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Unifying Biological Image Formats with HDF5: The biosciences need an image format capable of high performance and long-term maintenance. Is HDF5 the answer?

Authors:

Matthew T. Dougherty,

Michael J. Folk,

Herbert J. Bernstein,

Frances C. Bernstein,

Kevin W. Eliceiri,

Christoph BestAuthors Info & Claims

Queue, Volume 7, Issue 9

Pages 20 - 25

https://doi.org/10.1145/1626135.1628215

Published: 01 October 2009 Publication History

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Abstract

The 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 technical phenomenon. Now it is an indispensable computational tool. It has produced a variety of incompatible image file formats, most of which are already obsolete.

References

[1]

BioHDF; http://www.geospiza.com/research/biohdf/

[2]

Crystallographic Information Framework. International Union of Crystallography; http://www.iucr.org/resources/cif/

[3]

DICOM (Digital Imaging and Communications in Medicine); http://medical.nema.org

[4]

EMDB (Electron Microscopy Data Bank); http://emdatabank.org/

[5]

FITS (Flexible Image Transport System); http://fits.gsfc.nasa.gov/

[6]

HDF (Hierarchical Data Format); http://www.hdfgroup.org

[7]

MEDSBIO (Consortium for Management of Experimental Data in Structural Biology); http://www.medsbio.org

[8]

METS (Metadata Encoding and Transmission Standard); http://www.loc.gov/standards/mets/

[9]

MPEG (Moving Picture Experts Group); http://www.chiariglione.org/mpeg/

[10]

netCDF (network Common Data Form); http://www.unidata.ucar.edu/software/netcdf/

[11]

NeXus (neutron, x-ray and muon science); http://www.nexusformat.org

[12]

NFS (Network File System); http://www.ietf.org/rfc/rfc3530.txt

[13]

OAIS (Open Archival Information System); http://nost.gsfc.nasa.gov/isoas/overview.html

[14]

OME (Open Microscopy Environment); http://www.openmicroscopy.org/

[15]

RDF (Resource Description Framework); http://www.w3.org/RDF/

Cited By

Reimer MBangalore LWaxman STan A(2020)Core Principles for the Implementation of the Neurodata Without Borders Data StandardJournal of Neuroscience Methods10.1016/j.jneumeth.2020.108972(108972)Online publication date: Nov-2020
https://doi.org/10.1016/j.jneumeth.2020.108972
Abdennur NMirny L(2019)Cooler: scalable storage for Hi-C data and other genomically labeled arraysBioinformatics10.1093/bioinformatics/btz54036:1(311-316)Online publication date: 10-Jul-2019
https://doi.org/10.1093/bioinformatics/btz540
Ljungquist BPetersson PJohansson ASchouenborg JGarwicz M(2018)A Bit-Encoding Based New Data Structure for Time and Memory Efficient Handling of Spike Times in an Electrophysiological SetupNeuroinformatics10.1007/s12021-018-9367-z16:2(217-229)Online publication date: 5-Mar-2018
https://doi.org/10.1007/s12021-018-9367-z

Index Terms

Unifying Biological Image Formats with HDF5: The biosciences need an image format capable of high performance and long-term maintenance. Is HDF5 the answer?

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Published In

cover image Queue

Queue Volume 7, Issue 9

Bioscience

October 2009

49 pages

ISSN:1542-7730

EISSN:1542-7749

DOI:10.1145/1626135

Issue’s Table of Contents

Copyright © 2009 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 01 October 2009

Published in QUEUE Volume 7, Issue 9

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Cited By

Reimer MBangalore LWaxman STan A(2020)Core Principles for the Implementation of the Neurodata Without Borders Data StandardJournal of Neuroscience Methods10.1016/j.jneumeth.2020.108972(108972)Online publication date: Nov-2020
https://doi.org/10.1016/j.jneumeth.2020.108972
Abdennur NMirny L(2019)Cooler: scalable storage for Hi-C data and other genomically labeled arraysBioinformatics10.1093/bioinformatics/btz54036:1(311-316)Online publication date: 10-Jul-2019
https://doi.org/10.1093/bioinformatics/btz540
Ljungquist BPetersson PJohansson ASchouenborg JGarwicz M(2018)A Bit-Encoding Based New Data Structure for Time and Memory Efficient Handling of Spike Times in an Electrophysiological SetupNeuroinformatics10.1007/s12021-018-9367-z16:2(217-229)Online publication date: 5-Mar-2018
https://doi.org/10.1007/s12021-018-9367-z

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