Cell and Developmental Biology Research Group

Department of Zoology, University of Oxford, UK

Terena Networking Conference

Lisbon, 22-25 May 2000

David M. Shotton and Thomas Boudier

(david.shotton@zoo.ox.ac.uk)

VIDOS VIDOS - a system for editing and - a system for editing and customizing videos over the Webcustomizing videos over the Web

Outline of my presentationOutline of my presentation

What are the problems when using videos over the Web?

The BioImage Database project: an introduction

An example of a scientific video:

the killing of virally-infected cells by cytotoxic T lymphocytes

Specific intrinsic metadata and Query by Content

The design and functionality of VIDOS

The applications of VIDOS

Conclusion: The future of image informatics

Videos on the Web: why so special?Videos on the Web: why so special?

Problems (for the user) Unusually large files ( >100 Mb) Time-critical visualisation Limited Internet transmission bandwidth No standard format (AVI, QuickTime, MPEG-2, Real, etc.) Multiplicity of compression algorithms

Solutions (for the video provider) Correct choice of server format(s) for download or streaming Creation of highly compressed preview movies Provision of on-line editing and customization tools to enable the

videos file to be adapted to the user’s specifications

The BioImage DatabaseThe BioImage Database

The BioImage Database is a recently developed searchable on-line database for multi-dimensional images of biological specimens, derived from all forms of microscopy:

Light, electron, acoustic and scanning probe microscopies

2D (x, y), 3D (x, y, z), video (x, y, time), 4D confocal (x, y, z, t)

Particular attention paid to image descriptors (metadata)

Work included development of novel tools for image visualization, format conversion, and video editing

http://www.bioimage.orghttp://www.bioimage.org

BioImage data sets BioImage data sets cover the full range cover the full range of microscopic of microscopic resolutionsresolutions

Carazo et al. (1999) Nucleic Acid Research 27: 280-283

Carazo & Stelzer (1999) J. Struct. Biol. 125: 97-102

The BioImage browse interfaceThe BioImage browse interface

Cytotoxic T lymphocytesCytotoxic T lymphocytes The immune system’s serial killersThe immune system’s serial killers

CTL-mediated target cell deathCTL-mediated target cell death

VAMPORTVAMPORT: Automated object and event : Automated object and event recognition - tracking of CTL movementrecognition - tracking of CTL movement

VANQUISVANQUIS - a video annotation interface - a video annotation interface

VIDOSVIDOS - a - a vivideo deo dodownload wnload sspecification systempecification system Allows one to edit and customize a digital video over the web

Adapts the video content, size, format and compression quality to its intended purpose, or to match the capabilities of one’s PC

The video may be in a VIDOS-enabled database like BioImage, or from anywhere else on the Web, including user’s web server

VIDOS gives the user video editing capabilities without the need to purchase expensive video editing software

By reducing the size of digital video files, VIDOS can improve corporate or personal efficiency by speeding network transfers, avoiding bandwidth bottlenecks, and reducing disc storage requirements

VIDOSVIDOS schematic diagram (simple) schematic diagram (simple)

VIDOSVIDOS schematic schematic diagramdiagram

(complex) (complex)

The The VIDOSVIDOS demonstration home page demonstration home page(http://vidos.zoo.ox.ac.uk/vidos)(http://vidos.zoo.ox.ac.uk/vidos)

The GALLOP test video previewThe GALLOP test video preview

Credits Photographer: Eaduard Muybridge, 1878Racehorse: AnnieJockey: unknown

Original video details:QuickTime FormatM-JPEG compressedCompression quality 0.615 frames, repeated x690 frames at 30 fps File size: 3,731 Kb

VIDOSVIDOS video selection procedure video selection procedure

The The VIDOSVIDOS selection interface selection interface

VIDOSVIDOS video customization procedure video customization procedure

The The VIDOSVIDOS customization interface customization interface

VIDOSVIDOS video download procedure video download procedure

The final The final VIDOSVIDOS- customized video- customized video

Original video: QuickTime format, M-JPEG compressed at quality 0.6, 90 frames at 30 fps

File size 3,731 Kbytes.

Customized video: AVI format, Indeo compressed at quality 0.3, 45 frames at 10 fps, 50% zoom

File size 91 Kbytes

Compressed file approximately 41 times smaller than original

The benefits of The benefits of VIDOSVIDOS For individuals in science, R&D, legal, government and defence sectors: video

editing capabilities, enhanced download times, reduced storage requirements, and format conversion to suit intended purpose and (limited?) capabilities of one’s own PC

In education and training: the ability to select and tailor video clips from a central resource for inclusion in live or computer-based training programmes

For the corporate business environment (e.g. a TV company with regional studios): a system for distributed client-based video editing from a centralized server

Coupled with a video database and a Query by Content system, VIDOS provides the means to edit and customize those videos selected by the query, prior to downloading them

FROM IMAGE TO KNOWLEDGEFROM IMAGE TO KNOWLEDGEImage Informatics in the Digital AgeImage Informatics in the Digital Age

Harvesting knowledge from digital images requires: a searchable image database - The BioImage Database an automatic video content analysis system - VAMPORT an interactive video annotation system - VANQUIS a query by content system - The ImageQuest Project A web-based video customization system - VIDOS

Together, these form a unique and powerful combination to facilitate the conversion of raw image data into knowledge

The futureThe future We now have an excellent working prototype of VIDOS (v2.1) This is the subject of an international patent application We have clear ideas for further enhancement of functionality We have recently rewritten the VIDOS server program as

multithreaded JAVA, to enhance concurrent client support We are forming a spinout company to develop, promote and market

BioImage, VIDOS and the various Query by Content tools We are adopting DOIs and the <indecs> rights metadata model Ingenta Ltd will host the BioImage Database, integrate it with their

BIDS bibliographic databases, and expand it to server other fields We seek partners and licencees to apply the VIDOS Web-based

video editing and customization technology in other areas

AcknowledgementsAcknowledgements

My BioImage Partners (database design and implementation)

Academic: Jose Maria Carazo, Ernst Stelzer, Andreas Engel and Ignacio Fita

Corporate: European Bioinformatics Institute, Silicon Graphics, and Informix Software Ltd, particularly Jon

Machtynger who wrote the VANQUIS code

My research assistants at Oxford

Thomas Boudier (1997-1998; quantitation of video compression artefacts, video object tracking, and VIDOS coding)

John Pybus (1999-2000; VIDOS re-coding)