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OME-XML & OME-TIFF

Show or hide the answer What is OME-XML and how does it relate to OME-TIFF?

OME-XML captures all image acquisition and experimental metadata along with the binary image data and packages it into an easily readable structure. See the OME-XML FAQ entry for details.

OME-TIFF stores binary image data in standard multi-page TIFF files, while using OME-XML in the header to preserve rich metadata. See the OME-TIFF for details.

For more technical information about OME-XML and OME-TIFF, see the File Formats.

Show or hide the answer Why TIFF? What about other container formats?

The one word answer is: compatibility. TIFF files are readable in a large number of existing software tools, and when coupled with OME-XML also flexible enough to accommodate the needs of the microscopy imaging community.

That said, OME-TIFF is merely one example of an alternate pixels container for OME-XML metadata; others are certainly possible. If you do not like TIFF for some reason, you can use the OME-XML format directly, or utilize a different container format. However, we urge you to consider using the OME-XML standard for metadata, rather than creating yet another incompatible metadata representation.

Show or hide the answer What file extension should I use when saving OME files?

We would recommend:

OME-XML file: filename.ome.xml

OME-TIFF file: filename.ome.tif

Show or hide the answer How can I check the validity of an OME-XML or OME-TIFF file?

We provide an online validator.

This will provide a basic indication of the validity of the file structure. It does not guarantee that the data written in the file structure is correct. The validator also only looks at one file at a time so multi-part OME-TIFF files will show as not being complete. At present it cannot analyse across the multi-part files.

It should be noted that Bio-Formats will still be able to read some files that the validator marks as invalid as it concentrates on reading what data it can, not validation.

You can also browse the source code for the validator which includes a script to run it from the command line.

Alternately, you can validate your file on the command line using Bio-Formats.

Show or hide the answer What does the online validator check?

The validator does the following steps:

  1. If OME-TIFF extract the OME-XML from the header.
  2. Examines the OME-XML block and determines the correct schema.
  3. Validates the OME-XML against that schema reporting any errors, and then checks with the other older/newer schemas too but just "for info".
  4. Scans the OME-XML and records all object IDs.
  5. Scans the OME-XML and checks all Refs and Settings objects point to an ID that is present in the file.
  6. If OME-TIFF examined the TiffData nodes and calculates the number of TIFF frames needed to make the file complete, then check the TIFF structure to see if there are enough frames present in the file. If not the file is still valid but incomplete (normally part of a multi-file OME-TIFF). Groups of files cannot be checked together yet.

This all is just checking the structure of the data. No attempt is made to make sure the data values make sense.

Show or hide the answer Why is my LSID being marked as invalid and not accepted?

The LSID specification defines the first three portions as case-insensitive, that is "URN:LSID:(Authority)". The remaining portion is case-sensitive. In OME-XML however we assume lower case for the first two portions "urn:lsid:", for "(Authority)", normally a domain name, any case is acceptable but lower case is recommended for consistency. The remaining portion is case-sensitive.

For full information on our use of LSID in OME-XML see: IDs and LSIDs in OME-XML

Show or hide the answer How do I validate a file on the command line?

First, download and install the Bio-Formats command line tools.

A full tutorial can be found here. In brief, you download and unzip the tools to produce a collection of command line scripts for Unix/Mac and batch files for Windows. The two commands we will use are xmlvalid and tiffcomment.

  • xmlvalid – a command-line XML validation tool
  • tiffcomment – extracts the OME-XML block in an OME-TIFF file from the comment in the TIFF's first IFD entry.

All scripts require loci_tools.jar is downloaded to the same directory as the command line tools.

Then to validate an OME-XML file sample.ome use: 

xmlvalid sample.ome

This validates the XML directly.

Then to validate an OME-TIFF file sample.ome.tif use: 

tiffcomment sample.ome.tif | xmlvalid

This extracts the OME-XML from the TIFF then passed it to the validator.

Typical successful output is: 

[~/Work/bftools]$ ./xmlvalid sample.ome
Parsing schema path
http://www.openmicroscopy.org/Schemas/OME/2010-06/ome.xsd
Validating sample.ome
No validation errors found.
[~/Work/bftools]$

If any errors are found they are reported. When correcting errors it is usually best to work from the top of the file as errors higher up can cause extra errors further down. In this example the output shows 3 errors but there are only 2 mistakes in the file. 

[~/Work/bftools]$ ./xmlvalid broken.ome
Parsing schema path
http://www.openmicroscopy.org/Schemas/OME/2010-06/ome.xsd
Validating broken.ome
cvc-complex-type.4: Attribute 'SizeY' must appear on element 'Pixels'.
cvc-enumeration-valid: Value 'Non Zero' is not facet-valid with respect 
   to enumeration '[EvenOdd, NonZero]'. It must be a value from the enumeration.
cvc-attribute.3: The value 'Non Zero' of attribute 'FillRule' on element 
   'ROI:Shape' is not valid with respect to its type, 'null'.
Error validating document: 3 errors found
[~/Work/bftools]$
Show or hide the answer Which version of the OME-XML schema is used by XXX?

OMERO

  • The Beta4.3.x (June 2011) version is using the 2011-06 OME-XML schema
  • The Beta4.2.x (July 2010) version is using the 2010-06 OME-XML schema
  • The Beta4.1.x (December 2009) version is using the 2008-09 OME-XML schema
  • The Beta4.0.x (March 2009) version is using the 2008-09 OME-XML schema
  • The Beta3.x (June 08-November 2008) version is using the 2008-09 OME-XML schema


OME-Perl server
The OME server is using the 2003 OME-XML schema

Show or hide the answer How often are new schema versions released?

About one to two time a year for Major releases. It is driven by users' requests for model changes.

The schema has two kind of releases Major and Minor. A major release happens once or twice a year, normally about February and September. These are key advances and add new functionality. Minor releases are bug fix releases and one or two may happen between Major releases.

The releases are now in sync with releases of OMERO and Bio-Formats.

For more information of the versioning of the releases see

Version Information

Show or hide the answer Some metadata is missing from your schema. What can I do?

Your first step is to suggest it on the forums or mailing list by sending us your use case.

This allows others to provide input to ensure the metadata is added in the most appropriate location so it can work in all cases. From there it will progress to a ticket on the Trac and after research to find the most general name for the term it can get rolled into the next schema release.

In the short term it is also possible to use StructuredAnnotations to store the value into the existing schema.

Show or hide the answer How can you represent binary image data in XML using plain text?

Binary data is represented in XML using Base64 encoding See RFC 1341 Section 5.2. Binary data is a string of numbers in base 2 represented by a series of bits (binary digits). These same numbers can be represented in base 64 using a series of base 64 digits. The convention for representing base 64 digits is to use the upper and lower case letters (52 digits), the numbers (+10 digits), and two punctuation characters '+' and '/' (total = 64).

Since each byte can represent a value from 0 to 255, we would need two base 64 digits to represent it. If we did that, we would need twice the storage to convert binary into plain text. Instead we can convert 3 bytes at a time into 4-digit base 64 numbers. This makes the plain-text representation of binary data "only" 1/3 larger.

Show or hide the answer Which TIFF IFD fields are required in OME-TIFF?

The only requirement is that the ImageDescription directory entry must be present in the first IFD, and populated with a valid OME-XML metadata block.

Otherwise, OME-TIFF files do not need any IFD fields beyond what would be required for a regular TIFF. Please see the TIFF specification for a list of IFD fields required for regular TIFFs.

Show or hide the answer What are the minimum requirements for creating an OME-TIFF file?

An OME-TIFF file is in essence a standard TIFF file with an OME-XML metadata block stored inside it. See the OME-TIFF specification for details.

The minimum OME-XML metadata block would conform to the OME-XML minimum specification.

Show or hide the answer Where can I get some sample data files?

We have a small collection of sample files available that are designed to demonstrate the format.

General simple samples are available from:
http://trac.openmicroscopy.org.uk/ome/browser/ome.git/components/specification/Samples

Also: OME-TIFF samples are available

Show or hide the answer What support is there for BigTIFF?

The Bio-Formats library and command line tools can work with BigTIFF files.

OMERO.importer has support for the format as it is using the Bio-Formats library but you should be aware that when working with very large files you may hit other limitations on image size related to the import and rendering support in the OMERO server.

The addition of the 'Big Image' support into OMERO in v4.2 has removed most, but not all, of these restrictions.

Show or hide the answer Does OMERO Support FLIM files and FLIM analysis?

OMERO currently supports the uploading and viewing of some FLIM files, specifically ICS, and STD file formats. Currently the OME-XML model does not support N-Dimensional Data as required by FLIM, so viewing FLIM data that has extra-dimensions such as phase, frequency and time will not be viewed correctly in insight, nor stored or retrieved correctly from OMERO.

We are actively working on adding FLIM to the OME Data Model, Bio-Formats, and OMERO. We have a Trac page which contains our progress so far in adding N-Dimensional data to OMERO.

There is also a detailed discussion on the mailing list.

We have announced our 6D and 7D solution which should provide a stop gap solution for some FLIM data until we can move to full N-Dimensional Data support.

Show or hide the answer Do you have any support for HDF (Hierarchical Data Format)?

While we have looked at HDF and would be interested to talk to anyone who wants to develop a general HDF solution for storing images and metadata, but we do not at present have an OME format.

Bio-Formats does support some proprietary formats that use HDF and we do make some use of HDF internally in our software.

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