Step 4 : Extract timestamps and apply corrections - LernerLab/GuPPy GitHub Wiki

a. In the Input Parameters GUI, click on the button Extract timestamps and its correction

b. In this step, GuPPy will eliminate the first few seconds of data (set by user in the Input Parameters GUI) and will do the timestamps correction for the eliminated data

c. GuPPy will display the signals that have been extracted for the user to inspect.

If everything looks good, you can proceed to the next step (Step 5).

If you see artifacts in the control and signal channel plot (as shown in the screenshot below), you can use GuPPy's artifact correction feature to select chunks of data you would like to keep, while excluding portions of the recording that have large artifacts. To do this artifact correction, follow the steps below:

• Select chunks of the data which do not have artifacts (i.e., chunks to KEEP) by moving the cursor on the plot to the start of the chunk and hitting the 'space-bar' on the keyboard
• Then move the cursor on the plot to the end of the chunk and again hit the 'space-bar' on the keyboard
• If you make a mistake and want to delete a particular coordinate, press the 'd' key on the keyboard. After chunk selection, close the window
• Closing the window will save the coordinates of all the chunks in a file

d. After selecting the chunks you want to keep, go back to the Input Parameters GUI and set the removeArtifacts? option to 'True', select removeArtifacts method and then click on the button Extract timestamps and its correction again

Note:

• Using concatenate method, all the selected chunks will be concatenated together.
• Using replace with NaN method, all the bad chunks (chunks with artifacts) will be replaced by NaN

e. After Artifacts removal using concatenate method, control and signal plot will look as shown below. Please note that the plot is plotted by just concatenating all the selected chunks

f. After Artifacts removal using concatenate method, control and signal will look as shown below.

g. In artifacts removal, ΔF/F is calculated for all the chunks separately. In case of concatenate method, all the chunks are concatenated together to get a final ΔF/F trace. In case of replace with NaN method, all the chunks will be shown separately and bad chunks with NaN values. Using this final ΔF/F trace, z-score is computed.

g. Now you can proceed to Step 5!