[ome-devel] The minimum 'requirements' for creating an OME-TIFF file, XML tag styles, and master list of OME-XML tags

[Andrew Patterson]

Hello Nick,

> I'm wondering what the specifications are for a bare minimum OME- 
> TIFF file. I initially found a page specifying the minimum  
> requirements for an OME-XML file (http://www.ome-xml.org/wiki/MinimumSpecification 
> )

Yes this is the minimum specification for the latest schema. As noted  
on the bottom of the page if you change the bf:BinData node to a  
TiffData node this will be a minimum specification for the XML block  
in a OME-TIFF file.

> but this is missing some of the tags found in the OME-TIFF  
> specification page (http://www.loci.wisc.edu/ome/ome-tiff-spec.html)  
> including the <TiffData /> tag.

These tags are optional so are not needed in a minimum specification.

>
> Also, is there somewhere I can find a 'master list' of all the tags  
> the OME-TIFF file format supports? I found what seems like a likely  
> candidate for what I want (http://www.openmicroscopy.org/site/support/legacy/ome-server/developer/xml-schemata 
> ) but it's really confusing and I'm not sure if one of those lists  
> contains all the elements of all the others (ie, my master list).

As noted on this page it is legacy information for working with the  
original OME server.

For the current schema look in the standard schema location:
http://www.openmicroscopy.org/Schemas/

This has a link to the current schema files and also some auto- 
generated documentation you may find useful.

> Lastly, as far as OMERO and bioformats is concerned, are </ome:OME>  
> and </OME> the same? The first is from http://www.ome-xml.org/wiki/MinimumSpecification 
> , while the second is from http://www.loci.wisc.edu/ome/ome-tiff-spec.html 
> . Would both styles of XML validate with the bioformats command line  
> tool, and would both successfully read into OMERO (meaning, would  
> files using either XML tag style both work)?


The characters before the colon in the node name are called the prefix  
and are used to specify the namespace the node belongs to. They are  
used to avoid naming clashes. XML has two main ways of locating the  
namespace of a node.
By default it will use the namespace of it's parent node to look for  
all child nodes without a prefix. If the child is in a different  
namespace it can either use a prefix or have it own xmlns Attribute.

In the top level node there is no parent so the xmlns Attribute must  
be specified. This is the case with our OME node.

All the following forms are valid:

<OME
  xmlns="http://www.openmicroscopy.org/Schemas/OME/2008-09"
  ...
 >

<OME:OME
  xmlns:OME="http://www.openmicroscopy.org/Schemas/OME/2008-09"
  ...
 >

<someNamespace:OME
  xmlns:someNamespace="http://www.openmicroscopy.org/Schemas/OME/ 
2008-09"
  ...
 >

The namespaces are normally handled automatically by your XML parsing  
library.

For more information see:
http://www.w3schools.com/XML/xml_namespaces.asp

Hope this helps,

Andrew

--
Andrew Patterson
ajpatterson at lifesci.dundee.ac.uk
Software Developer, Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression, University  
of Dundee