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Analyze spike trains including peristimulus time histogram analysis and interspike interval histogram analysis.

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This app can be used to analyze spikes data and create peristimulus time histogram or interspike interval histogram.

Download the file Spike_Train_Analysis.opx, and then drag-and-drop onto the Origin workspace. An icon will appear in the Apps Gallery window.
NOTE: This tool requires OriginPro.

Click on the Spike Train Analysis icon in the Apps Gallery window, a toolbar with two buttons will appear: PSTH Analysis (peristimulus time histogram) and ISI Histogram (interspike interval histogram).

  • PSTH Analysis

    1. Click PSTH Analysis button in the toolbar. In the opened dialog, choose columns for Event Markers, Spikes and ID for Unit respectively. Spikes column shows spike timestamps, ID column indicates which unit (neuron) each spike belongs to, and event markers column indicates timestamps for a particular stimulus type.
    2. In Choose Spike IDs branch, check Use All Unit IDs, all spikes will be used in the analysis. Otherwise, select IDs in the Select Spike IDs list box, and it will analyze spikes for each chosen ID.
    3. In the Settings branch, specify the pre and post time for each stimulus, bin size, quantity to calculate: count (average counts over all stimuli), probability or Hz (count divided by bin size), and whether to calculate 99% confidence interval.
    4. Check Show Peristimulus Time Histogram option, peristimulus time histogram plots will be created in the report.
  • ISI Histogram

    1. Click ISI Histogram button in the toolbar. In the opened dialog, choose columns for Spikes, Event Markers (optional) and ID for Unit (optional) respectively. If Event Markers column is chosen, set pre time and post time in Event Marker Settings group. If ID for Unit column is chosen, select spike ID in Choose Spike IDs group.
    2. In Settings branch, specify Bin Scale (linear or log), bin begin, bin end and bin size, and Normalization (count, probability or spikes per second).
    3. Check Show Inter Spike Interval Histogram option, interspike interval histogram plots will be created in the report.

Sample OPJU File
This app provides a sample OPJU file. Right click on the Spike Train Analysis icon in the Apps Gallery window, and choose Show Samples Folder from the short-cut menu. A folder will open. Drag-and-drop the project file STAEx.opju from the folder onto Origin. The Notes window in the project shows detailed steps.
Note: If you wish to save the OPJU after changing, it is recommended that you save to a different folder location (e.g. User Files Folder).

Four units are supported: Count, Probability, Hz and Normalized Firing Rate. They are defined as follows:

  • Count: Mean Spike Count per Event
               Count = (Spikes per bin) / (Number of Events)
  • Probability: Normalized Spike Count
               Probability = (Spikes per bin) / (Number of Timestamps)
  • Hz: Firing Rate
               Hz = Count * (Bins in a sec)
  • Normalized Firing Rate
               Normalized Firing Rate = (Firing Rate) / (Number of Timestamps)

where Number of Timestamps = number of spikes within PSTH/ISI range for the selected ID(s).


v1.21 1/19/2024 Added Normalized Firing Rate unit.
v1.1 12/11/2023 Fixed probability unit bug.

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