Author: Jeffrey Kuhn (jkuhn at ccwf.cc.utexas.edu)
The University of Texas at Austin
Versions: 2001/2/14: first version
2001/7/17: shows paths and path lengths
Limitations: Requires a binary or thresholded 8-bit stack. Source: MultiTracker_.java Installation: Copy MultiTracker_.class to the plugins folder and restart ImageJ. Description: MultiTracker uses ImageJ's particle analyzer to track the movement of multiple objects through a binary or thresholded stack. The object number and coordinates may be optionally written to the image stack at the end for verification. This filter is based on the Object Tracker plugin filter by Wayne Rasband. A test stack, contributed by Ross Lang, is available.
Here is a procedure for tracking particles by hand:
Decrease the brightness of your stack by one value. Run "Click Forward" to on your stack (just once) and use the mark tool (with the WHITE foreground color) to follow one point through the stack by clicking on it repeatedly. Rewind (save a copy first) and track another point through your stack. When you have marked as many points as you like, save your stack, and threshold it. You will get black dots on a white background (the colors get inverted by the threshold).
Go to the first frame and use the magic wand tool to select a point. Then hit "measure" to get the centroid. Repeat for the next point, etc. When you have marked all of the points in order, select the background (to insure that the ROI encompasses the entire image) and use the new multitracker tool to get the coordinates for each point in the stack in the requested order. Make sure that there are exactly as many measurements as there are particles (i.e. 3 measurements for 3 particles). If the right number of measurements are found, the multitracker plugin will use them for the initial positions and ordering of the particles.
Setting the measurement order is particularly crucial if you are marking by hand. This allows you to repeat the measurement several times (to compensate for measurement error) and keep the marked points in the same sorting order every time. This makes averaging and other statistical analysis much easier.
See Also: Object Tracker, Manual Tracking, SpotTracker, MTrack2, ParticleTracker and MTrackJ plugins
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