ParticleTracking

ImageJ Plugins for Particle Tracking

This is a suite of ImageJ plugins for performing 2D particle tracking.

2023/03/29 First batch of uploads

• Point.java
• Traj.java
• MovieNormalizer_.java
• Particle_Tracker.java
• Particle_Tracker_totInt.java
• Trajectory_Linker.java
• PartTracker_TrajectorySorterInt.java

File descriptions:

Utility files:

• Point.java: Class for storing coordinates of Each Points
• Traj.java: Class for storing Points classified as belonging to the same trajectories

Preprocessing (optional):

• MovieNormalizer_.java: Computes the time average of the movie (mean image) and normalizes each frame by dividing by the mean image

_Processing: _

• Particle_Tracker.java: group above threshold pixels in Points, computes their position by the intensity weighted centroid method and outputs spatiotemporal position and the size (nb of pixels) of each points

• Particle_Tracker_totInt.java: Same as Particle_Tracker but:

  1. the position of each Point is computed as the average position of the pixels (no intensity weighted centroid)
  2. the mean intensity of each Point is an output

• Trajectory_Linker.java: connects points into a trajectory following a minimal proximity in the next frame algorithm

PostProcessing:

• PartTracker_TrajectorySorterInt.java: selects trajectories longer than a user defined threshold and saves them as text file

Instructions:

Preparation:

• Upload the ParticleTracking folder in the IJ Plugin directory
• Get jtransforms-2.4.jar from croelmiyn/FourierImageAnalysis/packages and upload to Plugin directory

Execution:

1. MovieNormalizer_ : runs without user inputs

2. Particle_Tracker (or Particle_Tracker_totInt):

• Open movie in ImageJ and decide on a threshold if relevant

• Execute: GUI interface pops up

  Parameters:

  • min_particle_radius: minimum radius a group of pixel needs to have to be considered a trackable point

  • separate: if checked, particles with multiple maxima will be split in several particles, using a Gaussian fit of their intensity profiles

  • Method for threshold: method for separating Points from background

  • CutOff: cutOff parameter for the method

    pixel counts as Point if:

    • cutoff_above_background: intensity > median(pixels) + cutOff * standardDeviation(pixels),
    • threshold: intensity > cutOff
    • percentile: intensity in the cutOff brighter pixel fraction
    • AbsThresh_above_bgd: intensity > mean(pixels_in_given_frame) + cutOff

• Output is a Result_Table containing the detected Points in each frame, which needs to be saved (PartTracked_).

3. Trajectory_Linker

• If FIJI: open the PartTracked_ as a ResultTable (File>Import>Results...)
• Run parameters:
  • Maximum Distance: maximum distance a particle is allowed to travel between 2 frames
  • print: if checked, the trajectories and cell positions will be displayed on the movie stack

4. PartTracker_TrajectorySorterInt: minimum_trajectory_length: minimum duration of a trajectory to be selected.