The OME-XML format ================== OME-XML is a `file format `_ for storing microscopy information (both pixels and metadata) using the OME Data Model. .. note:: OME-XML as a file format is superseded by OME-TIFF, which is the preferred container format for image data making use of the OME Data Model. The purpose of OME-XML is to provide a rich, extensible way to save information concerning microscopy experiments and the images acquired therein, including: - dimensional parameters defining the scope of the image pixels (e.g. resolution, number of focal planes, number of time points, number of channels) - the hardware configuration used to acquire the image planes (e.g. microscope, detectors, lenses, filters) - the settings used with said hardware (e.g. physical size of the image planes in microns, laser gain and offset, channel configuration) - the person performing the experiment - some details regarding the experiment itself, such as a description, the type of experiment (e.g. FRET, time lapse, fluorescence lifetime) and events occurring during acquisition (e.g. laser ablation, stage motion) - additional custom information you may wish to provide about your experiment in a structured form (known as :doc:`/developers/structured-annotations`) Features and applications ------------------------- The OME-XML file serves as a convenient file format for data migration from one site or user to another. The OME-XML file captures all image acquisition and experimental metadata, along with the binary image data, and packages it into an easily readable package. The `paper `_ describing the design and implementation of the OME-XML file appeared in Genome Biology. .. note:: OME-XML files can be read by potentially any software package - you do not need OME image management software to use OME-XML. Some specific features of the OME-XML file format: - OME-XML files may contain one or more sets of 5-D pixels, for example raw data from a microscope, the deconvolved data, and a volume rendered view. - OME-XML files contain all the metadata associated with an image, including the experimental (e.g. cells, genes) and acquisition (e.g. microscope light sources, filters, detectors) metadata. - OME-XML Image pixels may be stored compressed directly in XML with base64 encoding. Compression of the pixels and the metadata is supported through widely-available patent-free compression schemes (gzip and bzip2). OME-XML Images are addressable by plane. - OME-XML files have a built-in mechanism for supporting arbitrary user-defined data that can be used globally or attached to Images, Features (objects inside Images), and Datasets. Mechanisms for OME-compliant systems to populate databases with these user-defined fields is part of the specification. See the :doc:`/developers/structured-annotations` XML Schema section. The OME-XML Schema .xsd files and technical documentation are available on the :schema:`Schema pages <>`.