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LineageTracker offers an ImageJ based framework which is easily extendible and has the capability to track cell lineages while being specifically designed to handle large cell displacements between frames. The methods are designed for fluorescent cells and have been used to analyse Schizosaccharomyces pombe (lower right), C2C12 mouse stem cells (upper right) or migrating RPE cells.

The segmentation step detects cells and measures features including for example intensity, size, shape and texture. A statistical scoring system calculates individual transition scores between cells in subsequent frames using a feature-based cost function. Details of this method have been published in M.J. Downey, D.M. Jeziorska, S. Ott, T.K. Tamai, G. Koentges, K.W. Vance, T. Bretschneider. Extracting fluorescent reporter time courses of cell lineages from high-throughput microscopy at low temporal resolution, PLoS ONE 6(12): e27886, 2011.

Three plugins are installed in the Plugins menu of ImageJ:

  1. Segmentation. The user can select from three pre-defined segmentation methods, or include customised segmentation methods. Parameters can be edited using an interactive preview.
  2. Experiment Viewer. View and edit the segmentation and tracking. Cell intensities can be examined and exported.
  3. Create from Open: Creates a new experiment using the images currently open in ImageJ. All images should be stacks with a single data channel per stack with the same pixel size and number of frames.

Exending the Software

The software can be extended using 'plugins' to add segmentation, tracking and analysis methods. A demonstration analysis plugin (Count Cells) is described from the plugins tutorial page. Further are availible in the plugins download section.

The plugins API is in a state of flux and new interfaces are being added as required. Any plugins hosted here (along with the tutorials and examples) will be updated to reflect any changes.

View the version history.

ImageJ Version Information:

Changes made in ImageJ since version 1.46 have caused problems with older versions of LineageTracker, preventing experiments from being re-loaded. These problems have been now been fixed so if you were affected by this problem, please download the latest version.


Current Version: 1.2.4
Release Date: 11th August 2013

Requires Java 1.6 and Fiji/ImageJ 1.44o or newer and Image5D. We recommend Fiji because it comes with Image5D pre-installed along with many extra image analysis methods. To install, download the jar file and copy it into the ImageJ plugins directory. If upgrading from a previous version, remove the old 'jar' file before installing the new one.


Sample image segmented by LineageTracker

Segmented yeast cells