ImageJ Plugin for manual cell lineage tracking.

We provide a step-by-step workflow to identify and track individual cells and their progeny using our ImageJ plugin ‘Live Plant Cell Tracking (LiPlaCeT)’, followed by instructions to visualize and analyze cell population dynamics using Paraview software (https://www.paraview.org/). The plugin is developed to work with hyper-stacks of 3D images or 3D images in time (4D) acquired with a microscope; one or two channel images can be analyzed.

LiPlaCeT plugin has been developed to facilitate cell tracking and cell lineage analysis within time-lapse experiments of 3D cell populations. Cell information, including 3D position through time, proliferation events and lineage relationships, is saved automatically in the Graphical User Interface (GUI). Annotated cell information can be transferred to Paraview to build cell genealogy trees to visualize mitotic events, detect cell cycle time, track the formation of cell lineages, and visualize individual and population dynamics related to growth and movement within the 3D population through time.

Manual tracking using LiPlaCeT is the main step to enable data analysis and visualization. We have chosen the Paraview platform to visualize tracking results because it has many functionalities such as visualization of data in 3D and time (4D), change the view positions, rotate, translate the data, zoom in, zoom out, screen shots, movies, a variety of colormaps, time inspector to move time by time, among many others functionalities. In addition, Paraview platform is easy to use following few steps