OME-XML - Open Microscopy Environment XML

OME-XML is a vendor-neutral file format for biological image data, with an emphasis on metadata supporting light microscopy. It can be used as a data file format in its own right, or as a way of encoding metadata within a TIFF or BigTIFF file (for which purpose there is the OME-TIFF specification).

The standard is maintained by the Open Microscopy Environment Consortium, and was last updated in June 2012.

Extensions

OME-TIFF - Open Microscopy Environment TIFF

A specification of how to embed OME-XML metadata within a TIFF or BigTIFF image file.

Tools

Bio-Formats

Bio-Formats reads proprietary microscopy image data and metadata, and converts them to OME-TIFF, a combination of TIFF and OME-XML.

Fiji

Fiji is an image processing package that supports the OME data model for images

OMERO

Repository software for organising, viewing, analysing and sharing biological microscopy images. It supports proprietary file formats but normalises to OME-TIFF/OME-XML.

Use Cases

JCB Data Viewer

A repository for viewing and analysing multi-dimensional image data associated with articles published in The Journal of Cell Biology. Its native metadata format is OME-XML.

The Cell: An Image Library

A resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. Its native metadata format for images is OME-XML.