CinePlex v3 Manual - Plexon Inc

7 Repeat Step 6 until all the coordinates are entered or repaired. Move the file
forward to the next episode of bad tracking coordinates and repeat.
8 When finished, from the File menu, click Save. The user may save and export
the new or updated positions like any other marker data.
4.6.7 Simple Place Cell Analysis
Suppose it is suspected that a certain neuron seems to fire only when the rat is in
his nest. As a procedural approach to test this hypothesis, a new Zone Interval
marker could be defined that defines the boundaries of the rat's nest. The generated
occurrences of this marker represent the intervals during which the rat was in
its nest. NeuroExplorer could then be used to search for correlations between
neural firing rates and this interval.
1 Advance the video until a frame shows where the outline of the desired Zone
(the nest) is clearly visible.
2 Define a new Zone Interval marker (see “Defining Markers” on page 175).
Label it “Rat In Nest”. In the Define New Marker dialog box, click Generate
Occurrences to open the Zones Editor dialog box (see “Zones Editor” on
page 256).
3 In the Coordinates of the Selected Zone area, click Add and then click the
left mouse button repeatedly in the video window in order to define the outline
of the nest. Before completely closing the contour, click the right mouse
button, which closes the contour.
4 In the Coordinates Marker to use list, select the appropriate Coordinates
marker, and click Generate Selected. This generates occurrences of the new
“Rat In Nest” marker. Click Done to close the Zones Editor dialog box.
5 To inspect the “Rat In Nest” intervals, use the Find Marker Occurrences
dialog box (see “Find Marker Occurrences” on page 253) to quickly
advance through all the occurrences of the “Rat In Nest” marker. It is also
possible to use the Marker Occurrences window (see “Marker
Occurrences Window” on page 229) to remove any undesirable “Rat In
Nest” occurrences.
6 From the File menu, click Export to NEX (see “Export to NEX” on
page 244) to write the data to a NEX file for subsequent analysis. The “Rat In
Nest” marker shows up as an interval variable in NeuroExplorer.
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