The Image Data Resource: a bioimage data integration and publication platform

Eleanor Williams, Josh Moore, Simon W. Li, Gabriella Rustici, Aleksandra Tarkowska, Anatole Chessel, Simone Leo, Balint Antal, Richard K. Ferguson, Ugis Sarkans, Alvis Brazma, Rafael E. Carzo Salas, Jason R. Swedlow (Lead / Corresponding author)

Research output: Contribution to journalArticlepeer-review

75 Citations (Scopus)
341 Downloads (Pure)

Abstract

Access to primary research data is vital for the advancement of science. To extend the data types supported by community repositories, we built a prototype Image Data Resource (IDR) that collects and integrates imaging data acquired across many different imaging modalities. IDR links high-content screening, super-resolution microscopy, time-lapse and digital pathology imaging experiments to public genetic or chemical databases, and to cell and tissue phenotypes expressed using controlled ontologies. Using this integration, IDR facilitates the analysis of gene networks and reveals functional interactions that are inaccessible to individual studies. To enable re-analysis, we also established a computational resource based on Jupyter notebooks that allows remote access to the entire IDR. IDR is also an open source platform that others can use to publish their own image data. Thus IDR provides both a novel on-line resource and a software infrastructure that promotes and extends publication and re-analysis of scientific image data.
Original languageEnglish
Pages (from-to)775-781
Number of pages7
JournalNature Methods
Volume14
Issue number8
Early online date19 Jun 2017
DOIs
Publication statusPublished - Aug 2017

Keywords

  • Data integration
  • Protein databases

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