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

Abstract : 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.
Type de document :
Article dans une revue
IEEE Transactions on Medical Imaging, Institute of Electrical and Electronics Engineers, 2018, pp.1-12. 〈10.1109/TMI.2018.2845884〉
Liste complète des métadonnées

Littérature citée [29 références]  Voir  Masquer  Télécharger

https://hal.inria.fr/hal-01821338
Contributeur : Peterlik Igor <>
Soumis le : jeudi 19 juillet 2018 - 15:50:37
Dernière modification le : vendredi 12 octobre 2018 - 15:55:22
Document(s) archivé(s) le : lundi 1 octobre 2018 - 01:40:15

Fichier

tmi_filogen.pdf
Fichiers produits par l'(les) auteur(s)

Identifiants

Collections

Citation

Dmitry Sorokin, Igor Peterlik, Vladimír Ulman, David Svoboda, Tereza Nečasová, et al.. FiloGen: A Model-Based Generator of Synthetic 3D Time-Lapse Sequences of Single Motile Cells with Growing and Branching Filopodia. IEEE Transactions on Medical Imaging, Institute of Electrical and Electronics Engineers, 2018, pp.1-12. 〈10.1109/TMI.2018.2845884〉. 〈hal-01821338〉

Partager

Métriques

Consultations de la notice

332

Téléchargements de fichiers

36