NeuroExplorer

This how-to guide contains an overview of data import methods.

Use File | Open… and then select your data file.

If you are using one of more than 50 supported file formats, the program will load your data file.

If NeuroExplorer complains about an unknown file extension or invalid file format, follow these instructions.

If you can load your data in MATLAB, you can either save MATLAB data in a .nex5 file, or transfer data from MATLAB to NeuroExplorer.

If your data is in Excel, you can copy and paste your data from Excel to NeuroExplorer.

NeuroExplorer supports more than 50 file formats and tries to identify the data file type from the file extension.

Some file extensions are used by several file formats and NeuroExplorer may be unable to identify the format of the selected file. For example, a .nev file can be either a Neuralynx data file or Ripple Neuro data file.

You can:

• Use the specific File | Import Data sub-menu, such as Plexon Data File or Neuralynx Data File, to open your data file.
• Specify what file format corresponds to a specific file extension:
  • Select View | Data Import Options…
  • Click the File Extensions… button
  • Select the file extension in the left column
  • Click in the right column and select the file type for the extension

You can create spike trains (1 × N or N × 1 matrices with timestamps in seconds) or continuous variables in MATLAB and transfer them to NeuroExplorer on the fly.

1. Select File | New.
2. Select MATLAB | Get Data From MATLAB | Open MATLAB As Engine. NeuroExplorer will open MATLAB as an engine.

When you run Open MATLAB As Engine, a new instance of MATLAB is opened. This instance has no variables in its workspace. Therefore, you need to create or load the data you want to transfer to NeuroExplorer.

After your data is available in MATLAB, select one of the MATLAB | Get Data From MATLAB commands to transfer the data to NeuroExplorer.

NeuroExplorer can use Copy/Paste to add data variables.

To paste timestamped variables such as BarPress and Reward from a spreadsheet:

In Excel

1. Select the cell range containing both variables.
2. Select Home | Copy.

In NeuroExplorer

1. Select the Data view of a file.
2. Select the Timestamps tab.
3. Right-click and select Paste.

NeuroExplorer will create two new Event variables and add them to the file.

Using the same approach, you can import continuous variables by right-clicking in the Continuous tab and time intervals by right-clicking in the Intervals tab.

You need to save the file using File | Save… or File | Save As… to make the change permanent.

NeuroExplorer can import continuous data from a multicolumn text file where each column corresponds to a continuous variable.

ContChannel1    ContChannel2
114.74609       -63.47656
56.15234        -358.88672
-187.98828      -63.47656
-48.82813       388.18359
-26.85547        285.64453

Use File | Import Data | Text File with Continuous Variables (no timestamps)….

• First line contains variable names – if selected, fields in the first line are used as variable names. The second line becomes the first row of data.
• First Data Point Timestamp – specifies the timestamp of the first data point in each continuous variable.
• Time Between Data Points – specifies the time step used to calculate the timestamp for each row.

For data row n, where n = 1, 2, …:

DataRowTimestamp = FirstDataPoint + (n-1)*TimeBetweenDataPoints

If the text file contains timestamps in the first column:

Time      ContChannel01
0.000400  114.746094
0.000500  56.152344
0.000600  -187.988281
0.000700  -48.828125
0.000800  -26.855469

Use File | Import Data | Text File with Continuous Variables (with timestamps)….

NeuroExplorer can import timestamps stored in the following text formats.

1. Multicolumn Table of Timestamps

Neuron01    Neuron02
0.01        0.001
0.3         0.05
0.5         0.1
0.4
0.6

Each column contains the timestamps of a neuron. The first line contains the names of all variables.

2. Pairs <name> <timestamp>

The text file contains pairs of the form name timestamp.

name is a character string. The first character should be a letter. If a number is used as the name, NeuroExplorer adds “event” at the beginning of the variable name.

timestamp is a number representing the neuron firing time or event time in seconds or time ticks.

Neuron01    0.01
Neuron01    0.3
Neuron02    0.001
Neuron02    0.05
Neuron01    0.5
Neuron02    0.1
Neuron02    0.4

Use File | Import Data | Text File with Timestamps… to import a text file with timestamps.

Sampling Frequency defines the internal representation of timestamps.

Internally, timestamps are stored as integers representing the number of time ticks from the beginning of the experiment. The time tick is:

1./Sampling_Frequency

Timestamp Units defines how timestamp numbers are treated. If timestamps are in time ticks, they are stored internally exactly as they appear. If they are in seconds, NeuroExplorer converts them to time ticks:

Internal_Timestamp_In_Ticks = Timestamp_In_Seconds * Sampling_Frequency

NeuroExplorer requires a Sentinel key to operate. Sentinel drivers need to be installed so NeuroExplorer can communicate with the Sentinel keys.

These drivers are installed when you run NeuroExplorer5Setup64.exe.

Error Messages and Troubleshooting

To speed up access to frequently used analyses, you can rearrange the order of analyses in the All Analyses list by dragging analyses up and down.

There is also a Recently Used Analyses list showing the last 10 analyses used.

The layout of the Analyses Panel is saved in:

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

To standardize the order of analyses across computers in a lab, rearrange the analyses on one computer, exit NeuroExplorer and copy the AnalysesPanelLayout.layout file to the corresponding folders on other computers:

C:\Users\<user_name>\Documents\NeuroExplorer 5\Layouts