Matthew T. Dougherty
Erez Zadok
Abstract
The biosciences need an image format capable of high performance and long-term maintenance. Is HDF5 the answer?
- BioHDF; http://www.geospiza.com/research/biohdf/.Google Scholar
- Crystallographic Information Framework. International Union of Crystallography; http://www.iucr.org/resources/cif/.Google Scholar
- DICOM (Digital Imaging and Communications in Medicine); http://medical.nema.org.Google Scholar
- EMDB (Electron Microscopy Data Bank); http://emdatabank.org/.Google Scholar
- FITS (Flexible Image transport System); http://fits.gsfc.nasa.gov/.Google Scholar
- HDF (Hierarchical Data Format); http://www.hdfgroup.org.Google Scholar
- MEDSBIO (Consortium for Management of Experimental Data in Structural Biology); http://www.medsbio.org.Google Scholar
- METS (Metadata Encoding and Transmission Standard); http://www.loc.gov/standards/mets/.Google Scholar
- MPEG (Moving Picture Experts Group); http://www.chiariglione.org/mpeg/.Google Scholar
- netCDF (network common Data form); http://www.unidata.ucar.edu/software/netcdf/.Google Scholar
- NeXus (neutron, x-ray and muon science); http://www.nexusformat.org.Google Scholar
- NFS (Network File System); http://www.ietf.org/rfc/rfc3530.txt.Google Scholar
- OAIS (Open Archival Information System); http://nost.gsfc.nasa.gov/isoas/overview.html.Google Scholar
- OME (Open Microscopy Environment); http://www.openmicroscopy.org/.Google Scholar
- RDF (Resource Description Framework); http://www.w3.org/RDF/.Google Scholar
Index Terms
- Unifying biological image formats with HDF5
Recommendations
Unifying Biological Image Formats with HDF5: The biosciences need an image format capable of high performance and long-term maintenance. Is HDF5 the answer?
BioscienceThe biological sciences need a generic image format suitable for long-term storage and capable of handling very large images. Images convey profound ideas in biology, bridging across disciplines. Digital imagery began 50 years ago as an obscure ...
Taxonomy of Image File Formats
ECONF '13: Proceedings of the 2013 Fourth International Conference on e-Learning "Best Practices in Management, Design and Development of e-Courses: Standards of Excellence and Creativity"Professionals, practitioners, students, and novice users are overwhelmed with the different image file formats. This paper, proposes taxonomy for image file formats after reviewing 82 different image file formats based on the following attributes: ...
The Biological Connection Markup Language
Motivation: Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on ...
Comments