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Nat Methods. 2017 Aug;14(8):775-781. doi: 10.1038/nmeth.4326. Epub 2017 Jun 19.

The Image Data Resource: A Bioimage Data Integration and Publication Platform.

Author information

1
Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK.
2
European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom.
3
Pharmacology & Genetics Departments and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
4
LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay, Palaiseau, France.
5
Center for Advanced Studies, Research, and Development in Sardinia (CRS4), Pula(CA), Italy.
6
School of Cell and Molecular Medicine, University of Bristol, Bristol, UK.
#
Contributed equally

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 data from several imaging modalities, including high-content screening, super-resolution and time-lapse microscopy, digital pathology, 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 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.

PMID:
28775673
PMCID:
PMC5536224
DOI:
10.1038/nmeth.4326
[Indexed for MEDLINE]
Free PMC Article

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