New Phase Analysis Reveals Phase Relationship between Single-Cell Activity and Local Field Potentials

NeuroExplorer 5.017 released on July 22, 2015 has two new analyses: Find Oscillations analysis and Firing Phase analysis.

Find Oscillations analysis identifies episodes of oscillatory activity in the specified frequency band in recorded analog signals. The algorithm is described in Klausberger, Magill, Marton, Roberts, Cobden, Buzsaki and Somogyi. Brain-state- and cell-type-specific firing of hippocampal interneurons in vivo. Nature, 2003 Feb 20;421(6925):844-8

The user specifies two frequency bands (for example, theta band and delta band). NeuroExplorer finds the segments of LFP signal where theta to delta frequency power ratio exceeds a certain threshold. The LFP signal is then band-filtered and oscillation cycle start times are identified via Hilbert transform. This analysis adds several new variables to the data file. The data viewer screenshot below shows the results of analyzing variable LFP01. NeuroExplorer added three new variables: Theta_Epochs, Theta_Filtered and Theta_ZeroPhase:

FIndOsc1D

The LFP01_Theta_ZeroPhase event is than used in Firing Phase analysis that calculates probability of a neuron firing in a certain phase of theta cycle:

FiringPhase

By the way, I added these new analyses after several users asked me whether a phase-of-firing analysis is available in NeuroExplorer.

Do you need new analyses or new features in NeuroExplorer? Please send your requests to [email protected]

Nex5 File Format

NeuroExplorer Version 5.016 (released on July 3, 2015) supports new .nex5 data file format that is more flexible than .nex file format:

  • Allows NeuroExplorer to save files larger than 2 GB
  • Allows to save unlimited metadata for the whole file and for every file variable in JSON format

nex5 format is designed to be similar to .nex format so that the code that reads and writes .nex files would need only small modifications to implement reading and writing .nex5 files.

Full .nex5 file format specification as well as C++ code and Matlab code for reading and writing .nex5 files are available in the following files:

 

Dealing with Noise and Artifacts in Data Viewer

Often you can visually identify periods of noise or artifacts in 1D Data Viewer:

scratching artifact2

In NeuroExplorer version 5.014 or later, you can identify time intervals corresponding to artifacts using mouse:

– Right-click in 1D View to invoke context menu:

1dmenu1

– Specify ‘Select Interval Variable…’ menu command. NeuroExplorer will display the following dialog:

Specify Interval Variable to Add Intervals to

– Click ‘Create New Interval Variable…’ button:

New Variable Name

– Let’s create a new interval variable with the name noise. Type ‘noise’ (without quotes) and click OK to close this dialog, then click OK to close Select Interval Variable dialog.

– Note that the cursor now has ‘plus interval’ graphic:

intadd

– Press the left mouse button at the start of the noise interval, then drag the mouse until the end of the noise interval and release left mouse button. The new interval is added to noise interval variable:

added interval

– Add a second interval:

2intervals

– Hit ESC key to exit Add Interval mode

– We want to analyze data that is NOT in the noise intervals. To make this possible, right-click in 1D view again and select ‘Invert Interval Variable’ menu command:

invertintvar

– In the Invert Interval Variable dialog, select noise variable to be inverted:

Invert Interval Variable

– Now noise_inverted interval variable contains time intervals corresponding to our data without noise:

noiseinverted

– We can use noise_inverted variable in a Data Selection page of analysis properties dialog:

Analysis Properties data sel

and the data in noise intervals will be ignored.

There is also a faster way to get rid of noisy data — you can delete all the data in specified time intervals. To do this, right-click in 1D view and select ‘On Mouse Click and Drag, Delete…’ menu command:

deletemenu

– Now when you click and drag with the left mouse button, all the data in selected time interval are deleted:

deleted2

deleted3

Note that delete operation cannot be undone right away. You will need to reload the data file to restore original data.

 

How to Save and Restore Your Work in NeuroExplorer

When you work in NeuroExplorer, the program creates a number of data and analysis results windows.  By default, these windows are not restored when you close and reopen the program.  If you would like to save and restore all your current work in NeuroExplorer, use File | Save NeuroExplorer State and File | Restore NeuroExplorer State menu commands:

saverestorestate

You can also restore the last analysis of this or previous NeuroExplorer analysis session using File | Restore Last Analysis menu command.  The program will do the following:

  • Load the data file used in last analysis
  • Select the variables used in last analysis
  • Run the analysis

See also Working with Results Files.

 

Working with Results Files

NeuroExplorer can save both graphical and numerical results of the analysis in a NeuroExplorer results file. Since each result has both graphics and numerical values, the results are saved in a set of files with common file name and different extensions.

You can use SavedResults | Quick Save Results menu command to save all the current results:

quicksaveresultsmenu

For example, if you run Perievent Rasters analysis on data file TestD21.plx and select Quick Save Results, the results will be saved in the following 5 files:

  • TestD21_plx Perievent Rasters.nexresult (text file with links to other files of this result)
  • TestD21_plx Perievent Rasters numres.txt (text file with numerical results)
  • TestD21_plx Perievent Rasters numres summary.txt (text file with the summary of numerical results)
  • TestD21_plx Perievent Rasters.png (.png file with graphical analysis results)
  • TestD21_plx Perievent Rasters.ntp (template file with analysis parameters)

By default, these files be saved in the folder:
C:\Users\<your_user_name>\Documents\NeuroExplorer 5\Results.

The .nexresult file is the file containing description of the analysis and the links to other result files. You can open this file in NeuroExplorer using SavedResults | Open Saved Results File menu
command.

When you open results file, NeuroExplorer loads graphics and numerical results files and shows a window with 4 tabs:

savedresperiraster

This window looks similar to the Graphical results window, but the results are not ‘live’ — you cannot adjust analysis parameters and recalculate the results.

However, you can replicate the results saved in the results file. Use SavedResults | Restore Analysis in NeuroExplorer menu command:

restoresavedres

NeuroExplorer will do the following:

  • Open data file used in the calculation of results
  • Select variables for analysis exactly as they were selected in the saved results
  • Run the analysis used in the calculation of results (using the same analysis parameters)

You can also use SavedResults | Results Folder Summary menu command to view all the saved results in a grid:

ResFolderSummary1

In this Results Folder Summary view you can:

  • Sort results by any of the columns by clicking at the column header
  • Open results file by double-clicking the row representing the file
  • Convert selected results to PowerPoint slides using right-click and selecting Add Slides… context menu command
  • Select results using Find combo box in the NeuroExplorer toolbar. The text in all the columns will be used when filtering the results. For example, to view only results saved in 2015, type 2015 in Find box:

resfind2