[ome-users] Questions about OME-XML and Java OME-XML library

[Andrew Patterson]

Hello Aaron,

I can provide you with some of the answers.

Most of the information can be encompassed in the current model.  
Where you will need to add additional information it can be placed  
inside the CA:CustomAttribute elements. These elements with content  
type <Any> can be attached to Datasets, Images, Regions, and to the  
topl level OME element. You can if you wish define you own version of  
the CA.XSD file with extra objects in the CustomAttribute block that  
means that files with your additions can be validated. If you do not  
wish to or your files are validated by someone un-aware for your  
additions then anything in the CustomAttribute will be accepted as  
valid provided it is well formed XML.

Where you may have a problem is at the moment an Image requires  
Pixels, which requires at lease one BinData or TiffData element. I  
guess you would have a filename/filesize at this point.

Now your questions:
[1] - Only the minimum specification has been defined and it is in  
draft. And this is the bare minimum required to display an Image.

The draft version is:

<?xml version="1.0" encoding="UTF-8"?>
<ome:OME xmlns:bf="http://www.openmicroscopy.org/XMLschemas/ 
BinaryFile/2007-06"
  xmlns:ome="http://www.openmicroscopy.org/XMLschemas/OME/2007-06"
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xsi:schemaLocation="http://www.openmicroscopy.org/XMLschemas/OME/ 
2007-06 file:ome.xsd">
     <ome:Image ID="Image:1" Name="Name92" DefaultPixels="Pixels:1">
         <ome:CreationDate>2006-05-04T18:13:51.0Z</ome:CreationDate>
         <ome:Pixels
              ID="Pixels:1"
              DimensionOrder="XYZCT"
              PixelType="int8"
              BigEndian="false"
              SizeX="2"
              SizeY="2"
              SizeZ="2"
              SizeC="2"
              SizeT="2">
             <bf:BinData Compression="none" Length="12">ZGVmYXVsdA==</ 
bf:BinData>
          </ome:Pixels>
     </ome:Image>
</ome:OME>
Note: the xsi:schemaLocation line is not finalised and the data in  
this sample is nonsense.

[2], [3] - Cannot help but the idea is that the levels are not rigid  
shapes your file must have. They are targets you file can reach for.  
If your file is level X then it will have everything needed to hit  
this level but may also contain more.

[4] - Yes these have been used in the past and are currently, I  
believe, used internally as part of BioFormats to convert between two  
OME-XML file shapes to make the import process more efficient. I  
would hope it would not be too onerous a task to convert other XML  
files to the OME-XML format using XSLT. You may need some additional  
pre/post processing to tie up internal file references.

Hope this helps,

Andrew




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