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{SCIFIO}: an extensible framework to support scientific image formats

Submitted by karopka on Sun, 2016/12/11 - 19:29
Title{SCIFIO}: an extensible framework to support scientific image formats
Publication TypeJournal Article
Year of Publication2016
AuthorsHiner, MC, Rueden, CT, Eliceiri, KW
JournalBMC bioinformatics
Volume17
Pagination521
ISSN1471-2105
KeywordsBio-Formats, Image analysis, ImageJ, open-source, SCIFIO
Abstract

BACKGROUND: No gold standard exists in the world of scientific image acquisition; a proliferation of instruments each with its own proprietary data format has made out-of-the-box sharing of that data nearly impossible. In the field of light microscopy, the Bio-Formats library was designed to translate such proprietary data formats to a common, open-source schema, enabling sharing and reproduction of scientific results. While Bio-Formats has proved successful for microscopy images, the greater scientific community was lacking a domain-independent framework for format translation. RESULTS: SCIFIO (SCientific Image Format Input and Output) is presented as a freely available, open-source library unifying the mechanisms of reading and writing image data. The core of SCIFIO is its modular definition of formats, the design of which clearly outlines the components of image I/O to encourage extensibility, facilitated by the dynamic discovery of the SciJava plugin framework. SCIFIO is structured to support coexistence of multiple domain-specific open exchange formats, such as Bio-Formats' OME-TIFF, within a unified environment. CONCLUSIONS: SCIFIO is a freely available software library developed to standardize the process of reading and writing scientific image formats.

DOI10.1186/s12859-016-1383-0
PubMed ID27927161
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