AxIS Data in NeuroExplorer

Transcription

1 AxIS Data in NeuroExplorer 1. Objective NeuroExplorer is a data analysis program for neurophysiology that can be used to analyze neural data collected with AxIS. This document describes the steps necessary to import AxIS files into NeuroExplorer, select electrodes to analyze, create a raster plot, and generate crosscorrelations. With the exception of cross-correlation analysis, everything may be performed in NeuroExplorer demo mode. 2. Importing Data from AxIS NeuroExplorer can import raw data (.raw) and spike files (.spk) from AxIS. This tutorial will focus on importing spike files for analysis. Spike files are generated by recording the data stream from a Spike Detector in AxIS and contain information about spike timing and waveforms. By default, NeuroExplorer only imports channels with active spiking. To visualize or compare all channels in a particular well, it is necessary to change this default setting to include channels without spikes. To import all channels, including those with zero spike counts, choose View Data Import Options. Under the Axion Files tab, check the box labeled Create variables for channels with zero counts. Axion BioSystems AxIS Data in NeuroExplorer 1

2 In the File menu, click Import Data, and select Axion Data File from the list. Import data from AxIS file Data panes NeuroExplorer assigns the data from AxIS into two different variable types for each electrode: one containing spike timestamp information, and one containing the spike waveforms. Click the tabs at the bottom of the main screen to change data panes to see the different variables. The Variables pane lists all of the variables. A checkbox beside the electrode name indicates the electrode is currently selected for analysis. Timestamp variables contain the timestamps for all of the spikes detected on that electrode. The Timestamps data pane shows the timestamp variables (one per column). In AxIS.spk files, timestamp variables are named according to the convention well location_electrode number, e.g. A1_11. In the Timestamps data pane, the electrode names are listed in the first row, and below each electrode name is a list of timestamps corresponding to the time a spike was detected on that electrode. Waveform variables contain the voltage waveforms for all of the spikes detected on an individual electrode. The Waveforms pane shows the waveform variables. The top left cell is a drop-down menu containing a list of all of the waveform variables. Waveform variable names contain a wf_ preceding the electrode name, e.g. wf_a1_11. The second column of this pane contains the timestamps of the detected spikes on the selected electrode. The remaining columns contain the voltage waveform information from every detected spike. The waveform length is specified in AxIS by the Spike Detector. Axion BioSystems AxIS Data in NeuroExplorer 2

3 3. Selecting Data to Analyze There are several options for selecting electrodes to analyze: 1. Manual selection: Select or deselect the checkboxes beside each electrode name in the Variables pane. 2. Command line filtering: Use the filter options at the top of the Variables pane to select electrodes that meet a specific criteria. Use * to represent any characters that will not be specified in the search. For example, A1* will select all electrodes from well A1. Filtering based on the number of timestamps, which corresponds to the total spike count on each electrode, or the mean frequency of the spikes is also available. Click Filter after entering the criteria. 3. Variables Panel: Select electrodes in the Variables panel. If the Variables panel is not present, select it in the View menu. The left column contains unselected electrodes, while selected electrodes are on the right. Click > or < to move an electrode between columns. Use Shift or Ctrl to highlight several electrodes at a time. Select all electrodes by clicking >>, or deselect all electrodes by clicking <<. Push Apply to make the changes take effect. Use the dropdown menu at the top to specify All variables, Neurons (timestamp variables), Waveforms, or other variable types. Filter options Variables panel 4. Performing Analyses NeuroExplorer provides a variety of analysis options. This guide provides step-by-step instructions for generating a raster plot and performing cross-correlation analysis. Further descriptions of these and other NeuroExplorer analyses can be found in the NeuroExplorer User Manual and Reference. Axion BioSystems AxIS Data in NeuroExplorer 3

4 4.1 Raster Plot A raster plot displays a mark (vertical line) at each detected spike time. Plotting several electrodes at once provides a visualization of spikes across different electrodes within a well, showing how they relate temporally. To generate a raster plot: 1. Select raster analysis: Click Analysis Select Analysis Type Rasters, or select Rasters from the Analysis panel. If the Analysis panel is not present, select it in the View menu. 2. Specify plot visualization details: Modify the default settings for x-axis length and tick height as desired. To create the raster plot in a new window, check Show analysis in a new window. 3. Click OK. Select Rasters Electrodes can be added or removed after the graph is created, using the Variables panel (see Section 3). To change the plot layout, right-click on the plot and select Edit Graphics. Recommended plot layout settings: 1. Single column: Select Block Properties and change Number of Graph columns to 1 and deselect Draw grid. 2. Move electrode names: Select Switch to Graph Layout Mode. Click and drag the electrode name to the left side of the plot. 3. Return to page view: Select Switch to Page Layout Mode to return to the page view. 4. Single x-axis: Select X Axis Properties. Under the Label tab, set Show Label to Bottom Graph Only. Under the Line tab, set Show Label to Bottom Graph Only. Under the Numerics tab, set Show Numerics (which graphs) to Bottom Graph Only. Axion BioSystems AxIS Data in NeuroExplorer 4

5 To export the graph to Microsoft PowerPoint, right click on the raster plot and select Send Graphics to Power Point. Specify a file location, slide title, and any comments, then click OK. Edit Graphics options 4.2 Cross-correlation Correlation analysis provides information about the way neurons are interacting. A crosscorrelogram shows the probability a spike occurred on an electrode at time t 0+t given a spike on a different reference electrode at time t 0. If spikes on the electrode of interest often occur very closely in time to spikes on the reference electrode, a crosscorrelogram between these two electrodes will have a peak centered near zero. The height and width of the peak of the crosscorrelogram indicate the degree of network synchronicity. To perform cross-correlation analysis: 1. Select electrodes: Select 5-10 active electrodes in a well to analyze. 2. Select crosscorrelogram analysis: Click Analysis Select Analysis Type Crosscorrelograms, or select Crosscorrelograms from the Analyses panel. 3. Specify multiple reference events: In the Analysis tab set Reference Event(s) to Multiple Reference Events (one for each column of graphs). 4. Select reference events: Click Ref. Events to specify which electrodes will be used as the reference events. 5. Select electrodes to analyze: Click Add All Variables Selected for Analysis to use all electrodes selected in the workspace as the reference events. 6. Open in new window: Check Show analysis in a new window to open the plot in a new window. 7. Click OK. 8. Adjust analysis settings: Settings may be adjusted in the properties panel after running the analysis, if desired. Axion BioSystems AxIS Data in NeuroExplorer 5

6 Specify reference events Click Results View Numerical Results Window to view the values of the cross-correlation analysis. The Results pane contains the values of the crosscorrelogram and the Summary pane contains relevant metrics from each crosscorrelogram curve. View numerical results Axion BioSystems AxIS Data in NeuroExplorer 6

7 Trademarks Axion BioSystems, Inc. and the logo are trademarks of Axion BioSystems, and may not be used without the express written permission of Axion BioSystems, Inc. All other brands, product names, company names, trademarks and service marks are the properties of their respective owners. Restrictions and Liabilities This document is provided as is and Axion BioSystems will assume no responsibility for any typographical, technical or other inaccuracies in this document. Axion BioSystems does not make any commitment to provide any changes, updates, enhancements, or other additions to this document to the User within any time frame or at all. This document might contain references to third-party sources of information, hardware or software, products or services and/or third-party websites (collectively the Third-Party Information ). Axion BioSystems has no control over and is not responsible for any Third-Party Information, including, without limitation the content, accuracy, copyright compliance, compatibility, performance, trustworthiness, legality, decency, links or any other aspect of Third-Party Information. The inclusion of Third-Party Information in this document does not imply endorsement with use of Axion BioSystems technology. Conditions of Use You are responsible for understanding and performing the protocols that are described within. Axion BioSystems makes no guarantee for any results achieved. These protocols are provided as a recommendation by Axion BioSystems based on its use and experience. Origin Axion BioSystems Microelectrode Arrays are manufactured in the United States of America. Copyright Notice 2014 Axion BioSystems, Inc. All rights reserved. This document may not be reproduced, distributed, modified or publicly displayed without the express written permission of Axion BioSystems. Title of Section Axion BioSystems AxIS Data in NeuroExplorer 7