LineageTracker
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) or C2C12 mouse stem cells (upper right).
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 submitted for publication.
Three plugins are installed in the Plugins menu of ImageJ:
- Segmentation. The user can select from three pre-defined segmentation methods, or include customised segmentation methods. Parameters can be edited using an interactive preview.
- Experiment Viewer. View and edit the segmentation and tracking. Cell intensities can be examined and exported.
- 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 reflext any changes.
View the version history.
Download
Current Version: 1.1.2
Release Date: 20th September 2011.
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.
