Open Microscopy Environment (OME)
Web:
http://www.openmicroscopy.org/
System Overview:
Features:
Binary files and source code download .
Large amounts of Documentation.
Software that interacts with a database to manage images.
Open development project.
Uses PostgreSQL.
Perl, Java, C, Html, XML.
Support for annotations.
OME allows bench biologists to easily define their own vocabulary and interfaces for image annotation
Templates allow an OME user to easily create customized Image Database applications for data entry (annotation), searching (browsing), and display. The current interface allows annotation by Category Groups.
The default DBMS is Postgres. Eventually, Oracle may be supported as well.
OME includes a light-weight web-based interface,
written in Perl running under Apache.
OME programmers have developed standardized file formats for the exchange of image data and database schema for simplifying the automated analysis of images.
Data Server, Image Server and Web Server ( Must be on the same machine as the data server) All of these server processes will run inside of Apache.
Disadvantages:
Installation as the Unix root user. However, download and unpack the source (or check it out of CVS) as the root user, since this imparts superuser permissions onto all of the files in the distribution. Unpack the OME source as a normal user; perform the installation as the superuser.
Difficult to install, requires setup of Perl, mod Perl, Apache and PostgreSQL.
Separate Image and Data server. These can all be on the same machine, or on separate machines.
Designed for UNIX environment.
What does OME do?
Defines a set of information common to all biological microscopy, a format for storing this information, and a mechanism for sharing it with other software.
Allows users to define new types of information specific to their experiments.
Provides a browser-based interface for searching and browsing images.
Provides a mechanism to use existing image analysis algorithms within the OME framework.
Provides a consistent interface between analysis algorithms, allowing the user to combine them in a controlled way that does not violate the algorithm's intent.
Provides an additional framework, the OME Java API , for accessing information stored in an OME database via a Java-based client application running on a remote machine.
How it works:
OME's design follows a standard client-server architecture.
A single installation of OME will usually be used for an entire laboratory or department.
The data and metadata for the images in an OME installation are stored on a centralized server.