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Calculate Score Gradient

From user-defined min and max values, calculates a score (0-10) of each spot from Trackmate.

Results Table Output

Exporting data from imageJ's result tables to the default CSV option can led to problems related to decimal case separators. If you found this error, we recommend the usage of Excel Functions, a plugin that allows trouble-free data exports to xlsx format.

Interface

Interface image

XML File

Two possible files can be used here:

  1. Trackmate's whole save file
    • Ideal option overall.
    • Mandatory if you only have spots and no tracks. In this case, a mean score of every spot on each frame will be calculated.
    • If there are any tracks, all spots outside them will get filtered out.
  2. Output of trackmate's Export tracks to XML file export action.
    • Only spots in tracks get saved in this file, so only them will be considered.

Source Video

The source video used for tracking. Ideally not the processed one, so you can set the ROIs better.

Fix Missing Spots

When tracking with Trackmate, not all frames in a video will have spots. That's because your target might not be visible in those frames. It's usually not moving as well. An uneven number of frames will create an unreliable score overall. This option fixes the missing spots by using an available adjacent spot and copying its coordinates.

There's no prejudice in setting this to True if you have a perfect tracking, with spots in all frames.

Display Plots

  • Box Chart: The starting edge of the box corresponds to the 1st Quartile (Q1, 25th percentile), and the ending edge corresponds to the 3rd Quartile (Q3, 75th percentile). The line crossing through the interior of the box indicates the Median (Q2). The whiskers reach the lowest and highest data points that are within 1.5 times the IQR from the box edges. Box Chart image

  • Dial Chart: Dial is set to the median score value. (If you have multiple tracks, montage of all track's dials is created)

    Dial Chart image

Open Frame

Opens the first frame of the video as a preview. Can be used to set the ROI in functions that require it. Ignores the file's EXIF rotation data.

Load Min/Max from XML

Gathers and displays the min and max position values from the current XML. It is required to click this button to check for calibration issues.

Change Max Score

Allows the user to change the max value by clicking on the preview image.

Change Min Score

Allows the user to change the min value by clicking on the preview image.

Stop

Stop changing max and min values.