The OME-TIFF File

In the OME-XML File binary image data is stored as compressed base64 (more info). This is convenient for data migration, but causes a performance penalty when used for data acquisition or visualization:

• Image planes are encoded separately, but without byte offsets stored in any sort of table of contents or linked list structure. As such, individual planes cannot be easily extracted until the entire file has been read.
• The entire dataset is stored within a single file. This is both a strength and a weakness: it is more difficult for part of the dataset to become lost, but reading such a large file requires significant overhead.

OME partners at LOCI have developed a variant of the OME-XML File specifically designed for data acquisition and storage. This format, called OME-TIFF, uses OME-XML in the standard TIFF header and stores binary image data in a multi-page TIFF file. This means that:

• Image planes are stored within one multi-page TIFF file, or across multiple TIFF files. Any image organization is feasible.
• A complete OME-XML metadata block describing the image is embedded in each TIFF file's header. Thus, even if some of the TIFF files in a 5-dimensional image are misplaced, the metadata remains intact.
• The OME-XML metadata block in an OME-TIFF file may contain anything a standard OME-XML file can, including multiple OME images with multiple sets of pixels.
• The only conceptual difference between OME-XML and OME-TIFF is that instead of encoding pixels as base64 chunks within the XML like OME-XML does, OME-TIFF uses the standard TIFF mechanism for storing one or more image planes in each of the constituent file(s).
• Storing image data in TIFF is a de facto standard, and essentially all image handling software can read TIFF-based formats, thus adoption and integration of OME-TIFF is straightforward.

LOCI maintains the OME-TIFF Overview and Specification. Thanks to Kevin Eliceiri and Curtis Rueden and the LOCI gang for all their hard work on OME-TIFF.