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

 

 

How to Customize Analyses Panel

There are two ways to select an analysis in NeuroExplorer – you can click at the analysis you want to run in the Analyses panel:

SelectAnalysis

or select an analysis via Analysis | Select Analysis Type menu command:

SelectAnViaMenu1

The fastest way is to use Analyses panel. However, now that NeuroExplorer has more than 30 analyses to choose from, you may have to scroll the panel to get to many of the analyses. To speed up the access to the analyses you use most often, you can rearrange the order of the analyses in the All Analyses list by dragging the analyses up and down in the list:

draganalyses

There is also Recently Used Analyses list that shows the last 10 analyses that were used.

The layout of the Analyses panel is saved in the file

C:\Users\<user_name>\Documents\NeuroExplorer 5\Layouts\AnalysesPanelLayout.layout

If you want to standardize the order of analyses on all computers in your lab, you can rearrange the analyses on one of the computers, exit NeuroExplorer and copy AnalysesPanelLayout.layout file to C:\Users\<user_name>\Documents\NeuroExplorer 5\Layouts folders on other computers.

Exporting Data to Text Files

NeuroExplorer version 5.002 was released on September 8, 2014. Here is a summary of what’s new in this version:

  • Coherence, Spectrograms and PeriEvent Spectrograms analyses now have all the spectral calculation options available in other spectral analyses (selection of 3 types of data preprocessing, 6 types of windowing functions and multi-taper options).
  • Burst Analysis now saves properties of each burst in Numerical Results:

Burst Properties

  • When exporting data or numerical results to text files, a user can select what character is used to separate items in a line (comma, space or tab; previously only tab was available). The new comma-separated output (.CSV file format) is especially convenient when working with Excel since this file format is natively supported by Excel.
  • When exporting data to text files, a user can now export waveform variables and marker variables (previously, NeuroExplorer could only export neurons, events, intervals and continuous variables).
  • You probably know that you can open a .nex file in NeuroExplorer by double-clicking at the file in File Explorer. For some reason, Windows sends several open file commands to NeuroExplorer when you double click at a .nex file. You could see some files opened twice, and some files generating a “sharing violation” error. This problem is fixed in NeuroExplorer 5.002 (and while we are talking about opening files, note that you can also open a .nex file by dragging the file into NeuroExplorer).

Numerical Results for PeriEvent Rasters Are Available in Version 5

Many NeuroExplorer users asked me why perievent rasters analysis lists only perievent histograms in the numerical results table.

The reason was that listing all the timestamps for each line of the perievent raster can use a lot of RAM and can slow down the program. For example, for a spike train with 10,000 spikes, we may have 10,000 raster lines containing up to 10,000 spikes in each raster line. This adds to 100 million timestamps which would use 800 MB of RAM. Besides, the user can analyze dozens of neurons, so using so much RAM may not work, especially for a 32-bit application that cannot use more than 2 GB of RAM. The situation is somewhat better for a 64-bit program, but the program would still be too slow.

In NeuroExplorer Version 5, I came up with a solution — the program stores some of the results of the perievent raster analysis in memory and calculates all the timestamps for perievent rasters on-the-fly:


PeriEvent Rasters Numerical Results

What I found interesting was that the graphical representation of the perievent raster:


PeriEvent Raster

creates an impression that each line of the raster contains many data points while in reality each line contains only a few points as we can see from numerical results above.

Complete numerical results for PeriEvent Raster analysis and for all the other analyses that did not provide all the results in version 4 (Cumulative Activity Graphs, Instant Frequency, ISI versus Time, Poincare Maps and Synchrony versus Time) are available in NeuroExplorer 5.001 and later.

If you purchased NeuroExplorer Version 5 license, download the latest Version 5 installer.  Otherwise, download NeuroExplorer Version 5 Demo today!