www.iplantcollaborative.org bisque: enabling cloud and grid powered image analysis ramona walls...
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www.iplantcollaborative.org
BISQUE:Enabling Cloud and Grid Powered
Image Analysis
Ramona WallsiPlant Collaborative
[email protected] from slides by Martha Narro, Nirav Merchant
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Motivation I
• High throughput imaging is essential for large-scale phenotyping.• Affordable robotics for image
acquisition are creating vast amounts of imaging data.
• Many laboratories have automated imaging setups, but lack a comparable analysis platform.
• Super resolution microscopy and multi-channel images are pushing the boundaries of storage and computational capabilities.
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Motivation II• New, improved analysis
algorithms are being published.• Biologists struggle to use
them.• Developers need images to
test algorithms.• Scientists need to compare
algorithms, reproduce results.
• Metadata is key for managing large datasets.• Sharing and collaborating with large image data
sets is challenging.
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BisqueImage Management, Analysis, Sharing System
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Why Bisque?• Biologists can
• Manage images• Choose from multiple analysis options • Overlay results to validate findings• Annotate images• Share images, results, annotations via secure link • Algorithm developers can
• Publish new analysis methods, easily make them web accessible
• Produce interactive plots, visualizations using built in API• Integrated with iPlant storage and computation
infrastructure for scalability
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How does it work?
Bisque
iPlant Data Store
High B
andw
idth
Trans
fer
iPlant Computational Infrastructure
High Bandwidth
Transfer
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Bisque Features
• Web application• Tiling, zooming, step through image stacks, play as
movie• Display 20K x 20K pixel images in web browser• Handles 100+ image, video formats• Import large image sets (≤ 40 GB via Bisque),
extremely large ones (> 40 GB via iPlant Data Store)• Scale analyses using distributed computing
(connected to XSEDE) and workflow engines (Pegasus, Condor)
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Import and Export
•support for multiple files•plugin free HTML5 uploads•drag/drop• import annotations•processing compressed files•compose 5D from multiple files
•on the file streaming export•dataset export•export annotations•compressed files: Tar, GZip, Zip, BZip
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Sharing
• Easy modes: • “Private” and
• “Published”
• Google style sharing for resources• Using E-mails of
collaborators
• Read-only or Full access
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Example Analysis: Seed Size
High resolution flat bed scanner image of seeds
Edge detection and analysis by Bisque
Source: Edgar Spalding
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ImageJ modules
• Bisque API for ImageJ• Dataset Cluster/parallel execution• Run image macros/plugins using
Web-interface• Currently requires hand editing of
macro files.• Working on semi-automated
conversion
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Bisque-iPlant Team
• Bisque (U. California, Santa Barbara)• B. S. Manjunath• Kris Kvelikval• Dmitry Fedorov
• iPlant (U. Arizona, Tucson)• Nirav Merchant• Martha Narro
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www.iplantcollaborative.org
• Main application:• bisque.iplanctc.org
• BISQUE video tutorials:• http://bovary.iplantcollaborative.org/client_service/
help
• Support• http://ask.iplantcollaborative.org
Useful Links