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, Bálint Antal, Richard K. Ferguson, Ugis Sarkans, Alvis Brazma, Rafael E. Carazo Salas, Jason R. Swedlow*

*Corresponding author for this work

Research output: Contribution to journalArticle (Academic Journal)peer-review

57 Citations (Scopus)
280 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). IDR links data from several imaging modalities, including high-content screening, multi-dimensional microscopy and digital pathology, with public genetic or chemical databases and 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 reanalysis, 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 for publishing imaging data. Thus IDR provides an online resource and a software infrastructure that promotes and extends publication and reanalysis 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 - 28 Jul 2017

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