The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging

Abstract

The Open Microscopy Environment (OME) defines a data model and a software implementation to serve as an informatics framework for imaging in biological microscopy experiments, including representation of acquisition parameters, annotations and image analysis results. OME is designed to support high-content cell-based screening as well as traditional image analysis applications. The OME Data Model, expressed in Extensible Markup Language (XML) and realized in a traditional database, is both extensible and self-describing, allowing it to meet emerging imaging and analysis needs.

Figure 1

The mode of acquisition defines the pixel image data. The meaning of a 2D-image recorded from a digital microscope imaging system varies depending on how it is collected. Almost all of the different modes in (a) and (b) can be combined to analyze cell structure and behavior. All of the parameters and configurations must be somehow recorded for the interpretation of the pixel data in an image. (a) The spatial, spectral and temporal context of an image is used to generate more information about the cell under study. Changing stage position, focus, spectral range or time of imaging all expand the meaning of an image. Modified from [33]. (b) The two aspects of the image data collection that define the pixel data. A variety of methods are used to generate contrast in modern biological imaging. In addition, the imaging method used to record the data also has meaning.

Figure 2

High-level view of the elements in the OME file schema. This figure (and Figures 3 and 4) should be read from left to right. A data type (for example, OME) is defined by a number of elements. In this case, OME is defined by Project, Dataset, Experiment, Image, and so on. Each of these elements can be defined by their own individual elements. The Image and Instrument elements are expanded in Figures 3 and 4. The full XML schema is available [24]. The full documentation for the schema is also available [25]. +, One or more elements of this type; ?, optional element or attribute; *, zero or more elements of this type; 1, choose one from a list of elements; D, the value of this element/attribute is constrained to one of several values, a range, or a text pattern (see the online documentation for more details [25]).

Figure 3

The Instrument element in the OME file schema. The data elements that define the acquisition system parameters are shown. For these descriptions, we have incorporated suggestions from many colleagues and commercial partners [32]. Symbols are as in Figure 2.

Figure 4

The Image element in the OME file schema. The data elements that define the an image in the OME file are shown. These include the image itself (Pixels), and a variety of characteristics of the image data and display parameters. Symbols are as in Figure 2.

Figure 5

Using STs for visualization in OME. Examples of the use of STs for visualization of data within an OME database are shown. These tools are Java applications that access OME via the OME remote framework [34]. All OME code is available [31]. (a) The Chain Builder, a tool that enables a user to build analysis chains by ensuring that the input requirements of a given module are satisfied by outputs from previous modules. This is achieved by accessing the STs for the inputs and outputs within an OME database. (b) The DataManager, DatasetBrowser and 5DViewer. The DataManager shows the relationships between Projects, Datasets and Images within an OME database. The DatasetBrowser modifies the display method for images within a given dataset depending on the values of data stored as STs within an OME database. The 5Dviewer allows visualization of individual images based on STs in an OME database.