Multicomponent CPM

During the last two decades a large amount of new simulation frameworks in the field of cell imaging has emerged. They were expected to serve as performance assessment tools for newly developed as well as for already existing cell segmentation or tracking algorithms. These simulators have typically been designed as single purpose tools. They generate the synthetic image data for one particular modality and one particular cell type.

Here, we introduce a multipurpose simulation framework, which produces the synthetic time-lapse image sequences of living endothelial cells.

Sample Data

The aim of this project is to properly simulate the development of vascular networks formed during the process called vasculogenesis in different modalities. Currently, we focus on fluorescence and phase constrast microscopy. Below, you will find some of our results:

Fig. 1: Labeled image (2D cross section)

Fig. 2: Phase contrast (2D cross section) - show sample video

Fig. 3: Fluorescence microscopy (2D cross section)- show sample video

Fig. 4: Labeled cell population (3D projection) - show sample video

Fig. 5: Phase contrast (2D projection) - show sample video

Downloading

The source codes written in C/C++, bison and lex are available here

In order to properly compile to project, you should first download our image processing library.

If you want to imitate the phase contrast microsopy (II a III phase of the simulation process), you will need the MATLAB environment.

References

Svoboda D, Kozubek M. Multimodal Simulation in Live Cell Imaging. In Simulation and Synthesis in Medical Imaging: Second International Workshop, SASHIMI 2017, Held in Conjunction with MICCAI 2017, Quebec, Canada, LNCS 10557, pp. 89-98, ISBN 978-3-319-68126-9. doi:10.1007/978-3-319-68127-6_10.

Svoboda D, Nečasová T, Tesařová L, Šimara P. Tubular Network Formation Process Using 3D Cellular Potts Model. In Simulation and Synthesis in Medical Imaging: 3rd Int. Workshop, SASHIMI 2018, Held in Conjunction with MICCAI 2018, Granada, Spain, LNCS 11037, pp. 90-99, 2018.

Svoboda D, Nečasová T, Image-based Simulations of Tubular Network Formation. In 17th IEEE International Symposium on Biomedical Imaging, 2020, pp. 1608-1612, ISBN 978-1-5386-9330-8.

Acknowledgement

This project was funded by Czech Science Foundation, grant No. GA17-05048S and by the Ministry of Education, Youth and Sports of the Czech Republic (Projects LTC17016 and CZ.02.1.01/0.0/0.0/16_013/0001775).