Using the Biological Collections Ontology to Advance Biodiversity Science
Using the JPEG2000 image format for storage and access in biodiversity collections.
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Transcript of Using the JPEG2000 image format for storage and access in biodiversity collections.
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Freeland, TDWG 2008. 24 Oct 2008
Using the JPEG2000 image format for storage and access in biodiversity collections.
Chris FreelandMissouri Botanical Garden
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Freeland, TDWG 2008. 24 Oct 2008
But first, an oversight…
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Freeland, TDWG 2008. 24 Oct 2008
Overview of JPEG2000
• Wavelet-based compression– Different than JPEG– Decompress without extracting entire file
• Proposed in 2000 to supercede JPEG– Hasn’t
• Slow adoption in museums & libraries– Poor (no) native browser support– Few open source options
• Faster adoption in medical imaging, other commercial applications
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Freeland, TDWG 2008. 24 Oct 2008
Parts of the format
• Part 1, Core coding system (JP2)– defines format; adopted as standard first.
• Part 2, Extensions • Part 3, Motion JPEG 2000 • Part 4, Conformance • Part 5, Reference software • Part 6, Compound image file format (JPM)• Part 7 has been abandoned • Part 8, Security (JPSEC) • Part 9, Protocols and API (JPIP)• Part 10, JP3D (volumetric imaging) • Part 11, JPWL (wireless applications) • Part 12, ISO Base Media File Format (common w/ MPEG-4)
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Freeland, TDWG 2008. 24 Oct 2008
Advantages of JPEG2000
• Region extraction• Compression
– Both lossless & lossy
• Self-containedness– XML metadata + image– Multiple objects can be bundled
together
• Progressive Transmission– Lower quality at early load
http://www.dlib.org/dlib/september08/chute/09chute.html
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Freeland, TDWG 2008. 24 Oct 2008
Region Extraction
“Give me x,y coordinates at z resolution.”
600ppi, 200MB TIF; encode to 100MB JP2
72ppi: 20KB JPG
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Freeland, TDWG 2008. 24 Oct 2008
“How many books in a ___?”
2 Biblioburros; 4,800 books*
*http://www.nytimes.com/2008/10/20/world/americas/20burro.html
Luis Soriano, with Alpha and Beto
1 Biblioburro = 2,400 books
BHL to date = 9 Biblioburros!
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Freeland, TDWG 2008. 24 Oct 2008
Storage requirement for a digital Biblioburro
• 2,400 books / Biblioburro– (9,238,295 pages / 22,118 books in BHL) = 418 pages / book– 1,002,437 pages / Biblioburro
• Avg size of each image file– RAW/TIF: 24MB; JP2: 2MB
• Drive space needed / Biblioburro– TIF: 24TB; JP2: 2TB
2,400 books 24 TB TIFs
2 TB JP2
= =
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Freeland, TDWG 2008. 24 Oct 2008
Self-containedness / metadata bundling
• Not just an image, but an image, its content & its context– Adobe XMP– Dublin Core– Your own XML
• TIF Headers & JPEG limit fields
• Can describe more than just an image– A whole web site
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Freeland, TDWG 2008. 24 Oct 2008
Barriers for adoption
• Lack of affordable, scalable serving options– Until recently, no open source server– Commercial options expensive
• No native browser support– Safari does, but via QuickTime– But why??
• PNG?• No motivation?
• Community skepticism
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Freeland, TDWG 2008. 24 Oct 2008
Encoding Software
• Commercial– Adobe Photoshop– LuraTech SDK– LizardTech
• Non-Commercial– Kakadu– ImageMagik– IrfanView
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Freeland, TDWG 2008. 24 Oct 2008
Decoding & Serving
• Commercial– LizardTech– Aware– LuraTech ICS– FSIV
• Non-Commercial– Kakadu– GSIV– djatoka
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Freeland, TDWG 2008. 24 Oct 2008
Part 6: JPIP
• Protocol and API for transmitting JP2• Designed for HTTP, but not restricted
to that carrier– Don’t need a browser
• Implementations are available, use is infrequent– HiRISE camera on
Mars ReconnaissanceOrbiter
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Freeland, TDWG 2008. 24 Oct 2008
Current use of JP2 in BHL
• Serve 85% (lossy) .jp2
• LizardTech decoder– Tiled on the fly– Cached for
performance
• GSIV browser-based client viewer
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Freeland, TDWG 2008. 24 Oct 2008
LizardTech ExpressServer
Browser GSIV.js
www.biodiversitylibrary.org
.jp2
.jpg
Internet Archive
/page/1274907
pageid: 1274907
BHLdb
http://www.archive.org/download/mushroomsofameri00palm/.../mushroomsofameri00palm_0010.jp2
images.mobot.org
A user requests Mushrooms of America, edible and poisonous, Plate X:http://www.biodiversitylibrary.org/page/1274907
locate:
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Freeland, TDWG 2008. 24 Oct 2008
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Freeland, TDWG 2008. 24 Oct 2008
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Freeland, TDWG 2008. 24 Oct 2008
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Freeland, TDWG 2008. 24 Oct 2008
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Freeland, TDWG 2008. 24 Oct 2008
The Future: djatoka
• Developed at Los Alamos National Laboratory, Research Library• Use of the ISO-standardized JPEG 2000 format [6] as the service
format; • Java-based open source solution built around the Kakudu JPEG
2000 library; • Geared towards reuse through URI-addressability of all image
disseminations including regions, rotations, and format transformations;
• Provision of a consistent, guessable URI pattern for image disseminations based on the ANSI/NISO OpenURL standard [7];
• Provision of an extensible service framework for image disseminations enabled by OCLC's Java OpenURL package;
• Availability of image disseminations in a range of image formats; • Availability of image disseminations for locally stored JPEG 2000
files, as well as for Web-accessible images in a variety of formats; • Configurable server-side, file-based caching; • Ajax-based client reference implementation, based on IIPImage
JavaScript Viewer, which allows panning, zooming, and selecting the URI of the current view.
http://www.dlib.org/dlib/september08/chute/09chute.html
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Freeland, TDWG 2008. 24 Oct 2008
References
• djatoka– http://www.dlib.org/dlib/july08/buonora/07buonora.html
• HUL: Page Image Compression for Mass Digitization– http://preserve.harvard.edu/massdig/hul_study/
• JP2 in Libraries and Archives– http://j2karclib.info/taxonomy/term/2
• JPEG 2000 - a Practical Digital Preservation Standard?– http://www.dpconline.org/docs/reports/dpctw08-01.pdf
• JPEG2000 site– http://www.jpeg.org/jpeg2000/
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Freeland, TDWG 2008. 24 Oct 2008
Contact
Chris FreelandMissouri Botanical Garden4344 Shaw Blvd.St. Louis, MO [email protected]
http://www.chrisfreeland.com