Publication details

FiloGen: A Model-Based Generator of Synthetic 3-D Time-Lapse Sequences of Single Motile Cells with Growing and Branching Filopodia

Authors

SOROKIN Dmitry PETERLÍK Igor ULMAN Vladimír SVOBODA David NEČASOVÁ Tereza MORGAENKO Katsiarina EISELLEOVÁ Lívia TESAŘOVÁ Lenka MAŠKA Martin

Type Article in Periodical
Magazine / Source IEEE Transactions on Medical Imaging
MU Faculty or unit

Faculty of Informatics

Citation
WWW https://doi.org/10.1109/TMI.2018.2845884
Doi http://dx.doi.org/10.1109/TMI.2018.2845884
Keywords simulation;3D time-lapse sequence;synthetic cell;cell deformation;filopodium evolution
Description The existence of diverse image datasets accompanied by reference annotations is a crucial prerequisite for an objective benchmarking of bioimage analysis methods. Nevertheless, such a prerequisite is arduous to satisfy for time-lapse, multidimensional fluorescence microscopy image data, manual annotations of which are laborious and often impracticable. In this paper, we present a simulation system capable of generating 3D time-lapse sequences of single motile cells with filopodial protrusions of user-controlled structural and temporal attributes, such as the number, thickness, length, level of branching, and lifetime of filopodia, accompanied by inherently generated reference annotations. The proposed simulation system involves three globally synchronized modules, each being responsible for a separate task: the evolution of filopodia on a molecular level, linear elastic deformation of the entire cell with filopodia, and the synthesis of realistic, time-coherent cell texture. Its flexibility is demonstrated by generating multiple synthetic 3D time-lapse sequences of single lung cancer cells of two different phenotypes, qualitatively and quantitatively resembling their real counterparts acquired using a confocal fluorescence microscope.
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