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Department of Computer Science

Download Plugins

Download the plugins and copy the class or jar file into the ImageJ plugins directory.

Analysis Plugins

Count Cells

Prints to the log window displaying the number of cells in each frame.

Source code Class File

Highlight Dividing Cells

Highlights dividing cells by overlaying circles of random colour.

Source code Class file

Segmentation Plugins

Multi-Channel Segmentation

Requires LineageTracker v1.1.0 or newer (Released 9th September 2011).

An updated version of the Seeded Growth Segmentation which takes multiple image channels into consideration. Incorporates the 'Semi-Automatic' segmentation which uses user-selected seeds to grow the cell nuclei.

Source Code Jar File

Tracking Plugins

Simple Nearest Tracking

An example of a tracking plugin which selects the closest cell in subsequent frames.

Source Code Class File

Plugin Collections

Multiple plugins may be combined into jar files for easy distribution. The name of the jar file must contain the word Tracker to be recognised by LineageTracker

Tracker Plugins 1

A collection of segmentation and analysis plugins:

  • Two threshold segmentation methods. An automatic method based on the 'Li' thresholding in ImageJ and an adjustable threshold which allows the threshold value to be modified.
  • Load tracking generated using MTrack3. The tracking files must be named after the experiment, followed by _tracked.MTrack3.
  • Make Stack From Cell: create an image stack containing the area around the chosen cell, following the cell as it is tracked.
  • Export tracking as MTrackJ files
  • Export a stack with the cell tracks drawn on.
  • Fast Manual Track: quickly add tracking by clicking on cells.
  • Quick Delete Cells: Remove cells outside of specified area and intensity values.
  • Set Image Scale: Duplicates the set image and timescale functions of the Edit Preferences plugin but can be used from a macro command.
  • Set Tracked To Validated: Sets the validated flag of cells which have been tracked.

Download the plugins (includes the source code)
Note: the name should begin Tracker with a capital T. If the name begins with a lower case T, it will need renaming before it will work on Linux or Mac with versions of LineageTracker earlier than 1.2.1

Requires the Apache commons-lang library (tested with version 2.4)

Cell Motion Analysis Plugins

A collection of plugins for analysing cell motion, developed in collaboration with the CMCB.

  • Count cells in frames
  • Create a Results Table holding cell speeds/distances and associated statistics. Tables are saved in the results/ directory of the experiment.
  • Filter cells based on speed, track lengths or distance moved.
  • Delete tracking for non-validated cells.

Download the plugins (includes the source code).

Requires the Apache commons-math library (tested with version 2.0).

LineageTracker Extensions

Headless Mode

Runs LineageTracker without opening a window to display the images. To use, copy LineageTracker_Headless.jar into the ImageJ Plugins folder. A new entry (called LineageTracker Headless will appear in the plugins menu). Simply replace any calls to

run("Experiment Viewer"...

with

run("LineageTracker Headless"...

in any batch processing commands. Since there is no image window, the running copy of LineageTracker will be invisible and it is important to remember to close it using

run("Run Plugin","close=true");

before trying to open another instance of LineageTracker.