Automatically analyze experimental data using CellData

Both experimentalists and modelers may wish to automate analysis of AxoClamp recordings from biological cell current sweeps. The CellData tool reads in AxoClamp files in binary (ABF) or text (ATF) format. If the file contains recordings from a current injection sweep, such as the protocols commonly used to characterize firing curves and intrinsic electrophysiological properties of single cells, the CellData tool will process the file to determine spike threshold points, action potential peaks, sag and steady state peaks. Then, it will allow the user to review and edit the points for accuracy (or choose a different strategy for determining the action potential threshold), before computing over 30 common electrophysiological properties of the cell.

CellData can be used independently of SimTracker. Both a compiled version and the MATLAB source code of CellData is available for download at http://mariannebezaire.com/simtracker/.

  1. From the Tools menu of SimTracker, choose the ’Experimental Comparison (CellData)’ option to open the CellData tool (Figure [fig:tutCellData:01])
  2. In the CellData tool, load data from an AxoClamp file by clicking the button ’Load AxoClamp file’ (Figure [fig:tutCellData:02]) and selecting the desired AxoClamp file (in ABF or ATF format) from the file picker dialog box that appears (Figure [fig:tutCellData:03]).
  3. As the recording data is imported, a dialog box will appear asking for additional metadata (Figure [fig:tutCellData:04]). Enter the cell type and location for the cell, using whichever nomenclature is appropriate to the user’s field of study. Also enter the name of the person who recorded the cell, for future reference. Then click OK.
  4. Once the recording data is read in from the cell, CellData will display some of the traces from the file in a graph at the lower right corner of the tool. The traces displayed will include recorded membrane potential from the most hyperpolarized trace, the most depolarized trace, and the trace from the current injection at the zero level, if performed (Figure [fig:tutCellData:05]). Overlaid on these traces will be the corresponding current injection plots.
  5. Users should look these over and ensure that the current injection timing looks correct and corresponds to the displayed potential traces, and then click the ’Verify Current Sweep’ button (Figure [fig:tutCellData:06]). A dialog box will then appear, confirming ’Current Sweep Verified’ (Figure [fig:tutCellData:07]).
  6. The lower right corner of the CellData tool will now display the some membrane potential traces from the current sweep, including the potential recordings corresponding to all hyperpolarized current injections and the most depolarized current injection (Figure [fig:tutCellData:08]). However, the traces must be further analyzed to calculate the electrophysiological properties of the cell. Click the ’Calculate Threshold’ button to start the analysis process (Figure [fig:tutCellData:09]).
  7. The threshold calculation process can be time intensive, so the CellData tool will display a status bar to alert the user to the progress of the calculation (Figure [fig:tutCellData:10]).
  8. A second window will appear, displaying one at a time the membrane potential recorded at each current injection. In this interface, users can choose from one of three possible threshold calculation strategies, visually observing how the point chosen depends on the threshold calculation used. Select ’1’ from the dropdown menu picker to set the calculation strategy for this sample cell (Figure [fig:tutCellData:11]).
  9. A line will be drawn through each threshold point calculated in the displayed membrane potential trace (Figure [fig:tutCellData:12], see red arrow). Users can browse through the membrane potential recordings from each current injection level by selecting the left or right arrow buttons (Figure [fig:tutCellData:12], see orange outline), while keeping track of which level they are currently viewing by looking at the description in the upper left corner of the window (Figure [fig:tutCellData:12], see red circle). Whichever threshold calculation strategy is chosen will be used to find the threshold points in the recordings from all current injection levels.
  10. When satisfied with the threshold calculation strategy chosen, push the ’Set Threshold’ button (Figure [fig:tutCellData:13]) and wait for CellData to calculate all spike threshold points from all current injection levels in the file. When the calculation has finished, the second window will close.
  11. Back in the CellData window, click the button to ’Verify & Analyze’ (Figure [fig:tutCellData:14]). Another status bar will appear in CellData to signal the progress of the review step, which can take awhile for large files.
  12. After the tool has identified all points of interest in the membrane potential recordings from each current step, the second window will again appear, allowing users to review and correct any point (Figure [fig:tutCellData:15]). The points found by the program include (for hyperpolarized traces) the trough point of the sag potential, (for hyperpolarized and subthreshold depolarized traces) the steady state potential, (for subthreshold traces only) the transient peak depolarization potential, (for suprathreshold traces) the action potential threshold, action potential peak, and afterhyperpolarization potential.
  13. Figure [fig:tutCellData:16] shows various buttons available for modifying the points automatically chosen by the CellData tool. To move or delete an incorrect point, either click the corresponding action button (Figure [fig:tutCellData:16]) and then select the point by clicking it with the mouse, or scroll through the table of points to the right side and select the checkbox next to the point, then click the appropriate action button.
  14. As when selecting the threshold, users may scroll through the membrane potential recordings associated with each current injection level, and may correct points at each level. When finished, click the ’Done with cell’ button to close the second window and return to the main CellData interface.
  15. Now CellData will display additional buttons for displaying and exporting the analyses of the cell, as well as a table of calculated electrophysiological properties (Figure [fig:tutCellData:17]) and, in the lower right corner, a graph that can be set to display several different analyses by making a selection from the drop-down menu above the graph (Figure [fig:tutCellData:18]).
  16. Click the ’Make Figures’ button (Figure [fig:tutCellData:19]) to display an interface where users can pick which graph types to display and the format in which to display them (Figure [fig:tutCellData:20]). Figures such as those pictured in Figure [fig:tutCellDataOut] will be displayed.
  17. Alternatively, click the ’Export Properties’ button to export the table of electrophysiological properties as a tab-delimited text file, comma-separated values text file, or Microsoft Excel file.

Tutorials