Evoked Amplitude Analysis

Overview

Goal:

Calculate the amplitude of evoked release (EPSP, EPSC, EJC, EJP) and determine the ‘average’ amplitude for a recording

Output:

  • Processed recording data with adjusted baseline

  • Exportable table of maximum and minimum amplitudes

  • Summary of the data

Plugins used:

Set up

Open a recording from file menu -> Open recording or Alt+o. Set the view mode to overlay by View menu -> overlay Select the channel to analyze in the channel dropdown menu.

Open plugins to use by Plug-ins menu -> select the desired plugin names. Plugins typically have user-input forms that appear in the control-panel as individual tabs.

Use the Process Recording Plugin to subtract the baseline. Find a x-axis region that best estimates the ‘baseline’ in the recording. Set the Baseline Subtraction method to Mean of x-axis range and enter the lower and upper bounds of the x-axis used to calculate the baseline for each sweep. Click Apply. The baseline of the sweeps should now be aligned at y=0.

Save the recording file by file menu -> Save recording data as....

Caution

.abf files cannot be overwritten by SimplyFire. Baseline subtracted traces should be stored under a new file name.

If the amplitude of the artefact is larger than the evoked response, use the Navigation Tools located around the plot to adjust the x- and y-axes so that the artefact is outside of the visible x-axis.

Alternatively, use the Navigation Plugin to set the desired x- and y-axes limits.

If not all sweeps should be analyzed (i.e. some sweeps failed to respond), use the Sweeps Plugin to hide unwanted sweeps. While the Sweeps Plugin is in focus, a sweep can be highlighted by clicking on or near the sweep. Pressing the Delete/Backspace/e key will hide the sweep from view.

The sweeps that are currently visible are indicated in the control-panel.

Analysis

Analysis is performed by the Evoked Analysis Plugin.

If the artefact is larger than the evoked response, set the Limit x-axis for analysis to: parameter to Visible window and adjust the plot so that the artefact is outside of the visible window.

Alternatively, set the Limit x-axis for analysis to: parameter to Defined range and enter the lower and upper x-axis limits for the analysis.

Click on Calculate Min/Max button. Minimum and maximum values per sweep (per channel, if multiple channels are analyzed) will be entered into the data panel.

Output

The results of the analysis can be found in the data panel.

The following properties for each sweep analyzed can be found:

  • Sweep number (starting from 0)

  • Channel number

  • Filename

  • Minimum y-value for the sweep

  • Maximum y-value for the sweep

Export the data

Selected entries in the data-panel can be copied onto the clipboard.

Shift+left click to select a range of entries or hold Ctrl to select multiple entries Ctrl + a to select all entries. Use the Esc/q key to remove all the highlights.

Data can be copied by Ctrl + c or right click on the data-panel -> Copy selected.

The copied data can be pasted into Excel or other programs of choice.

The data-panel can also be exported to a comma separated value (CSV) format by file menu -> Mini Analysis -> Export data table. All data visible in the data-panel are stored in the exported file.

Summarize the data

A summary of the discovered minis can be added to the results-display. The results-display is found in the results tab under the plot.

Right click on the data-panel -> Report all or Report selected or press the Report stats on the control-panel. Averages and standard deviation of maximum/minimum y-values will be added to the results-display. Additionally, the indices of channels and sweeps sampled will be indicated.

The result can be found in the results-display.

Clear the data

When opening a new recording file, the data in the data-panel are cleared.

The entries can also be deleted by selecting the entries and using Delete/Backspace/e key.

Alternatively, the Delete all button in the control-panel can be pressed.