2010 | Melissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, Jason R. Swedlow
Metadata is crucial for sharing image data in the biological sciences to prevent duplication, promote integrity, and facilitate scientific discovery. Multidimensional microscopy image data, acquired from various platforms with proprietary file formats (PFFs), pose challenges for standardization and sharing. This paper describes an open standard format for microscopy image data, urging the community to adopt open image data standards and ensure all imaging platforms support these formats to build an open image data repository.
The importance of open access to large datasets in biology is well established, with protocols and principles for data sharing emerging. However, access and sharing require significant effort and investment. The success of genomic data sharing, where standards were developed and adopted by the community, provides a model for the imaging community to follow. The paper reviews current online biological image repositories and provides recommendations for the use of open standardized data formats.
The JCB DataViewer is an open repository for original image data in the life sciences, allowing access to original data and metadata. It is based on the Open Microscopy Environment (OME) and Bio-Formats projects. The repository is freely available to the public and aims to merge with a definitive public repository of image data in the life sciences.
The paper emphasizes the need for standardized file formats that support rich metadata structures. It outlines recommendations for the use of PFFs, including associating metadata with image data, ensuring metadata is readable by third-party software, and requiring commercial software to support open metadata specifications. The development of standardized image data and metadata formats is crucial for the success of scientific image repositories.
The OME has developed a data model and XML file format for biological imaging, which is widely used. The paper advocates for the adoption of these standards to ensure the long-term accessibility and usability of image data. The community must demand support for these formats in commercial platforms to ensure public and charity-funded scientific data is publicly available. The paper concludes that open, standardized formats are essential for the future of scientific image repositories.Metadata is crucial for sharing image data in the biological sciences to prevent duplication, promote integrity, and facilitate scientific discovery. Multidimensional microscopy image data, acquired from various platforms with proprietary file formats (PFFs), pose challenges for standardization and sharing. This paper describes an open standard format for microscopy image data, urging the community to adopt open image data standards and ensure all imaging platforms support these formats to build an open image data repository.
The importance of open access to large datasets in biology is well established, with protocols and principles for data sharing emerging. However, access and sharing require significant effort and investment. The success of genomic data sharing, where standards were developed and adopted by the community, provides a model for the imaging community to follow. The paper reviews current online biological image repositories and provides recommendations for the use of open standardized data formats.
The JCB DataViewer is an open repository for original image data in the life sciences, allowing access to original data and metadata. It is based on the Open Microscopy Environment (OME) and Bio-Formats projects. The repository is freely available to the public and aims to merge with a definitive public repository of image data in the life sciences.
The paper emphasizes the need for standardized file formats that support rich metadata structures. It outlines recommendations for the use of PFFs, including associating metadata with image data, ensuring metadata is readable by third-party software, and requiring commercial software to support open metadata specifications. The development of standardized image data and metadata formats is crucial for the success of scientific image repositories.
The OME has developed a data model and XML file format for biological imaging, which is widely used. The paper advocates for the adoption of these standards to ensure the long-term accessibility and usability of image data. The community must demand support for these formats in commercial platforms to ensure public and charity-funded scientific data is publicly available. The paper concludes that open, standardized formats are essential for the future of scientific image repositories.