Automation in cytomics: a modern RDBMS based platform for image analysis and management in high-throughput screening experiments

  • Authors:

  • E. Larios;Y. Zhang;K. Yan;Z. Di;S. LeDévédec;F. Groffen;F. J. Verbeek

  • Affiliations:

  • Section Imaging and Bioinformatics, LIACS, Leiden University, Leiden, The Netherlands;Centrum Wiskunde and Informatica, Amsterdam, The Netherlands;Section Imaging and Bioinformatics, LIACS, Leiden University, Leiden, The Netherlands;Department of Toxicology, LACDR, Leiden University, Leiden, The Netherlands;Department of Toxicology, LACDR, Leiden University, Leiden, The Netherlands;Centrum Wiskunde and Informatica, Amsterdam, The Netherlands;Section Imaging and Bioinformatics, LIACS, Leiden University, Leiden, The Netherlands

  • Venue:
  • HIS'12 Proceedings of the First international conference on Health Information Science
  • Year:
  • 2012

  • Bioscientific data processing and modeling

    ISoLA'12 Proceedings of the 5th international conference on Leveraging Applications of Formal Methods, Verification and Validation: applications and case studies - Volume Part II

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Abstract

In cytomics bookkeeping of the data generated during lab experiments is crucial. The current approach in cytomics is to conduct High-Throughput Screening (HTS) experiments so that cells can be tested under many different experimental conditions. Given the large amount of different conditions and the readout of the conditions through images, it is clear that the HTS approach requires a proper data management system to reduce the time needed for experiments and the chance of man-made errors. As different types of data exist, the experimental conditions need to be linked to the images produced by the HTS experiments with their metadata and the results of further analysis. Moreover, HTS experiments never stand by themselves, as more experiments are lined up, the amount of data and computations needed to analyze these increases rapidly. To that end cytomic experiments call for automated and systematic solutions that provide convenient and robust features for scientists to manage and analyze their data. In this paper, we propose a platform for managing and analyzing HTS images resulting from cytomics screens taking the automated HTS workflow as a starting point. This platform seamlessly integrates the whole HTS workflow into a single system. The platform relies on a modern relational database system to store user data and process user requests, while providing a convenient web interface to end-users. By implementing this platform, the overall workload of HTS experiments, from experiment design to data analysis, is reduced significantly. Additionally, the platform provides the potential for data integration to accomplish genotype-to-phenotype modeling studies.