DotLinker

Global optimization of particle linking.

editing

Description

The most popular algorithm of particle tracking takes two separate steps. The first step is dot detection (segmentation) and then the second step is particle linking. Many tools readily assemble these two steps as a single set. Especially for the linking step, we rarely find a tool that does only the linking step. DotLinker loads position coordinates of particles and links them along timeline to estimate their trajectory.

DotLinker was created, as in some cases, we are successful in segmenting particle objects and that we already have their coordinates data. Majority of tracking tools packages image segmentation (detection) step and particle linking step as a single tool, but this tool is specifed only for the linking step.

Input: Text data with list of particle coordinates for each frame (CSV).

Output Text data with estimated tracks.

Dependency

ImageJ ver 1.41k or higher

Installation

Download the plugin from the link below, and copy the file into the plugin folder of ImageJ or Fiji.

Usage

Scripting

An example of accessing the plugin from a script is linked below.

[DotLinker2016.py]()

This script does:

  1. Opens an already segmented sequence of epitherial cells.
  2. Do particle analysis to measure the pixel coordinates of each cell at each frame. The results appears in the normal ImageJ results table.
  3. Using those coordinates, DotLinker links cell positions along time. Tracks are estiamted and shown in another table “Tracks”.
  4. Each cells is filled with a grayscale value, to indicate their relative increase/decrease in cell area.

Repository

https://github.com/miura/DotLinker

References