BEST NetworkCollaborate, Create, Learn

A Biomedical Education, Skills and Training Community

Technical Committee19/02/2013

Progress Report

It all about access

The BEST Portal

Access point to:• Project information

• Partners • Results of Trials

• Content • Tools

Progress• Mock-ed up• In development• Sourced seed content

Virtual Labs• Mock-ed up• In development

Progress• 3 vLabs contributed• 2 in development • Some descriptions created

Virtual Lab - Page• Description• Learning Objectives• Screenshot• Ability to Try • Ability to “Adapt”

Learning Tools InteroperabilityLMS Integration

Single sign on;Grade Book Integration;

Single sign on;No Grade Book IntegrationCurrent UNSW-Med installation SP5.

Service Packs 10 and 11 needed.

Implications: older Explorer (default) version;Not compliant with Smart Sparrow;

>> Add Firefox to SOE;

Australian Medical Image BankAn initiative of the BEST Network

VS

High availability Image Server

Learning

BEST VS Repository

Scanning Hosting Content Development and hosting

Content Development Tools

Management tools

BEST PortalContent Repository and

Management System

At home

On the go

In class

Reminder:

• High resolution scan produces large (~2GB) SVS files (or using existing SVS files);

• Copying the files to a HD and uploading to a storage server;

• Tiling each SVS file is to produce a set of tiles to match the multiple target Zooms;

• Uploading the tiles to S3;

Australian Medical Image BankProcessing procedure

• Highly durable storage infrastructure designed for mission-critical and primary data storage.

• Recovery - stores data in multiple facilities and on multiple devices within each facility.

• checksums on all network traffic to detect corruption of data packets when storing or retrieving data.

• Systematic data integrity checks - automatically self-healing.• Version control.• Designed for 99.999999999% durability and 99.99%

availability of objects over a given year.

Australian Medical Image Bank Amazon S3 Storage

AMiB• Cloud-based, Fast• Shared• Members only/ public

Progress• 500 images from UNSW• 20 from Umelb

Next:• Agree on metadata • Search, Snomed;

http://www.best.edu.au/amib/viewer/anat6801

• Based on OpenLayers (Openlayers.org), which is an open source JavaScript library to load, display and render maps from multiple sources on web pages.

• “Caching” The tiles loaded from a CDN - Content delivery network: high availability and high performance.

• The slide viewer is HTML5 based – any device;

Australian Medical Image BankImplementation - Virtual Slide Viewer

• Notify the user for testing and confirmation. • Users review the slide, add in cataloguing information, and add the slide

to the AMIB catalogue.• Database implementation is depending on the data format. Need to

facilitate a standardized list of properties that will be used for cataloging and searching.

• Implementation (my-SQL) Each entry coupled with the matching tiles hierarchy.

• Every database request produces required zoom level tile group and the corresponding information.

• The database schema is going to support the implementation of additional annotations and user generated data that is going to be added to the images as actual deployment commences.

Australian Medical Image BankCataloguing process

In order for us to do that we will need:• To analyze the best 10 UNSW slides with the most

complete Lotus-notes meta data information;• To create the rules with which all the UNSW slides

are going to comply.• To generalize a format that fits other slide batches

from different sources that may include different data sets;

• Normalize all the information and make sure all slides are consistent.

Australian Medical Image Bankmetadata analysis

Virtual Slide ViewerFinalize specs

HTML5 Metadata Scale ruler (Zooms) Nav/Inset-Box Illumination (bright/dark) Ability to get a link to a

specific view? Collection Navigation?

Next:• Integration with

Annotate

http://www.best.edu.au/amib/viewer/anat6801

Action ItemsObtain all relevant AMiB images (IP issues) Finalize image metadata definitionFinalize Viewer capabilitiesFinalized contribution of existing content

With metadata (descriptions, learning objectives etc)