Generator Platform of Benchmark Time-Lapsed Images Development of Cell Tracking Algorithms: Implementation of New Features Towards a Realistic Simulation of the Cell Spatial and Temporal Organization

Leonardo Martins, Pedro Canelas, André Mora, Andre S. Ribeiro, José Fonseca

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

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    Abstract

    Recent developments in live-cell microscopy imaging have led to the emergence of Single Cell Biology. This field has also been supported by the development of cell segmentation and tracking algorithms for data extraction. The validation of these algorithms requires benchmark databases, with manually labeled or artificially generated images, so that the ground truth is known. To generate realistic artificial images, we have developed a simulation platform capable of generating biologically inspired objects with various shapes and size, which are able to grow, divide, move and form specific clusters. Using this platform, we compared four tracking algorithms: Simple Nearest-Neighbor (NN), NN with Morphology (NNm) and two DBSCAN-based methodologies. We show that Simple NN performs well on objects with small velocities, while the others perform better for higher velocities and when objects form clusters. This platform for benchmark images generation and image analysis algorithms testing is openly available at (http://griduni.uninova.pt/Clustergen/ClusterGen_v1.0.zip).

    Original languageEnglish
    Title of host publicationSimulation and Modeling Methodologies, Technologies and Applications - International Conference, SIMULTECH 2016, Revised Selected Papers
    PublisherSpringer Verlag
    Pages52-74
    Number of pages23
    ISBN (Print)9783319698311
    DOIs
    Publication statusPublished - 2018
    Publication typeA4 Article in conference proceedings
    EventINTERNATIONAL CONFERENCE ON SIMULATION AND MODELING METHODOLOGIES, TECHNOLOGIES AND APPLICATIONS -
    Duration: 1 Jan 1900 → …

    Publication series

    NameAdvances in Intelligent Systems and Computing
    Volume676
    ISSN (Print)2194-5357

    Conference

    ConferenceINTERNATIONAL CONFERENCE ON SIMULATION AND MODELING METHODOLOGIES, TECHNOLOGIES AND APPLICATIONS
    Period1/01/00 → …

    Keywords

    • Cell tracking
    • Cluster tracking
    • Microscopy
    • Synthetic time-lapse image simulation

    Publication forum classification

    • Publication forum level 1

    ASJC Scopus subject areas

    • Control and Systems Engineering
    • Computer Science(all)

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