Tutorial:Single Channel Measurements

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Idealization and Stats

  1. If you haven't already, simulate basic model sim.qdf
  2. Create a new model (File -> New model)
  3. Estimate closed and open amplitudes
    • Method 1: grabbing by eye
      1. select a bit of baseline data
      2. right-click the closed (black) state and choose "Grab"
      3. select a bit of data from the middle of an opening
      4. right-click the open (red) state and choose "Grab"
    • Method 2: grabbing all at once with Amp
      1. select a bit of clean data containing open and closed intervals
      2. right-click the background of the model and choose "Grab all amps increasing"
      3. Verify the amps by pointing at each state until the tool-tip shows
  4. Try idealizing a selection of data -- when analyzing long files, this will save time if you have made a mistake or there is a problem with the analysis
    • Select a bit of data
    • Right-click "Idl" on the right under "Modeling"
    • Data Source: Selection
    • Method: SKM
    • Re-estimate: yes
    • Click "Run"
    • Check the idealization to convince yourself that it is correct, and that significant events have not been missed. If you chose a long selection to idealize, you can view a shorter segment in the high-res window by highlighting it in the low-res window. Note: You can view the idealized trace above the simulated data by checking the Idl show above box located on the toolbar. You can hide the idealized trace from the display by un-checking the Idl show box – this will not undo the analysis.
  5. Right-click "Idl" on the right under "Modeling"
    • Data Source: Whole file
    • Method: SKM
    • Re-estimate: yes
  6. Click "Run"
    • When it finishes, the data is overlaid with a red idealized trace
  7. Open the Results window (View -> Results)
  8. Scroll through the amplitude histograms (one per data segment), verifying that the pdf curves match the histograms
  9. Right-click a histogram for curve-fitting, or to extract it to a text file or excel worksheet.
  10. Click the "Segments" tab to see a table of stats vs. data segment
    • you can select a range of cells and press Ctrl-C to copy to the clipboard
  11. Click the "Select" tab to plot the stats
    • Click "Show var..." and choose a stat to plot it vs. segment number
    • Click "Show var..." and choose "custom" to plot one stat vs. another on a scatter plot
    • right-click a point in a plot to show the original data segment
    • right-click the background of a plot to:
      • toggle histogram view
      • logarithmetize the y axis
      • fit to a line or curve
      • copy the image, or create an excel worksheet
  12. Click "Reports" and choose "SKM Report" to create a Word document with all stats and any visible "Select" plots.

Fitting Histograms

  1. If you haven't already, simulate basic model sim.qdf
  2. Idealize it as above
  3. Open the Histogram window (View -> Histogram)
  4. Resize it so the third pane (green) is big enough
  5. Make sure Data Source is "file"
  6. Right-click the green icon and choose "Properties"
    • Class: 1 (open)
    • log: yes (log x binning, so the mean time is visible as a peak)
    • Autoscale: yes
  7. Click OK, then left-click the green icon to run it
  8. Right-click the histogram, choose "Curve fitting"
    • Curve type: Exponential(log 10 x)
  9. Click "Fit" until the curve matches the histogram
  10. Read Tau and Amp, then click "Close"

For difficult fits, you may have better luck with the other algorithms -- click "Options" to switch algorithms.


Prev: Single Channel Measurements Outline Next: Single Channel Kinetics
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