Linking Methods

All the linking methods, described in the paper will be available after the official publication of the paper.

For now, the result plots from the paper can be interactively explored here

Ground Truth Generation

In order to generate the ground truth data, described in the paper, use the following procedure:
  • Download LinkingPaper.jar

  • Get the ground truth XML files from the Particle Tracking Challenge website. (In the example below “MICROTUBULE snr 1 density low.xml” will be used)

  • For each of the XML file generate a temporary file with extension .xml.txt as follows:
    java -cp ./LinkingPaper_.jar TrackConvertorXMLtoTXT ./MICROTUBULE\ snr\ 1\ density\ low.xml

  • Now, having “MICROTUBULE snr 1 density low.xml.txt” in the same folder, we can continue to generate different conditions (different levels of false positives and false negatives). Every time, a file “detections.xml.txt” will be created, where the most important columns are 1) x-coordinate, 2) y-coordinate, 3) time-stamp of that specific detection, 4) intensity of the detection (is not used in the paper, dummy value), 5) ID of the original track, other columns are not used. To generate the track, run for example:
    java -cp ./LinkingPaper_.jar:./ij.jar ws.smal.sos.eval.linking.PrepareDetections ./MICROTUBULE\ snr\ 1\ density\ low.xml.txt 100 2.5 0.1 0.2
    This will process 100 frames and will result in:
    load : MICROTUBULE snr 1 density low.xml.txt
    processed with R = 2.5 to remove: 0.2 to add: 0.1
    loaded 6597
    lost 1281
    added 620
    saved 5921