Metadata matters: access to image data in the real world

Author:

Linkert Melissa112,Rueden Curtis T.11,Allan Chris32,Burel Jean-Marie3,Moore Will3,Patterson Andrew3,Loranger Brian3,Moore Josh2,Neves Carlos2,MacDonald Donald3,Tarkowska Aleksandra3,Sticco Caitlin11,Hill Emma4,Rossner Mike4,Eliceiri Kevin W.11,Swedlow Jason R.32

Affiliation:

1. Laboratory for Optical and Computational Instrumentation, Department of Molecular Biology and Department of Biomedical Engineering, Graduate School, University of Wisconsin at Madison, Madison, WI 53711

2. Glencoe Software, Inc., Seattle, WA 98101

3. Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK

4. The Rockefeller University Press, New York, NY 10065

Abstract

Data sharing is important in the biological sciences to prevent duplication of effort, to promote scientific integrity, and to facilitate and disseminate scientific discovery. Sharing requires centralized repositories, and submission to and utility of these resources require common data formats. This is particularly challenging for multidimensional microscopy image data, which are acquired from a variety of platforms with a myriad of proprietary file formats (PFFs). In this paper, we describe an open standard format that we have developed for microscopy image data. We call on the community to use open image data standards and to insist that all imaging platforms support these file formats. This will build the foundation for an open image data repository.

Publisher

Rockefeller University Press

Subject

Cell Biology

Reference19 articles.

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2. Ensuring the Integrity, Accessibility, and Stewardship of Research Data in the Digital Age;Committee on Science, Engineering, and Public Policy (US), and Committee on Ensuring the Utility and Integrity of Research Data in a Digital Age,2009

3. Megascience. ’Omics data sharing;Field;Science.,2009

4. The Open Microscopy Environment (OME) data model and XML file: open tools for informatics and quantitative analysis in biological imaging;Goldberg;Genome Biol.,2005

5. 4DXpress: a database for cross-species expression pattern comparisons;Haudry;Nucleic Acids Res.,2008

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