First, because the aerogel may be somewhat distorted during extraction, we may partially lose the ability to accurately determine where on the sky the particle originated.
Can anybody elaborate on how the incoming direction of the particle in a track can be determined?
If my understanding is correct, the stardust team expects interstellar particles to originate from the sagittarius region (the center of our galaxy) and therefor the collector has been directed to this region while collecting IS particles.
After finding a track the incoming direction is given by the line going through the axial center of the track. If it matches the expectations, the particle is considered to be interstellar. If it originates from somewhere else (a low angle track), ist is considered to be from within the solar system.
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An interstellar dust stream was detected in the 1990s by the Galileo and Ulysses missions originating from the direction of the constellation Ophiuchus (which is near Sagittarius and the center of the Galaxy). As Stardust was cruising about the Solar System on its way to meet up with Comet Wild 2 it opened up the aerogel collector and oriented it so that the Interstellar Dust Collector side was pointed directly into the oncoming stream.
That means that dust particles from that stream should have impacted with the aerogel coming straight in ( about 90 degrees to the idealized surface).
In general, the angle of the tracks tell us from what direction the particles came. That's why we expect that the low angle tracks seen by some were probably made by interplanetary dust or ricochets of cometary dust off of the spacecraft.