Metadata matters: access to image data in the real world

By M. Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, William J. Moore, Andrew J. Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald and 6 more. Journal of Cell Biology, 2010

984 citations recorded by the source corpus.

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.

Subfields: Biophysics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/cd4a32103ed6560b34df75bd34ab1ca23062cdb0

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Citations in the corpus

Critical review on biofilm methods (2017, methodology): “The format, Open Microscopy Environment (OME-Tiff), is now standardized and tools exist to convert most proprietary file formats into this (Linkert et al., 2010; Rueden & Eliceiri, 2007), allowing a wider choice of processing software.”
TrackMate: An open and extensible platform for single-particle tracking. (2017, methodology): “By being an open source Fiji plugin that uses modular libraries such as Bio-formats [57], SciJava [18], ImgLib2 [58], etc. , it is relatively straightforward to adapt TrackMate to new modalities and use cases.”
ImageJ2: ImageJ for the next generation of scientific image data (2017, background): “includes a wrapping of the Bio-Formats library [51], which enables a wide variety of supported images throughout all ImageJ operations.”
Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes (2011, positive): “Any image file format understood by Bio-Formats (Linkert et al., 2010), which currently supports over 100 different formats, may be used for tracing.”
The ImageJ ecosystem: Open‐source software for image visualization, processing, and analysis (2020, methodology): “26 The Bio-Formats library, 33 which is included with Fiji, plugs into SCIFIO, integrating its additional file formats more seamlessly into ImageJ.”
Biological Imaging Software Tools (2012, background): “Despite its recognized value, image metadata capture and annotation has not yet become widespread for bioimaging experiments 57 , though efforts are underway in certain areas.”
TrakEM2 Software for Neural Circuit Reconstruction (2012, methodology): “TrakEM2 has been written using the Java programming language and uses numerous image processing libraries including ImageJ (Wayne Rasband), mpicbg (Stephan Saalfeld), LOCI bioformats [37], ImgLib (Stephan Preibisch, Stephan Saalfeld, Tobias Pietzsch and others), ImageJ 3D Viewer [38], Stitching [39]”
OME Remote Objects (OMERO): a flexible, model-driven data management system for experimental biology (2012, methodology): “Bio-Formats is an image translation library that reads >100 proprietary file formats and translates them into this common data model that can then be accessed by other software tools 1 .”
High-Content Screening for Quantitative Cell Biology. (2016, background): “Open Microscopy Environment (OME) offers two possible solutions to these problems, with the development of Bio-Formats [53] and the OMERO server [54] (Box 2).”