title: Open tools for storage and management of quantitative image data.
abstract: The explosion in quantitative imaging has driven the need to develop tools for storing, managing, analyzing, and viewing large sets of data. In this chapter, we discuss tools we have built for storing large data sets for the lifetime of a typical research project. As part of the Open Microscopy Environment (OME) Consortium, we have built a series of open-source tools that support the manipulation and visualization of large sets of complex image data. Images from a number of proprietary file formats can be imported and then accessed from a single server running in a laboratory or imaging facility. We discuss the capabilities of the OME Server, a Perl-based data management system that is designed for large-scale analysis of image data using a web browser-based user interface. In addition, we have recently released a lighter weight Java-based OME Remote Objects Server that supports remote applications for managing and viewing image data. Together these systems provide a suite of tools for large-scale quantitative imaging that is now commonly used throughout cell and developmental biology.
authors.affiliation: Division of Gene Regulation and Expression, College of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, Scotland DD1 5EH, United Kingdom.
authors.forename: Joshua
authors.initials: J
authors.lastname: Moore
authors.forename: Chris
authors.initials: C
authors.lastname: Allan
authors.forename: Jean-Marie
authors.initials: JM
authors.lastname: Burel
authors.forename: Brian
authors.initials: B
authors.lastname: Loranger
authors.forename: Donald
authors.initials: D
authors.lastname: MacDonald
authors.forename: Jonathan
authors.initials: J
authors.lastname: Monk
authors.forename: Jason R
authors.initials: JR
authors.lastname: Swedlow
mesh_terms: D003628:Database Management Systems; D016247:Information Storage and Retrieval / Q000379:methods*; D008853:Microscopy; D012984:Software; D014584:User-Computer Interface