sigInspect user`s manual
Contents
1. S Save All R Replay 0 sound on V overview Figure 1 Main window of the sigInspect GUI with loaded 4 channel signal Using the GUI The sigInspect GUI with loaded signals can be seen in Figure 1 The main window consists of time se ries plot with selected second of given multi channel signal and spectrogram calculated from currently selected channels Basic controls Switching between seconds can be done using the left and right arrow keys When you reach the last second of current signal and hit right you get to the first second of subsequent signal and vice versa You can of course use corresponding buttons called previous and next or signal and second selector boxes with the same effect To have a clear view of all your channels you will probably need to adjust gain amplitude of the signals This can be done either by the gain slider on the left or by pressing up or down arrow keys Channel selection There are several operations that affect only the selected channels A annotation when you mark a specific 1s signal segment as an artifact B audio playback when audio is on and C spectrogram calculation Channel selection can be done using the numpad keys 1 9 number keys top row of your keyboard with ENG layout or with checkboxes on the right next to each signal You can also invert selection using the i key or select all with the a key Audio Sig2. NORMALIZE _SIGNAL_PER CHANNEL QUANTILE ARTIFACT_TYPES ARTIFACT_COLOR ANNOT_DEFAULT_FILENAME ARTIF UNSURE 24000 150 5 1 002 0 1 tr sigInspectAnnot mat signal sampling frequency in Hz 3 distance on the y axis between channels max number of prallel channels to plot decimate signals by this factor upon load e g to save memory amp processing time automatically adapt gain slider to signal use this quantile of signal amplitude for gain adaptation normalize each channel parallel signal sep arately use this quantile of signal amplitudes for per channel normalization cell array with artifact type abbreviations max TODO types color to plot artifact segments shown in overview only default name for sigInspect annotation when save button is hit is replaced by current date and time SHOW_SIG_INFO 1 show signal info from interface overview window OVERVIEW_DECIMATE_FACTOR 20 decimate signals by this factor before view in the overview window this is multiplied with the basic DECIMATE_FACTOR OVERVIEW_GAIN 10 increase gain in overview window to adapt for decimation spectrogram plot SPECTROGRAM NFFT 1024 points to be used in spectrogram FFT Win dow length is set to the same value overlap is 50 SPECTROGRAM_FREQ_LIMS 0 3000 limit spectrogram to this frequency range in Hz DISABLE_SPECTROGRAM 0 disable spectrogram will use the free space for sign
3. by typing v you turn on the overview window which shows whole current multi channel signal Current second is marked by red rectangle you can select any second by clicking on it in the overview window 2 siginspectOverview oa signal overview Show annot C none all maxCleanSegment SU ee 1 Figure 2 Overview window showing 4 channel signal from Figure 1 with annotation The overview window can also display annotated artifacts just select the all radio button at the top All clean segments with no artifact assigned will remain in default color blue while artifact seconds will turn red can be changed in the settings To see how long is the current longest artifact free segment select maxCleanSegment radio button This will mark all shorter clean segment red so that you have a quick idea how long clean contiguous segment of your signal is left The overview window uses further resampling to speed up display see OVERVIEW_DECIMATE_FACTOR in the Settings section of this guide Keyboard shortcuts For the sake of speed and usability many controls can be accessed through simple keyboard shortcuts mostly single button Most of the shortcuts are written directly in the GUI you can e g press o to toggle sound on off f to toggle spectrogram or hit number keys to select or deselect channels Settings To accomodate sigInspect to your needs it may be necessary to alter some of its
4. GUI tool that Allows you to inspect and annotate multi channel signals Can I start sigInspect without signals No signals or interface must be provided on startup Can I change interface during runtime No this is currently not supported Signals are overlapping what shall I do You can A change signal gain using keys or slider on the left or B change the PLOT_STEP settings field What is the interface The term interface refers here to an object of class sigInspectDataInterface which can be used to tailor the GUI to multiple data sources see the Advanced data loading section for details Do I need the interface No you do not have to worry just start the sigInspect the basic way with signals as a parameter it will initialize sigInspectDataBasic interface for you Can I annotate segments shorter than the whole current view 1s No this is not possi ble But trust us this way it is much faster and it may also be really hard to identify beginning and end of an artifact References 1 Bakstein E Schneider J Sieger T Novak D Wild J and Jech R Supervised Segmentation of Microelectrode Recording Artifacts Using Power Spectral Density Proceedings of the 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society Milan Italy August 2015 2 J H Falkenberg and J McNames Segmentation of extracellular microelectrode recordings with equal power in Proceedings of the 25th Annu
5. Inspect allows playback of thresholded signals which is useful for artifact identification as well as for simple overview of neuronal activity To hear audio playback Sound on checkbox at the bottom has to be checked use o shortcut to toggle sound at least one channel must be selected and threshold has to be set lower than at least some parts of some of the selected channels Threshold is indicated by the black horizontal lines surrounding each channel in the time series plot and can be adjusted by the thr slider on the left or by hitting the and keys SigInspect plays only signal parts exceeding currently set threshold in selected channels This can be used to play back only firing patterns of close neurons If you wish to hear the whole signal including neuronal background set threshold to 0 If you wish to replay current second use the r key hit Replay button or change channel selection Annotation Annotation can be done by the artifact type buttons at the bottom or corresponding F1 F12 keys The number and types of artifacts are up to you and correspond to the ARTIFACT_TYPES field in the settings When you hit a button you assign it to all currently selected channels If the currently selected channels have this artifact type already assigned you will unmark them You can assign from zero to all your defined artifact types to each second of each channel The labels on each button also sh
6. al International Conference of the IEEE Engineering in Medicine and Biology Society 2003 vol 3 pp 24752478 3 M Aboy and J H Falkenberg An automatic algorithm for stationary segmentation of extracellular microelectrode recordings Med Biol Eng Comput vol 44 no 6 pp 511515 Jun 2006
7. al plot ENABLE_WHOLE_SPECTROGRAM 0 Adds a w toggle to switch between current second and whole signal spectrogram Beta audio START_WITH_SOUND_ON 0 start with sound turned on USE_BEEP 0 beep when going to another signal USE_AUDIOPLAYER 1 use audio playback by audioplayer matlab audioplayer instead of play PLAY_VIA_LINTERNAL_PLAYER 1 use more sophisticated audio may prevent audio dropouts and other problems on some systems INTERNAL_PLAYER_DBG 0 show debug messages from internal player works only if audioplayer is chosen PLAY_ SOUND_IN_SYNC 0 synchronized audio mode CHECK_CONST_SAMPLES 1 check signal for constant samples visualize them in color though the Object programming is not very common in Matlab implementing your own interface is very simple as you will see below In OOP terms In Object Oriented Programming OOP terms such as in Java the sigInspectDatalInterface is an interface you have to inherit in your own class This is done in Matlab using the sign after your function name The sigInspectDataInterface has two abstract methods getSignallds and getSignalsById signaliId which you have to implement to have a valid class It may be also useful to define a constructor for your class which allows you to e g pick data to view right on the object initialization You can see an example class below Reference getSignallds 1 function signalIds getSignallIds obj signallds i
8. ct class as the language defines no interfaces and ignores the subtle distinctions between the two Example interface The following example code creates an interface to load signals from all csv files present in a directory In this example the csv files contain three channel micro EEG signal in columns The example ignores error checking dir file existence for the sake of brevity 1 classdef sigInspectDataCsv lt sigInspectDataInterface 2 define class inherit sigInspectDataInterface abstract class 3 properties 4 dirPath 5 end 6 methods 7 constructor just store the path set settings 8 function obj sigInspectDataCsv dirPath 9 obj dirPath dirPath 10 obj settings SAMPLING_FREQ 6000 6kHz sampling rate it obj settings PLOT_STEP 1 5 distance between channels on the y axis 12 obj settings ARTIFACT_TYPES Type A Type B Unsure 13 end 14 return list of signal ids load all csv files from a directory 15 use filenames as signallIds 16 function signalIds getSignallIds obj 17 lst dir obj dirPath csv 18 signalIds lst name 19 end 20 21 read signals based on signalId filename 22 function signals chInfo getSignalsById obj signalId 23 chinfo 24 signals csvread obj dirPath signalId 25 end 26 end 27 end Using the interface Once you have your class implemented it is very easy to use it amp initialize interface using i
9. default settings If you use your own data interface the settings can be changed easily from there see the Ad vanced data loading Section for more details If you use sigInspect without defining your own sigInspectDataInterface you can change settings easily using example code in Section Default interface All the main available settings are summarised in Table 1 the most important ones are in bold Advanced data loading sigInspect DataInterface To provide the possibility to connect sigInspect to your existing database and to make configuration for multiple data sources easy you can implement the sigInspectDataInterface and connect the GUI to whatever data source you are using When you call sigInspect you simply provide an instance of your implemented interface as the only parameter The two main things you have to implement are two methods getSignalIds which returns a list of signal identifiers a cell array of strings and getSignalsById signalId which returns a multi channel signal matrix for given signalld You can also override the default settings within your interface this way you can easily adapt sigInspect for multiple data sources you work with Even Table 1 Overview of available sigInspect settings field name default value meaning basics amp signal handling SAMPLING_FREQ PLOT_STEP PLOT_CHANNELS DECIMATE_FACTOR ADAPT_GAIN_TO_SIGNAL ADAPT_GAIN_QUANTILE NORMALIZE_SIGNAL_PER_CHANNEL
10. n automatic annotation in a mat file 3 run sigInspect with the same interface load the annotation 4 update the artifact annotation manually to your taste To see different argument types of sigInspectAutoLabel check out its inline help For example your artifact labelling code could look like this 2 1 use the Basic interface data in mat file 2 intf sigInspectDataBasic mySignals mat 3 change the settings 4 intf settings ARTIFACT TYPES Automatic MyArtifl MyArtif2 5 run autoLabel with the default method 6 sigInspectAutoLabel intf myAutoAnnot mat j 7 run sigInspect 8s sigInspect intf 9 now click the load icon in the toolbar and open myAutoAnnot mat Artifact types handling No matter what artifact types you set in your interface the sigInspectAutoLabel function uses only 0 1 clean artifact classification The number of artifact types you define will only be used to resize annotation matrix for each signal to appropriate dimension It may be a good idea to use artifact types in the form intf ARTIFACT_TYPES AUTO myTypel myType2 so that you keep record of the original automatic annotation Artifact classification methods While sigInspectAutoLabel is gateway function for user s convenience artifact classification itself is performed by the function sigInspectClassify This function also implements all classification methods mentioned below Artifact classificati
11. ol allows concurrent visualization of multiple parallel channels playback and spectrogram plot of selected channels to identify specific firing patterns and especially annotation of individual channels Parallel signals are displayed in one second segments which can be easily annotated using the GUI controls or shortcut keys SigInspect also contains tools for automatic annotation of microelectrode recording data based on published methods This can provide starting point for manual annotation and speed up the data cleaning process considerably Quick start Signal A signal in sigInspect is assumed to be a row vector with samples in columns a multi channel signal is a matrix with channels in rows SigInspect shows always one second segment of all channels in current signal A signal can have one to unlimited number of channels Loading a signal the simple way The simplest way to start viewing and annotation is to call sigInspect with signals as a parameter Multiple signals can be passed in a cell array instead user can then choose the displayed signal using the signal selector The second parameter is sampling frequency in Hz default value 24k Hz is set if second parameter is omitted 1 1 single multi channel signal matrix as input 2 size signal C x N matrix C channels N samples 3 sigInspect signal samplingFreq signal chan in rows samples in columns 4 5 2 multiple signals cell array as inpu
12. on is done on a set of features computed from the raw signal by sigInspectComputeFeatures the feature set varies from method to method psd deviation from ideal spectrum The psd method is designed to detect artifacts with very strong frequency components and is based on our 2015 EMBC paper 1 The classifier stores a mean Power spectrum or Power Spectral Density PSD calculated on clean portions of a training set of 60 ten seconds long microEKEG recordings Manual annotation of the training data was performed by 5 trained experts using previous version of the sigInspect tool Classification threshold was set to maximum accuracy on the training data More details can be found in the paper Other methods Other more accurate classification methods are still under development Please stay tuned About license SigInspect is distributed under the Lesser General Public License https www gnu org licenses lgp1 3 0 en html which means you can use sigInspect free of charge for research educational commercial or any other purpose but you should keep the license when using larger portions of the code If you publish results processed with our tool we expect you to give us appropriate authorship credit e g by citing our paper 1 We will be very happy if sigInspect helps you in your research If you are happy or unhappy with our tool we will be glad if you let us know FAQ What does sigInspect do sigInspect is a Matlab
13. ow numbers of all selected channels that have given artifact assigned Annotation can be saved to a mat file either by clicking the save icon in the toolbar the Save all button at the bottom or by hitting s By default annotation is saved to current directory as sigInspectAnnotyyyy mm dd HHMMSS mat where yyyy mm dd HHMMSS is current date and time to change this see ANNOT_DEFAULT_FILENAME in the settings Annotation can be loaded from a mat file using the load icon in the toolbar The format of saved annotation is a cell array of the same length as the number of signals Each cell contains annotation for given multichannel signal in a C x S x A logical matrix where C is the number of channels S signal length in seconds and A number of defined artifact types For example annotation 3 2 1 is one when the 3rd channel contains artifact of type 1 in 2nd second Saved annotation also contains interface type artifact types and signallds to verify that you are loading annotation that fits to currently loaded data when metadata do not fit sigInspect offers you to match repair the metadata Number shortcuts work obviously only up to 10 channels tenth channel is controlled by 0 This method is commonly used in Deep Brain Stimulation surgery for nuclei identification If you switch the overview window on you can also show signal segments annotated as artifact in color Overview window By checking the overview checkbox or
14. s a cell array of strings unique signal identifiers This function is called only once during sigInspect initialization After that sigInspect stores the signallds internally getSignalsBylId 1 function signals chInfo getSignalsById obj signalld This function is called whenever the viewed signal changes and new one has to be loaded Here signals isa C x N matrix where C is the number of channels and N is the number of samples Thus all channels have to be of the same length use trailing zeros if one of the channels is shorter The other output chInfo is a single string which is shown in time series plot title You can use this parameter to provide info about individual channels such as in Figure 1 all text beyond the 18t245p3x signalld in the plot title If you do not need additional signal info just return empty string settings The last attribute of the abstract class is the settings structure By default this is an empty structure i e it is not abstract so you do not have to define within your interface However it may be very useful for defining settings for your data source Settings are defined simply by assigning the settings structure a field of the same name as the property you want to change For example you can change the sampling frequency within your interface as follows 1 intf myInterface 2 intf SAMPLING_FREQ 10000 3 sigInspect intf 4in Matlab it is in fact an abstra
15. sigInspect User s Manual Eduard Bakstein eda zzz cz July 13 2015 sigInspect is a Matlab GUI tool for inspecting multi channel recordings Is particularly useful for extracellular microelectrode recordings and allows visualization playback and annotation of segments containing artifacts SigInspect was developed by the NEURO group http neuro felk cvut cz at the Department of Cybernetics Faculty of Electrical Engineering Czech Technical University in Prague Contents Overview 1 Quick start 2 Signal s aA fowls Qo oe hd Gok Bae i eek hp CIRO SR oe SS ee ee ee Gee a G h 2 Loading a signal the simple way 2 2 Loading signals from a mat fille 2 2 2 Using the GUD 5 Soe sts gree Sk a ord eats EA we in ty GY oP ee Gh ys Bee ad gee 4 bs 3 Settings seek wack ta Ae es oe OE GP eR SE Rw eM a a 4 Advanced data loading sigInspect DataInterface 4 In OOP terns 2 5 oS oe eek Pa Re Raa ee ee ee OA ee Se as 6 Reference ochre ok oe eb a DE eh ee NG A ee ee eS a bed 6 Example interface sot a sraa doh Re he ele ek eRe a eee AG ee 7 Default interface siginspectDataBasic ooa a ee T Automatic artifact annotation Beta 8 Artifact types handling ya e e oea a a A a a A ee 8 Artifact classification methods ooo 000 ee 8 About license 9 FAQ 9 Overview sigInspect is a graphical user interface GUI application for Matlab developed for inspection and annotation of extracellular microelectrode recordings MER The to
16. t 6 s signall signal2 signal3 7 sigInspect s samplingFreq Loading signals from a mat file In case sigInspect is called without parameters an Open file dialog will pop up upon intialization asking you to select a mat file with data The mat file has to contain signals in a cell array the format described above in a variable called signal signals or data Otherwise your signals will not be found and the application will issue an error 2 siginspect a Baran 2 18t245p3x 1 cen unknown 2 ant unknown 3 pos unknown 4 sha unknown a a 900 800 700 600 SORE AN RY TORS TI IRTE EL al iji aa EEA T I P IT per ena e a r ap e n rn l il i mp pape rma e qir j i w wren z dha ad as dadda La aa wei sul lly noth bald dub aL au ad ad wd i Nu Ind hast sda Kala ba 500 LA a a Nie Mm T e SD hoad uaa A NA l had uda dulia Jail dhia Wi Jal didn uf tay ial wud ili i empeg perea A s uhi i til i a id ji palu hadi 400 no ge es al Ny wa ri rin Ci a in i Qdots wb awa EUR ASE Fee TP NN AAP HNL ME MER UPAR Pe T T A AA IA OT A RTP ego RE RMN IR HO Pire yal Jia a al avd the ba Mf ad tut da Lada a al of had a Sh adc ad al la lb dl of dt mib aaah Jatha alk ot thts af bd 300 s n F1 TYPE1 34 F2 TYPE2 1 F3 UNKNOWN Signal 18t245p3x v Second 2 v lt PREVIOUS NEXT gt
17. ts constructor intf sigInspectDataCsv csvDemo change additional settings optional intf settings NORMALIZE_SIGNAL_PER_CHANNEL 0 run sigInspect sigInspect intf Bw NR an Default interface sigInspect DataBasic When you provide sigInspect with a cell array of signals or a path to a mat file with data it will initialize the default interface sigInspectDataBasic which accepts these on the input see inline help for details The main disadvantage of calling sigInspect with signals directly is that you have no possibility to change settings other than to hard code them in sigInspect m directly A simple workaround is to initialize the basic interface yourself as follows 1 prepare data initialize the Basic interface 2 signals signall signal2 signal3 3 intf sigInspectDataBasic signals 4 change the settings 5 intf settings ARTIFACT_TYPES Wavy Spiky Other 6 run sigInspect 7 sigInspect intf Automatic artifact annotation Beta To assist you with manual artifact annotation in your signals the sigInspect tool provides you with several methods of artifact detection This tool is fine tuned for microKEG data and in its initial release it is intended as a starting point for manual signal inspection rather than as a stand alone tool The workflow is following 1 initialize data interface of your choice 2 run sigInspectAutoLabel on this interface which will result i
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