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Using OME Server

What is OME?

The Open Microscopy Environment (OME) is a set of software that interacts with a database to manage images, image meta-data, image analysis and analysis results.

What does OME do?

  • OME 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.
  • OME allows users to define new types of information specific to their experiments.
  • OME provides a browser-based interface for searching and browsing images.
  • OME provides a mechanism to use existing image analysis algorithms within the OME framework.
  • OME 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.

OME's Architecture

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. OME administrators can choose to place these server programs on the same machine, or on separate machines, depending on their particular needs and resources.

OME includes a light-weight web-based interface, written in Perl running under Apache, that can be accessed from any computer with a standard Web browser. OME 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. Java remote clients developed against this framework provide more advanced visualization and interaction functionality than the Web interface, however must be installed separately on each client computer.

In addition to our Shoola Java Client, there exist externally developed Java programs such as VisBio and ImageJ that have the functionality, either intrinsically or via a plugin, to interact with images and metadata stored in OME.

There is an included command-line tool, ome, for administering and otherwise controlling your OME installation.

OME Past, Present and Future

The features and capabilities described in these pages are current as of OME 2.6.0. To learn more about what is planned for the future, see the OME development roadmap.

OME Perl Server Docs

  • OS X Installation Guide: A guide for installing OME Perl Server on Mac OS X using the graphical installation wizard.
  • FindSpots User Guide: A guide for using OME's FindSpots - automated 3D particle finding and tracking software.
  • Tutorial: Quantitative MATLAB image analysis in OME: This is a step-by-step walkthrough explaining how to convert a legacy image analysis algorithm implemented in MATLAB into an analysis module so that it can be executed by the OME analysis engine against images and meta-data stored in OME.
  • Image Table Tools can be used to develop table-based displays of annotated images. These displays are suitable for dissemination of supplemental data for publications involving large microscopy image sets. The manual describes the use, configuration and implementation of these tools.
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