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The OME-TIFF format

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OME-TIFF file structure

The following section discusses various considerations when designing OME-TIFF filesets distributed over multiple files.

Single versus multiple files

Splitting a fileset across multiple files can have advantages in terms of acquisition but also processing purposes. The OME-TIFF file format can support any image organization. However, using one TIFF file per timepoint per channel with the focal planes for that timepoint and channel stored sequentially within the TIFF makes for very easy creation of TiffData elements (see Tubhiswt).

The main downside of splitting OME-TIFF over multiple files is their inherent fragility to common file-system operations such as file renaming or file copying which have the potential to “break” the fileset.

See OME-TIFF sample data for examples of single OME-TIFF file versus OME-TIFF distributed over multiple files.

File size

The TIFF file format internally uses 32-bit byte offsets. The largest offset which can be represented is 4GB, making this value the upper limit of the file size supported by the design.

The OME-TIFF file format supports the BigTIFF file extensions allowing the use of 64-bit byte offsets to overcome this size limit.

The main limitation of the BigTIFF file extension is the degree of its adoption in the community. Although OME Bio-Formats and OMERO will handle OME-TIFF using the BigTIFF file extension, other tools might not be able to open it.

Metadata redundancy

Storing multiple planes per OME-TIFF file and keeping the OME-XML metadata embedded in every file header is recommended (see the Tubhiswt) but is not always practical. Normally, the OME-XML metadata block is small in comparison with the binary pixel data in the file, but in some cases, it may be disproportionately larger.

Common reasons for this situation include:

  • storing each image plane in its own TIFF file
  • having a large amount of metadata such as plane-specific timestamps
  • having many structured annotations in the OME-XML.

For example, if you have a dataset with 1,000 time points, with each plane recorded at 512 × 512 as uint8 pixel type, storing each plane in its own file uncompressed requires ~256KB of disk per file, and ~256MB total. But if you have 5MB of corresponding OME-XML metadata, embedding a copy of that metadata in every file would result in a dataset nearly 20 times larger than before, requiring ~5.5MB of disk per file, and more than 5GB total.

One of the advantages of reproducing the OME-XML metadata across files is redundancy. If one of the constituent files survives data loss, the metadata survives. The space tradeoff of this duplication is acceptable when compared to the bulk of the pixel data in most cases, provided a suitable number of planes are stored in each TIFF.

Companion file vs master OME-TIFF file

Since the 2011-06 version of the OME-XML schema, it is possible to store partial OME-XML metadata blocks in some or all of the TIFF files pointing to a master file containing the full OME-XML metadata (see the technical specification for more details).

The master file can be either a master OME-TIFF file or a companion OME-XML file (see the Multi-file OME-TIFF filesets).

Using a companion OME-XML file allows information that can only be generated at the end of the acquisition to be easily appended without the need to manipulate existing TIFF IFDs. It has the same drawbacks as those highlighted above in the sense that this companion file needs to be preserved as part of the fileset to prevent metadata loss.

See also

Proposed tweak to µManager data files in 2.0
Community discussion about usage of companion file in OME-TIFF filesets