Vanderbilt Discovery Grant is funding David Pistons plan
for high volume image data storage, management and processing..
database improve image access
by Leigh MacMillan
During bursts of dynamic imaging, the microscopes in Vanderbilts
Cell Imaging Shared Resource can generate data at a rate of more
than 240 megabytes per minute, says David Piston, the cores
scientific director. Thats about one CD-ROMs worth of
images every three minutes, he says.
Where do you store all of these data, and how do you access and
analyze the images efficiently? These are the kinds of questions
being addressed by imaging bioinformatics, Piston says. He was recently
awarded a Vanderbilt Discovery Grant to implement a plan for high
volume image data storage, management, and processing.
Pistons plan involves creating a centralized repository for
storing images and structuring that repository so that access is
efficient. Simply having a large amount of disk space doesnt
guarantee access to it in a timely fashion, he says.
Traditionally, data have been stored on individual disk servers.
The problem with this scheme, Piston says, is that an individual
during large file transfer can monopolize a single
server and the network, leaving other disk servers sitting idle.
To overcome this problem, Piston will generate a parallel file system
essentially a group of servers transferring data in parallel,
instead of independently.
To manage the stored images for analysis and sharing with other
investigators, Piston will implement a database scheme developed
by the Open Microscopy Environment (OME, http://www.openmicroscopy.org).
OME is an open source software project to develop a database-driven
system for quantitative analysis of biological images, Piston says.
It is a collaborative effort among academic and industrial labs
that was started in 2000. The first versions of OME programs
standardized file formats for image data and database schema
are nearing completion.
Having an image database will allow researchers to systematically
deposit data and selectively extract images from simple queries
to the database. Keyword searches or other cross-referencing techniques
will provide investigators with the opportunity to compare images
from different laboratories and experiments, Piston says.
Piston has teamed up with Alan Tackett at Information Technology
Services to install, maintain and back up the parallel servers.
In addition to using existing expertise at ITS, this arrangement
will allow much wider access to these services once we get them
established, Piston says. The server and database system will
benefit many different groups, including users of the Cell Imaging
Shared Resource, the In Vivo Imaging Center, which Piston also directs,
and the newly created Vanderbilt Institute of Imaging Science under
the leadership of John Gore.
We expect this server and database system to greatly advance
image informatics and to accelerate progress in biological and biomedical
research at Vanderbilt, Piston says.
In addition to providing user-friendly storage and access to image
data, Piston expects the new system to speed data analysis. The
OME database will interface with both existing commercial image
processing software and with new analysis routines.
Piston and colleagues are developing one such new routine for specialized
particle analysis. They are using so-called deformable models to
track moving subcellular particles such as mitochondria and
insulin granules, which they image to study glucose-stimulated insulin
secretion over the time course of an experiment. The new
semi-automatic and automatic methods will allow analysis, processing,
and visualization of large three- and four-dimensional data sets.
The server and database system will make these kinds of analyses
possible, Piston says.