TRAgen (track generator)

This web page is a supplementary material to the paper TRAgen: A Tool for Generation of Synthetic Time-Lapse Image Sequences of Living Cells presented at 18th International Conference on Image Analysis and Processing (ICIAP 2015) hold in Genova, Italy in September 2015.


The paper introduces a tool, capable of generating 2D image sequences showing simulated living cell populations together with ground-truth images for evaluation of cell tracking tasks. The simulated events include namely cell motion, cell division, cell death, and cell clustering up to tissue-level density. TRAgen features complete cell cycle with shape changes due to rounding and elongation of a cell just before its division.

It is primarily designed to operate at inter-cellular scope, that is, it predominantly focuses on interaction between cells. It does not handle explicitly any intra-cellular structures such as protein molecules, chromatin territories, or mitochondria. Instead, the implementation provides mean for user to inject his/her own texture to be overlaid over the generated cell mask.

User can control the rate of cell divisions, average speed of cells, and temporal and spatial sampling of the simulation to steer complexity of the tracking task.

It is designed to provide a sequence of 2D images with labelled masks together with lineage trees to provide a complete tracking ground-truth data. We believe that prospective authors of newly developed tracking algorithms may easily add appropriate textures to these masks and tailor appearance of the obtained testing images specifically to the context of their needs, e.g., to phase-contrast or fluorescence microscopy, or to images with different SNR. The generated testing images obtained in this way, may become yet more realistic and thus more relevant for the evaluation.

Sample Sequence

The main aim of this project is to handle movement and inter-cellular interaction of cell digital phantoms. In the following two images (screenshots of selected time-lapse sequences), you can inspect all implemented forces affecting the motion and interaction of individual cells in the population. The left image shows the overall cell population while the right one focuses on four selected cells.

The emphasis on movement and inter-cellular interaction basically boils down to the activity of "pure" displacing and altering shape of cell masks. Thus, the implementation/generation of the content to be filled into the masks as well as outside them, and addition of microscopy and acquisition effects, such as blur, uneven illumination, various kinds of noise, is greatly simplified in the videos below:

Download and License

The program is written in C++. It uses OpenGL (with GLSL ver 1.5), GLEW, and GLUT libraries for drawing on the screen and rendering into memory buffers. It uses GNU GSL for random number generations. Last but not least, it uses the CBIA i3dlibs for I/O image formats operations plus some additional image manipulation to obtain (superficially) realistic images of the cells.

Source code with CMake configuration script (developed and test in Linux OS), and input data is available. The application has currently no input parameters and does not allow for modification during run-time. Changing parameters of the simulation is available only by changing the source codes and recompiling them.

The TRAgen (the above provided source code and data) is freely available under the GNU GPL license. Copyright belongs to the authors below and Centre for Biomedical Image Analysis (CBIA) at Masaryk University.


This project was funded by Czech Science Foundation, grant No. GA14-22461S.