CinePlex v3 Manual - Plexon Inc

5
5.8 Aligning Tracker Coordinates to Frames
If neural and video data files are collected using a Plexon NDAQ and CinePlex
Studio with tracking enabled, then the temporal relationship between Frame
markers, the arrival of strobe codes to the MAP digital input card, and video
tracker coordinates are depicted in the following illustration of the Activity window:
Note:
Note: the above screenshot depicts the timing assuming that the automatic corrections
for (see previous section) are not enabled.
When the video frame is available, CinePlex Studio immediately timestamps the
file and stores the time in the AVI file along with the video frame image. When
CinePlex Editor initially reads the AVI file, the time for each frame becomes a
Frame Marker time, which appears as the blue tick marks in the previous illustration.
After CinePlex Studio acquires the video frame, it feeds the video image to the
tracking algorithm. Some time later, the tracking algorithm determines the tracking
positions and CinePlex Studio encodes the tracking positions using the
VideoTracker protocol and outputs a burst of strobed data words. The time
between the frame timestamp and the sending of the strobe codes depends on
how quickly the tracking algorithms finish, but the first strobed data word always
occurs before the start of the next video frame. The words within a burst are
clocked out at a constant rate every two milliseconds.
When strobed data words arrive at the MAP, the MAP timestamps them as it
reads them in, and then stores them as events in the PLX file. When CinePlex
Editor in turn reads these strobed events from the PLX file, they become occurrences
of a Scalar marker named Strobed; in the preceding illustration, these
occurrences appear as brown tick marks. Also, if CinePlex Editor recognizes that
the strobed codes are in VideoTracker protocol, it decodes them into occurrences
of one or more Coordinates markers (see “Table 5-1” on page 5-278). CinePlex
Editor then assigns times to the Coordinate marker occurrences. The assigned
times are derived from the time of the first strobed event in each burst of strobed
events. As a result, CinePlex Editor assigns times to the tracked positions that are
later than the timestamps of the corresponding video frames; in the preceding
illustration, the tracked positions (Position 1) are the red tick marks and the video
frames are the blue tick marks.
This time offset between the frame time and the tracking coordinates, although
realistic, is not desirable in some cases. For example, one can simplify subsequent
analysis when the coordinates corresponding to a video frame are equal to
the time of the video frame. One can do this with CinePlex Editor, by using the
284 CinePlex