpath genpath d Users GEMS z 5 8 02 10 15 31 addpath genpath d Users clear rele clear r clc clear mole addpath genpath d Users GEMS bdfmainfig findobj tag bdfparams guidata bdfma fs bdfparams fs rele addpath genpath d Users GEMS ele L ES di Figure 6 Launching GEMS in MATLAB command window l A Start up figure will pop up as shown in Figure 7 The boxes show the default files To change them click on the open file icon next to each entry The left hand side of the figure 1s associated with raw files On the left hand side the first box is the main bdf mat or txt file which contains the main raw rec
21. L markers Remove current plots Process controls 1242 uv Save Markers Add Points Delete Points d Type channel numbers to detele their markers 1021 uv Wave orphans v 1136 uv Choose Markers Type channel numbers to detele their markers using amplitude limits 1267 uv Amplitude bounds Lower Upper Remove Markers 3034 uv 54 Maps Activation Maps Amplitude Maps Velocity Maps Interval Maps 5130 uv Downstroke width Maps Plot x y t Ke Flashlight Movie Export electrograms 1976 uv 56 Figure size 100 x gt 40 60 80 100 120 140 160 180 200 20 0 220 starttime window sec c Figure 14 Auto markers EN GEMS AT x y t File Edit View Insert Tools Desktop Window Help GN ban DR P P E o o o A og A A d n ESO a a a oi AW wg KA E LA Ce Kata ESA Pr SEN Gei E Es ui py d suf a 4 9 JS A Kal K BW ono d wl 8 0 04 o a 9 SE d CES EE Ti at 8 GE ALS io be e f PRA o dije Se F on AS Bag BD og w ch Wa d E M uu sat a i al E a a ge a 1868 QU ua ga o 50 100 150 46 Ai a285 44 n EK w SS 0 60 Figure 15 Plot x y t 12 Post processing 1 To check the markers closely click on the green button Select channels using buttons at the bottom right of Figure 14
22. LL waves to txt file button Figure 19 You can also save the displayed figures to image files using the green Save figure snapshot button Figure 19 OR you can save all the waves to separate image files 1 image file for each wave by pressing the yellow Save ALL waves to image files button or you can Save the current wave per subplot to an image file using the Save data to image button under each subplot NOTE log text files are saved with every image file containing the list of parameters used to generate the figure this will allow the users to re generate the figures at a later time with ease 14 Flashlight movie From the parameters figure you can choose if you want the movie to be black and white or colour the starting and ending time for the movie whether you want to manually group the different wave numbers and associate them with colours You can either create an avi file or save the frames to tif images then combine them to make a movie of desired extension using the flashlightMovieFileType parameter Saving to the tif files option can be used when you have a long data recording and MATLAB runs out of memory when creating the avi file Creating the tif files might take some time To create a flashlight movie press the Flashlight Movie button yellow circle in Figure 14 a A new figure will pop up Figure 20 a The figure represents the electrode configuration map with the marked events mo
23. U Egbuji AJ Pullan and LK Cheng Automated gastric slow wave cycle partitioning and visualization for high resolution activation time maps Ann Biomed Eng 39 1 469 483 2010 Doi 10 1007 s10439 010 0170 8 23 Contributors Dr Jonathan C Erickson GEMS founder developer Dept of Physics Engineering Washington amp Lee University Lexington VA USA Dr Rita Yassi GEMS manager developer Department of Engineering Science The University of Auckland New Zealand Mr Nira Paskaranandavadivel GEMS developer Auckland Bioengineering Institute The University of Auckland New Zealand Dr Gregory O Grady Dept of Surgery amp Auckland Bioengineering Institute The University of Auckland New Zealand Mr Peng Du Auckland Bioengineering Institute The University of Auckland New Zealand Dr Leo Cheng Auckland Bioengineering Institute The University of Auckland New Zealand Prof Andrew Pullan Dept of Engineering Science Auckland Bioengineering Institute The University of Auckland New Zealand Mr Tim Angeli Auckland Bioengineering Institute The University of Auckland New Zealand Dr John Egbuji Auckland Bioengineering Institute The University of Auckland New Zealand Dr Wim Lammers Dept of Physiology United Arab Emirates University Al Ain UAE Ms Emily Hargrave Thomas GEMS developer Auckland Bioengineering Institute The University of Auckland New Zealand Mr Simon Bull Auckla
24. ackplotVal Boolean True Stack plots False Grid plots cols Integer Number of columns of subplots Filter Settings FiltType E Integer Filter type FitLims pen cpm Filter limits Nxtnd Integer Number of samples for extended filter Baseline Settings basesubYal False Boolean True Baseline is removed held Integer Level of wavelet decomposition zerolvl Integer Number of scales to reconstruct largest scales for baseline subtraction sortchans False Boolean True Sort channels ShowFFT False Boolean Controls whether to show figure with FFT of signals displayed in main window FFTlims 0 0 1 15 String Controls the freguencies for which the FFT is computed Tau n 2 400 String SOBI integer time lags sobipkLbl True vi Boolean Controls whether to label peaks in SOBI components frequency spectra pmax val 10 25 Integer Threshold for peak labeling useSymm False v Boolean Controls whether to use the symmetric version of SOBI Figure 11 Default Parameters 9 Main GEMS figure controls 1 This main figure contains the raw recorded data as shown with the example in Figure 12 To stack the subplots plots for each electrode in one column select the Stack Plots check box green circle in Figure 12 Loose axis checkbox determines scaling of y axis of plots When loose axis is checked all y axis limits will be set equal to one another This is useful when comparing the amplitudes across channels To remove
25. add points as before 18 Useful Hints 1 In the main GEMS figure if you are not planning on using the pre screen and planning on processing all or most channels try this order of operating to save time it takes time to plot so every time you change something MATLAB tries to delete all the plots and then plot them again So if you have a lot of channels try to set everything for a single channel then type all channels later that way you save time a Type a single channel number any it doesn t matter in the channel box at the bottom b Select your baseline removal filter time period and if you want to stack or keep the grid view c Once you are happy with this then type in all the channel number in the channel edit box at the bottom That way it only has to delete a single plot then plots the rest after Due to the way GEMS keeps track of all the associated windows and plotting routines you cannot open multiple bdf mat files From time to time if you are clicking around you may mess up the plotting and callback routines When this happens the best course of action is to close GEMS and start fresh by re launching Therefore as soon as you mark events or cluster them SAVE your work 19 Glossary of parameters The table below lists the parameters the user can modify and a brief description of each parameter These parameters can be accessed from the main GEMS figure and the AT figure as described before The def
26. amples expect to wait a few seconds SG Filter smoothing filter where polynomial order and window size can be set Moving median baseline removal method where the window size 1S specified NOTE some filtering methods will require the appropriate toolboxes 1 e DWT requires wavelet toolbox To apply the baseline drift removal and the filtering user must click on Filter to see any changes in the viewed signals Channel box black circle in Figure 12 Enter the channels in this box that you wish to display You can enter MATLAB style lists such as 1 20 40 48 or 1 2 20 40 41 48 or 60 5 80 display every 5 channel starting from channel 60 and ending at channel 80 The number in parentheses indicates the total number of channels available for viewing Note that the channel list will be automatically sorted excluding any duplicated or invalid channels if the sortchans parameter is set to 1 If sortchans is set to 0 channels are displayed in the order specified 8 The Play Stop button controls automation of scrolling through or playing back data 9 To change the time for the display window change start time and the length of the displayed window NOTE you can use the slider to move through time start time in purple circle time for the subplot window is in grey circle in Figure 12 10 The Data Scroll menu orange circle in Figure 12 Fwd advances time by 60 sec or to max allowable FastF wd advances time by
27. as 40 22 L ne ENEE 41 23 AS 43 1 Software overview This user friendly GUI module is intended to facilitate and accelerate electrode data analysis to guickly visualize and guantify a series of activation maps and velocity fields It incorporates algorithm for automatically detecting activation times and partitioning each individual slow wave event so that isochronal maps and velocity field maps can also be generated with minimal manual tedious labour This manual will help guide you through the usage of the module point out some of its features and illustrate its capabilities Any comments or questions should be addressed to GEMS management team by email gems academic O gmail com 2 System requirements Operating Systems e Windows 7 e Windows XP 2 1 Binary To use GEMS you will need the Matlab Complier Runtime MCR installed on your machine The MCR will be supplied with GEMS exe 2 2 Open Source To use GEMS you will need the following installed on your machine 1 MATLAB R2009a or above For more information on how you purchase and install MATLAB please visit Mathworks 2 The wavelet toolbox is needed for some baseline drift and filtering methods Winrar or equivalent To download winrar for free visit Winrar 4 For developers perl is required for some functionalities to work For window users to download perl for free visit ActivePerl LA 3 Installation 3 1 Binary 1 Download GEMS zip a
28. ault values of these parameters are stored in AusrGUlDefaultsi defaultParams m If you change them for your experiments make sure you save them into a separate file using the Save Parameters button for safe keeping Table 1 List of parameters Group Parameter name Description BDF Parameters Set data to be resampled or not upon resamp loading efs Resampling frequency per second List of electrodes channels to show in the main GEMS figure and to be considered for processing Starting time of viewing signals in the main showchans GEMS figure and hence the starting time for initializeTime the processing data Length of the viewing window in main GEMS figure and hence the duration of the dataSegmentLength processed data minSliderMove main GEMS figure maxSliderMove main GEMS figure Sets loose or tight y axis controls vertical space occupied by signal in each subplot in yscaleVal the main GEMS figure stackplotVal GEMS figure cols GEMS figure FiltType Filter type to apply on raw signal FiltLims Filter limits to apply on raw signal FiltPoly Polynomial order for filtering FiltWind Filtering half window size basesubMethd Ivid baseWindSize zerolvl scales for baseline subtraction sortchans Controls whether to show figure with FFT of ShowFFT signals displayed in main window Nxtnd Number of samples for extended filter FFTlims Controls the frequencies for which the FFT REES a
29. bypass this pre screening step by just typing the number of channels you are interested in processing in the GEMS main figure black circle in Figure 12 for example 1 256 will plot channels 1 to 256 E Pre screening Control File Edit View Insert Tools Desktop Window Select cha Select good channels Select all channels Unselect all channels Clan 1135 1234567 8 91011 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 KZ Figure 13 Pre screening Original selected channels 11 Auto marking 10 11 To auto detect activation times ATs in the main GEMS figure press the Detect ATs FEVT button on the main GEMS figure light brown circle in Figure 12 This will detect ATs for the viewed channels and viewed time Wait until the algorithm finishes detecting events When it s done the AT figure will pop up see Figure 14 a NOTE don t alter anything in the main GEMS figure after you do this It might alter other important things and cause problems If you check the Plot clustered waves orange circle in Figure 14 a the plots will change displaying the clustered waves in different colours Figure 14 c If you check the Plot wave numbers then the wave numbers will be displayed on top of each marked event Unclustered ATs or orphans will be plotted in green squares with red outlines To view all the
30. can have artificially large values for the energy at the edge check to see if we believe these are real slow wave events Any putative slow wave occurring within BoundaryCheck seconds of either side of the segment are subjected to a further test for accuracy Smoothing window sec smooths the energy spectrum with a moving boxcar window of Smoothing window seconds FEVT critical parameters optimized for gastric slow waves n threshold multiplier multiplies the noise estimate running median to set the actual event threshold level A value between 4 6 15 typical Tradeoff lower eta increases sensitivity but decreases positive prediction value and vice versa Performance is dependent upon actual value set In GEMS this parameter can be found under the Parameters Figure Detection parameters thresh Ty running median window half width determines time window over which running median 1s calculated In practice this should be several times larger than the active waveform timescale 1 e deflection and recovery to baseline Performance is essentially independent of this parameter otherwise For gastric signals 15 30 sec is recommended Larger values lead to slower computation In GEMS this parameter can be found under the Parameters Figure Detection parameters rmhw Tr refractory period specifies the minimum time between two putative ATS Should be set long enough to account for fractionated waveforms
31. d obsoleteFunctions folders NOTES The obsoleteFunctions folder contains functions which are no longer used but we keep them just in case If you want to add any functions to this folder please ensure that the entire m file is commented so that it will not be considered in the path The analysis scripts folder contains functions which we are not really interested in we will eventually clean it up 5 As you click on the function you are interested in in the Functions list listbox the path to that function gets displayed in the Path editbox at the bottom of the figure NOTE you can scroll through the function names by hitting the letter you are interested in while you are in the Functions list listbox For example if I want to find zchan function I can just hit a on my keyboard and it will take me to the function that start with z As you keep hitting z the selection moves to the next function that starts with z 6 Once you select a function from the Functions list listbox the sub functions will be listed in the Sub functions listbox The sub functions are the functions found inside the chosen function in the Functions list listbox 7 Once you select a function from the Functions list listbox a list of the functions where the selected function is called from will be displayed in the Called from functions listbox 8 If you click on any of the functions in the Sub functions or Called from functions listbox the function
32. des controls 2111 uv 10372 uv 2241 uv Hee Create config file Choose config file 20 40 60 80 100 120 js FEVT controls Detect ATs FEVT 3675 UV 5365 uv 4 f Pla H 40 60 80 100 120 20 40 60 80 100 120 0 80 120 starttimeAvindow sec 1234 A 5678910 Num Chans 193 Figure 8 GEMS figure 7 Electrode configuration file You can either read the txt file or create it o amp 2 If you are using the default example files then the electrode configuration file EE GEMS Generate Electrode Matrix is already defaulted in the start up figure To read a configuration file press the Choose config file button green circle in Figure 8 and locate the electrode configuration file on your machine To create a configuration file press the Create config file button blue circle in Figure 8 A window should appear as shown in Figure 9 File Edit View Insert Tools Desktop Window Help elect PCBs generatio Select the PCBs _Wte an electrode configuration fe TOTMOGO OS TOTMOSORS To mmu ch OKS 29 30 31 32 TOTIMOO oR TOTIMOO OF TOTMOGO OI rOommooE3 T6 nmuo ph To mnmuao mhi TO TIMOO mhi TOTMOO DOS Tomm cK TOTIMOO ORS I Qnm o ocu TO TIMO O ORS Figure 9 Generate Electrode Configuration File 5 In the figure select which PCB generation you want from the Select PCBs generation list box red circle in Figure 9 A preview of a si
33. e il sobipkLbl components freguency spectra Controls whether to use the symmetric useSymm version of SOBI thresh Detection Parameters Multiple of rms noise estimate Spikes too large in signal will not be etamax declared multiple of rms noise refractory Refractory period between slow waves smoothWinSz method Smoothing window width of sneo signal Detection method simple sneo differ Detect downward deflections only using DownDeflOnly peak detector kernel x detection sig UpDeflOnly Nedge Size of peak detector kernel Half width of running median threshold detection Metric used to define the baseline noise level in a signal mabdev rms std Determines how to define the activation time w in FEVT window min maxdiff Check putatitive events near boundary of finite data segment using local min criterion Disallow spikes within first 15 samples 1 2 second Prevents an artificial spike in SNEO from being recognized Intermediate output of FEVT detection signal Minimum event duration to be considered a spike Empty means no amplitude threshold criteria applied Empty means no deriv threshold criteria applied Order of polynomial for baseline fitting to local spike waveform Option to print more infomartion during detection main matlab cmd prompt Option sets whether to use mex implementation in FEVT detection callback Threshold to determine if a peak or trough has been established Detect upward deflecti
34. file will open up in MATLAB This is to assist you change the functions 9 The total number of functions used in GEMS again excluding the analysis_scripts and obsoleteFunctions folders is displayed in the Total number of functions text box 10 The total number of code lines used in GEMS again excluding the analysis_scripts and obsoleteFunctions folders is displayed in the Total number of lines text box NOTE The Sub functions or Called from functions listboxes might contain more than the realistic used functions This is a limitation of the search because sometimes we have parameters the same name as a function so the search doesn t know any better Function Call Tree File Edit View Insert Tools Desktop window Help y Functions list Sub function A Rsigz elm Aumplitudehapsclbk v2 Linterpolatedplot v2 Bayly velocity Cnfgshaowichans Contents Contents Contents ExperimentDir Exporthiarks2Mat_v4 ExzportMarks txt v2 FFT compute GEMS MOBD MOBDneg MapHelp eo iert SCDplots So defaults SsmoothDeriy Spatialiap SquidDataLoad SubplotsBine lbk_ampl_ applytoall v2 SubplotsBtn Clbk_armpl_v2 subplotsBtnzSibk applytoall v2 subplotsBtnstibk interval subplotsBtnscClbk interval applytoall subplotsBtnsCGilbk 2 ssubplotsBtnatlbk vel applytaall v2 subplotsBtnsClbk vel v2 TOAcaliback FEWVT v2 TestfztizolayF ilt TriCubicCurveFit hs Untitled Salled from functions
35. g 13 Time Amplitude Velocity Interval Downstroke width maps You can view the activation times amplitude interval and velocity maps by using the buttons on the ATs marked figure green circle in Figure 14 Activation Maps Amplitude Maps Interval Maps Velocity Maps and Downstroke width Maps Corresponding figures with each of the buttons will pop up as shown by the activation times example in Figure 19 Black points circles represent electrodes for which a data point exists for that particular wave Red circles represent electrodes which did not record an activation time for that wave i GEMS v1 3 Isochrone Maps File Edit View Insert Tools Desktop Window Help Display options C Use global scale L Display electrode numbers C Display conduction blocks Plot contours Spacing between 2 rnntnurs Colormap calibration Save data Save ALL waves to txt file Save figure snapshot Save ALL waves to image files Co NES Wave Number 1 Save data to imag v r Next Save data to txt file 218s 218s 216s 214s 212s 210s 208s 206s 204s 202s Wave Number 2 Save data to imag n cn VI AAA rm Next Save data to txt file 234s 232s 230s 228s 226s 2245 2228 220s Wave Number 3 Save data to image A REND Next Save data to txt file Cn E 250s
36. he movie Top left electrode number of the selected patch only used if flashlightSlectPatch flashlighTopLeftElec parameter is set to true The number of rows of the selected patch only used if flashlightSlectPatch parameter flashlightPatchRows is set to true The number of columns of the selected patch only used if flashlightSlectPatch flashlightPatchCols parameter is set to true avi saves to avi file tif saves frames to tif files which can then be combined to make a flashlightMovieFileType movie Interpolate unmarked sites in each frame flashlightInterpTimes similar to interpolating isochrone plots 20 For developers open source only If you are changing some code in a certain function and want to know where the function is getting called from follow the following instructions 1 Ensure you have perl installed in your machine For instructions on how where you can obtain that please refer to Section 2 2 Add the path to your GEMS folder addpath genpath path directory 3 Run funcTree m This might take some time as it is searching all the relevant functions used in GEMS and how they are connected Once finished a figure as shown in Figure 22 will pop up 4 All functions found are listed alphabetically list 1s sorted by taking functions which start with capital letters first in the Functions list listbox These functions are the functions inside GEMS folders excluding the analysis_scripts an
37. he user friendly GUI applications Further explanations of each stage are provided below Prompt User Saved Processed Data File Electrode Recorded Data Configuration File File User pre set default e Load saved file Generate file Use pre set defaults e Load saved file Y Raw Recorded Data Pre processing Stage Visualize data Filter data Baseline removal Pre screen bad channels lm ge M Filtered Data Processing Stage e Auto detect activation times e Manual data correction Cluster REGROUPS Save marked data O O J MEME ccc c eg c NU mu cC 4 Make Propagation Display Contour a a a Marked Clustered Events ee n Maps e Activation times Post processing Stage Amplitudes e Velocities Time intervals e Width of downstroke Movies Save Data Non interpolated data to text files Maps to image files Movies to files Figure 5 GEMS flow chart 6 Launching 6 1 Binary Double click GEMS exe and move to step 1 6 2 Open Source a Launch MATLAB either by double clicking on the icon on your desktop or by using Start Programs Matlab or by locating it on your machine Add GEMS directory and subdirectories by typing in the MATLAB command window addpath genpath path directory see Figure 6 a for example addpath genpath d Users rita GEMS Launch GEMS by typing in MATLAB command window
38. is parameter can be found under the Parameters Figure Partition parameters N FIT POINTS 21 2FEVT detection ATs are detected based on a Non linear Energy Operator NEO method The algorithm implemented here computes either the energy as a function of time for an electrode signal V t or of the first difference of the signal diff V t Then the energy is analyzed to find times at which it 1s statistically very high The basis of the idea is that serosal records of gastric slow wave events that have a relatively steep decrease at the onset followed by a slow recovery The NEO operator is very sensitive to relatively steep drops in a signal as it is proportional to A o the amplitude squared multiplied by the frequency squared Brief description of AT detection parameters Method sneo differ defines the method to use to detect ATS sneo computes the energy as a function of time E V t of a signal electrode diffE computes the energy of the first difference of the signal as a function of time E diff V t Detection Threshold specifies that ATs are potentially detected at times for which the energy exceeds detectionThreshold estimated RMS noise in signal Refractory time sec specifies how far apart large bumps in the energy must be separated to be considered separate slow wave events I have found that values in the range of 3 5 seconds work well Boundary Check sec Because finite data segments
39. k on the channel number check box on the right hand side of the pre screen figure green circle in Figure 13 NOTE if the channel is somewhat good or if you are unsure about it then select it you can always delete the markers later BUT you CANNOT add channels later 4 If you want to select all channels then unselect the bad ones then press the Select all channels button black circle in Figure 13 5 If you want to unselect all channels press the Unselect all channels button purple circle in Figure 13 6 At the bottom of the figure pink circle in Figure 13 there is an edit box which has the list of the original channel list in the GEMS main figure just before the pre screen button was pressed You can also edit this box by either adding or removing channel numbers it is not connected to anything it 1s just made for manual editing like a scrap box for the user to type channels in may be if they are unsure of it or want to revisit it later 7 Once you are done click finish blue circle in Figure 13 and WAIT for the GEMS figure to update itself to include all the good channels The total number of selected channels will appear on the top right hand side of the figure yellow circle in Figure 13 8 Make sure that the time selected in the GEMS figure is what you want to include for the detection 1 e the time for the window should be the duration of the experiment if you want to process the entire file NOTE You can completely
40. lustered view the new point will be added to orphans NOTE As you click on Add Points button the Delete Points will be disabled When you click the Delete Points button the button will change to Deleting Points in pink Figure 17 b To delete markers point to the marker you want to delete with the mouse and use the left mouse click Use the right mouse Page 23 of 48 10 click to delete the last marker and that will automatically finish the deleting process NOTE As you click on Delete Points button the Add Points will be disabled To manually cluster events check the Manual Cluster checkbox brown circle in Figure 14 a Select which wave you want to cluster from the drop down box once you select that click on Choose Markers This will lock the wave drop down box to ensure you finish one wave at a time You can then start selecting which points you want to add to that wave Select using the left click last point to select use the right mouse click this will select the last point and also stop the selection process As you are selecting the points will turn into a pink box to show you the points you selected as shown in Figure 18 The code will ensure you have a single point per wave number per channel it will automatically set the older marker to an orphan if double ups occur If you are clustering points and want to add them to a new wave number ensure that the new wave number is a successive number from the current
41. marked events press the View ALL markers button NOTE for large files this might take a long time red circle in Figure 14 b To remove all the plots click on the Remove current plots button black circle in Figure 14 b In the command window it will indicate which axes it s up to in the deleting stage If you want to remove the markers of an entire channel then type in the channel or channel numbers in the Type channel numbers to delete their markers edit box purple circle in Figure 14 a and then press the yellow Delete Markers button If you want to remove the markers of channel s based on amplitude lower and or upper bounds then type in the channel or channel numbers in the Type channel numbers to delete their markers using amplitude limits edit box light green circle in Figure 14 a Then enter lower and or upper bounds in the appropriate boxes and then press the Remove Markers button Plot x y t button generates an x y t plot of the autodetected ATs as shown in Figure 15 Essentially it plots activation times on the z axis above the physical location of the corresponding channel The different coloured points correspond to individual slow wave events That is the software incorporates an algorithm to discern which points belong to each individual slow wave To export the visible electrograms select Export button yellow circle in Figure 14 a This will generate a figure which will contain the axes you are looking at
42. mat file so it can be re read press on the Save Groups button To load a saved group press the Load Groups button User will be prompted for a mat file To save the displayed results into a text file press the Save Stats to txt button Insert Tools Desktop Window Help Group List grp_035_094 grp 135 146 D 101 456 grp 101 156 grp 038 091 grp 011 022 larp 009 121 grp 007 018 arp 162 183 op 052 061 grp 068 069 Statistical Analysis Amplitude Velocity Interval Average STD Average STD Average STD Average E mm SMM TEA CE PET TES E PRES y Save Groups OO LoadGroups Figure 21 Statistical Analysis 16 Saving data Data can be saved to a mat file and a txt file Other Functions Export Marks to mat file or and Export Marks to txt file OR by pressing the Save Markers button pink circle in Figure 14 which will save the data to mat files The text file is in the format accepted in SmoothMap the mat file is saved in the format that can then be read again into GEMS for future re analysis 17 To re load analysed data Launch MATLAB and GEMS as described above Read the analysed mat file in the box on the right hand side of the start up figure and press Done You can plot activation times amplitude maps etc delete or
43. maximum wave numbers 1 e if currently you have 5 waves then the next wave number to manually cluster should be 6 do not skip numbers 1 e you can t start selecting wave number 10 NOTES the manual cluster option can also be changed in the main default parameter figure if you uncheck the Manual Cluster box GEMS will autocluster so 1f you don t want GEMS to autocluster keep this box checked REMEMBER if you do that save the parameter file so next time when you read it back in GEMS knows not to auto cluster GEMS ATs marked DER File Edit View Insert Tools Desktop Window Help Other Functions Display control dAUsersyas0024BackedUpDirector GEMSAGEMS v1 DYexampleFilesXExampleFile markeddata pig10exp2 OTo300 mat 0 Global y axes Plot clustered waves Plot wave numbers C Dont Plot Markers 2033 uv Wiew ALL markers Remove current plots Type channel numbers to detele their markers C Manual Cluster Wave orphans v Vu Choose Markers 1136 uv Type channel numbers to detele their markers using amplitude limits Amplitude bounds Lower 1267 uv Upper Export 3034 uv 5130 uv electrograms 1976 uv 220 starttimeAwindow sec GEMS ATs marked DER File Edit View Insert Tools Desktop Window Help Other Functions dAUsersyas0024BackedUpDirector GEMSAGEMS v1 DYexampleFilesXExampleFile markeddata pig10exp2 OTo300 mat Global y axes Display control Plot clustered
44. n extends the surface to estimate the time at the point under investigation c f Bayly et al Estimation of Conduction Velocity Vector Fields from Epicardial Mapping Data IEEE Trans Biomed Eng Vol 45 No 5 May 1998 The algorithm is known to be sensitive to the seed electrode the point at which the cluster is seeded from which it expands outward REGROUPS critical parameters DTmax Difference between actual and estimated AT This should be set to about 10 25 of the expected measured slow wave propagation cycle period For example if a gastric slow wave period is 20 s 3pm then DTmax should be between 2 5 s Tradeoff setting a lower value increases likelihood of a false positive being included in a cluster setting value too high increases chances of misclustering an activation time that is part of another slow wave In GEMS this parameter can be found under the Parameters Figure Partition parameters DTMAX Ncrit Determines minimum number of points in a cluster at which polynomial curve fitting for estimation is turned on Nerit must be gt 6 In practice we have found a slightly higher value 8 16 works well and that the algorithm is fairly insensitive to this parameter Tradeoff Lower value of Ncrit increases likelihood of local over fitting leading to poor estimation of ATs higher value of Ncrit turns on polynomial fitting at a later time making for poorer estimation of ATs on a global scale In GEMS th
45. nd Bioengineering Institute The University of Auckland New Zealand Functions available on File Exchange GEMS management would like to acknowledge the following authors for their contribution Author Function URL i SS M Jianwen Luo sgsdf gram poly http www mathworks it matlabcentral fileexchange 5556 luojw ieee org m savitzky golay smoothing and differentiation filter content sgsdf gram poly m Ben Barrowes suplabel m barrowes alum mit edu Rasmus Anthin rgbconv m http www mathworks com matlabcentral fileexchange 4265 rasmus anthin surgi rgbconv m cal science com i s Ji Jaco de Groot outlier m http www mathworks com matlabcentral fileexchange 1 1106 _j grootQuclac uk ma E Aslak Grinsted samexaxis m http www mathworks com matlabcentral fileexchange 7169 _ag glaciology net _Samexaxis nice subplots with same x axis le Aslak Grinsted parseArgs m http www mathworks com matlabcentral fileexchange 3696 ag glaciology net subaxis m subaxis subplot content parseArgs m http www mathworks com matlabcentral fileexchange 3696 mm ih subaxis subplot content parseArgs m Don Orofino MoviePlayer http webscripts softpedia com script Scientific Engineering don mathworks co Folder Ruby Signal Processing Interactive MATLAB Movie Player m 34707 html
46. nd save it on your computer 2 Extract the zip file You will have GEMS_pkg exe License folder and exampleFiles folder 3 Double click on GEMS pkg exe this will prompt you to install MCR Follow the prompts 4 To launch GEMS go to Section 6 1 3 2 Open Source l 2 2 Create a GEMS folder in your machine Download GEMS rar and save it inside the GEMS folder Extract all the files inside GEMS rar If you have winrar installed this usually can be done by right clicking on GEMS rar and then selecting Extract Here When extraction 1s finished you should be able to see a set of folders as shown in Figure 1 To launch go to Section 6 2 Size Type Date Modified Folder 30 07 2010 4 48 p m analysisTools Folder 30 07 2010 4 48 p m batchDetectFiles Folder 30 07 2010 4 48 p m C bdFviewerqui Folder 30 07 2010 4 48 p m O CallingTree Folder 30 07 2010 4 48 p m O DataLoad Folder 30 07 2010 4 48 p m extras Folder 30 07 2010 4 48 p m 9 FunctionFlowChart Folder 30 07 2010 4 48 p m O FunctionsR elating2SmoothMap Folder 3 08 2010 2 10 p m obsoleteFunctions Folder 30 07 2010 4 48 p m plotting Folder 30 07 2010 4 48 p m prsa Folder 30 07 2010 4 48 p m GRemovebaseline Folder 30 07 2010 4 48 p m C spikedet Folder 30 07 2010 4 48 p m C sguidviewergui Folder 30 07 2010 4 48 p m GuserManuals Folder 13 08 2010 3 22 p m _jusrGUIDeFaults Folder a 08 2010 2 22 p m wave matlab Folder 30 07 2010 4 49 p m
47. ngle PCB orientation will appear in the Electrode preview window below it yellow circle in Figure 9 The orientation of the electrodes within the PCBs used can be changed using the Orient PCBs list box green circle in Figure 9 The new orientation will appear in the Electrode preview window NOTE all the other PCBs used for the experiment will follow the same orientation The user can then select how many PCBs they had in rows and columns blue circle in Figure 9 The corresponding number of PCBs will appear as list boxes in the figure 8 Select PCBs from the list boxes based on the orientation used in the experiment 9 When finished press the pink button Write an electrode configuration file User will be prompted for a file name and will be asked if they wish to use this configuration for the main GEMS program If not then user will be reminded to read an electrode configuration file 10 To check the orientation of the electrodes press the Orient Electrodes button yellow circle in Figure 8 and Figure 10 will pop up You can close the electrode config figure or leave it open File Edit View Insert Tools Desktop Window Help 99999 9 9 9 9 9 9 9 9 9 9 90 99 9 9 9 9 9 9 9 9 9 9 9 9 90999999 99 99 9909 9 9 9999999 9 9 9 9 EECH 909999 9 8 5 9 9 9 9 9 9 9 99999 9 9 99 99 99 9 9 9999999 99 9 9 9 9 9 9 G 9999999 6 6 6 9 9 amp 9 9 9909069666069 6G 60 6 9 9 9 9 9 8 9 9 5 9 8 9 9
48. ons only rmhw baselineMetric defSpikeTime checkEdge Tb mxstat minEventDur ampThresh derivThresh polyorder verbose useMex amplthresh Half window length for amplitude detection Sets delta T allow queued point membership into growing region window_half_length Partition Parameters DTMAX doBaylyEst Do Bayly curve to estimate activation time oe ei CC Cesair FitOrder surface ar powrs estimate of the next points station ime N_FIT_POINTS estimate of the next points activation time vam Turn on bayly estimation only after this many points are in the cluster must be N BAYLY gt 6 seo mee ARES SEED ELEC based off of CM of Nevents criterion manualCluster Manual or automatic clustering Determines type of interpolation to plot isocrhones inverse nearest v4 bayly off WARNING nearest and v4 produce misleading plotTimelnterp interpolations ett Je isoLabels lines wegen td minPlotRatio wave number reguired to plot maps nen Plots ATs at half electrode spacing or on plotHlafElecSpace electrodes True plot contour plot only for the AT maps no surfaces False plot contour surface plots for the AT maps contourOnly Disconnected at the moment Velocity threshold value used to determine if a conduction block exits E g if the parameter is set to 0 3 this indicates that a conduction block will exist if the velocity between adjacent electrodes is less than 30 of the average
49. orded data refer to Section 4 The second box is for the parameters Users have 3 options 9 403Ip3 a qeueA wi ln d a Use the default parameters saved in the defaultParameters m function file b Set parameters by clicking on the Ser Parameters button this will open up the parameter figure and you can set the parameters as desired Remember to click on Change Parameters then press Close Me Never close this figure using the close button X c Load in a mat file this is usually available if you have used GEMS before and you saved it The third entry is the electrode configuration file If not entered GEMS will read some default file 1t has The fourth entry is the channel number to show when the main GEMS figure is launched The box on the right hand side is related to mat files which have analysed data When user uses this there will be no need to set the other files on the left hand side of the figure everything is saved in the analysed data file If user opens analysed file then you can skip to Section 11 NOTES After the first time you read bdf or txt file which contains the raw data a mat file will be generated so from then on you can use the mat file as it will be faster to read At load time GEMS checks to see if the parameter fs in the mat file matches the requested re sampling frequency in the default m file If these two values do not match GEMS at
50. ot the same as saving them If you change some parameters make sure you press Change Parameters before you press Save Parameters To load a set of parameters click on Load Parameters Once done click on Close Me button this will hide the figure NOTE DO NOT close the figure using the X button at the top right hand corner If you do by mistake you will need to re run GEMS again and risk losing all your current work mainly marked events You can also get this figure back from the AT figure Other Functions Set Parameters E GEMS Parameters Figure File Edit View Insert Tools Desktop Window Hel E BDF Parameters Detection parameters parameters Partition Parameters Parameters Map Plotting Parameters Plotting Parameters Flash Movie Parameters Movie Parameters Change Parameters Load Parameters Category Parameter Name at arde Description Data Loading resamp Boolean True Data is resampled upon loading efs Hz Frequency per second Display Parameters showchans 1D array List of electrodes channels to show in the bdf figure when it is generated initializeTime sec Starting time of viewing signals in the bdf figure dataSegmentLength sec Length of the viewing window in bdf figure minSliderMove sec Minimum amount slider can move by maxSliderMove sec Maximum amount slider can move by yscaleVal Boolean True loose y axis False tight y scale maximizes vertical space occupied by signal in each subplot st
51. ted on the test subject so keep careful notes Auto detect bad channels under development Re detect ATs this will launch execution of FEVT algorithm The figure will be re plotted with the corresponding ATs for each channel Re filter this will refilter the signals Change the filtering parameters as desired in the parameter figure before selecting this option Statistical Analysis refer to Section 15 Flashlight Display creates avi movie files This is the same as pressing the Flashlight Movie button Set Parameters launches the parameters figure User Manual launches the user manual NOTE If you change any settings parameters in the main GEMS window you need to re launch the AT marked figure from the main window to reflect these changes If you only change the detection parameters using the Parameters figure then you do not need to re launch the AT marked figure GEMS ATs marked BE File Edit View Insert Tools Desktop Window Help Other Functions m C Global y axes Display controls IT Plot clustered waves Plot wave numbers US Plot Markers WI View ALL markers IIS AT Remove current plots TOS E Process controls T Save Markers gt M er Na el gt channel cle their markers amplitude limits Amplitude bounds Lower Upper E Remove Markers gt d gt L Activation Maps Amplitude Maps Velocity Maps Interval Maps
52. tempt to reload the data from the original bdf or txt file resampling at the rate specified in the default m file The practical consequence is that if you are creating a mat file from scratch you must do two things 1 resample your data prior to saving it in the mat file and 2 make sure the frequency saved in your mat file field fs matches the value stored in default m file Otherwise an error will be thrown and your data will not load If user wants to process an entire file all channels and all time check the Process entire file checkbox in Figure 7 Once finished click on Done and a GEMS figure will pop up see Figure 8 which shows the first 120 seconds of the first 10 channels this 1s the default setup NOTES If you are reloading marked files from this step the main GEMS figure will not be generated If the analysed data was saved using an old version of GEMS user might be prompted to read in the original bdf mat file NOTE GEMS has default files that can be used to run GEMS In the open source the files are pre set in the boxes User can press the Done button and the main GEMS figure should pop up For the binary the user can locate the example files in the exampleFiles folder The included files are as follows Raw data files ExampleFile rawdata pigIOexp2 0To300 mat and ExampleFile rawdata pigl0exp2 0To100 mat These can be read in the Read in the main bdf txt mat file box
53. velocity value for condBlockThresh that wave number True user inputs limits manually for maps Determines whether to plot white black Flash Movie e flashlightET Flashlight movie end time flashlightDT Flashlight movie time step size Show only the trailing refractory tail Map Plotting Parameters Leading wavefront edge will not be flashlightRefracOnly shown flashlightFPS Frame per second playback speed flashlightBW vice versa foshighesecyies _ mevesoral deecederen 0 flashlightUseCycles movies or all detected events flashlightUseColors Use colours for the movie flashlightManualColors Set manual colours for the movie 1 Does not mark channels 2 Marks channels with no ATs in the selected time period 3 Marks channels with no detected flashlightMarkChanls ATs True splits the screen of the movie to 2 sections half of it will contain user specified image and information and the other half is the movie If user selects the BW movie the default will be red on either white or black False default setting of movie generation flashlightWithInfo no extra information True Display real time on top of the movie False Offset the display start time by flashlightDispRealTime OffsetTime parameter flashlightOffsetTime Offset the display start time True User to select a patch from the electrode matrix to create the movie False Entire electrode matrix is considered for flashlightSelectPatch creating t
54. ving through time The current or counter time depends on user choice in the parameters figure will increment at the top of the figure as the movie plays Once it is done a new figure will pop up which will allow the user to re play the movie fast forward etc If you selected manual colour assignment for the waves to generate the movie a figure will pop up Figure 20 b To manually group the wave numbers and associate them with colours type the number of colours you want in the Number of Colours box then hit enter The number of colours will be generated automatically on the right and next to each colour an edit box will appear Enter the wave numbers you want to group into each colour as shown with the example in Figure 20 b when you are done press Done A figure will appear and show the movie being created To create movies with half of the screen containing information about the movie set the flashlightWithInfo parameter to true If you use the black and white option with this setting the movie will come with red as default If you want to mark the electrodes which contain no detected ATs in the time period of the movie set flashlightMarkChanls parameter to 2 in the Parameters Figure If you want to mark the electrodes which contain no detected ATs at all then set flashlightMarkChanls parameter to 3 Flashlight File Edit View Insert Tools Desktop Window Help Sei k ASTA A a D EJ ad Frame 3 of 1396 EE
55. waves Plot wave numbers C Dont Plot Markers View ALL markers Remove current plots 2033 uv d Delete Points Type channel numbers to detele their markers bas Vu 1021 uv C Manual Cluster Wave orphans v SE la 1136 uv Choose Markers Type channel numbers to detele their markers using amplitude limits 1267 uv Amplitude bounds Lower Upper 3034 uv 5130 uv Export electrograms 1976 uv Figure size 190 x ENE Set tuna sg tos b Figure 17 Adding and deleting markers GEMS ATs marked OK File Edit View Insert Tools Desktop Window Help Other Functions a Display control dAUserswyas0024BackedUpDirectorGEMSAGEMS v1 0texampleFilestExampleFile markeddata pig10exp2 OTo300 mat Global y axes Plot clustered waves Plot wave numbers C Dont Plot Markers View ALL markers Remove current plots Process controls Save Markers a Add Points A T Delete Points d 4 5 6 8 10 11 12 Type channel numbers to detele their markers Vu Manual Cluster Wave Type channel numbers to detele their markers using amplitude limits L i Amplitude bounds Lower Upper Remove Markers Maps Activation Maps AD Amplitude Maps Velocity Maps Interval Maps Downstroke width Maps Plot xy t Flashlight Movie Export electrograms Figure size me a Figure 18 Manual Clusterin
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