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OME-XML Comments On Release

Release 1 - 5th June 2007

Corrections

Secondary Emission Filter & Secondary Excitation Filter

In LogicalChannel both should be of type FilterID and Emission is spelt incorrectly.

Old 

<xsd:attribute name="SecondaryEmmisionFilter" type=" EmFilterID "/>
<xsd:attribute name="SecondaryExcitationFilter" type=" ExFilterID "/>

New 

<xsd:attribute name="SecondaryEmissionFilter" type=" FilterID "/>
<xsd:attribute name="SecondaryExcitationFilter" type=" FilterID "/>

by Andrew & Curtis

Fix Spelling Mistakes

  • SecondaryEmmisionFilter -> SecondaryEmissionFilter
  • Zstart -> ZStart
  • Zstop -> ZStop
  • Tstart -> TStart
  • Tstop -> TStop
  • OpticalAxisAvrg -> OpticalAxisAveraged
  • Tunable -> Tuneable
  • Repetitation Rate -> RepetitionRate
  • Amplification-Gain -> AmplificationGain

by Andrew & Chris & Curtis

Correct Copyright

Add "University of Wisconsin at Madison" to the list of copyright holders. by Andrew & Kevin & Jason

Correct Filter in instrument

Old 

<xsd:element name="Instrument">
...
		<xsd:sequence>
			<xsd:element ref="Microscope"/>
			<xsd:element ref="LightSource" maxOccurs="unbounded"/>
			<xsd:element ref="Detector" maxOccurs="unbounded"/>
			<xsd:element ref="Objective" maxOccurs="unbounded"/>
			<xsd:element ref="Filter" maxOccurs="unbounded"/>
			<xsd:element ref="OTF" maxOccurs="unbounded"/>
		</xsd:sequence>
...
</xsd:element>

New 

<xsd:element name="Instrument">
...
		<xsd:sequence>
			<xsd:element ref="Microscope"/>
			<xsd:element ref="LightSource" maxOccurs="unbounded"/>
			<xsd:element ref="Detector" maxOccurs="unbounded"/>
			<xsd:element ref="Objective" maxOccurs="unbounded"/>
			<xsd:element ref="FilterSet" minOccurs="0" maxOccurs="unbounded"/>
			<xsd:element ref="OTF" maxOccurs="unbounded"/>
		</xsd:sequence>
...
</xsd:element>

Proposed Changes

Change to the regex used for IDs

The current regex is a little lax and with some help from Chris I have come up with a new format. It is longer and does require the ID name to occur twice which is a little ugly but this seams to be unavoidable if they are to work as either LSIDs or internal ids.

Old - for Project 

    (urn:lsid:)?(\S+\.\S+)+(:Project)(:\S+)

New - for Project 

    ~np~(urn:lsid:([\w-\.]+\.[\w-\.]+)+:Project:\S+)|(Project:\S+)~/np~

Valid - Old 

urn:lsid:ome.wibble:Project:1123
a.b:Project:c
uurn:lsid:a.b:Project:c
urn:lsid:a.ww12312541___---ww.d.d.b:Project:c
rn:lsid:a.b:Project:c
urn:lid:a.b:Project:c
urn:lsid:ome.wi~%#bble:Project:1123
~np~^.^:Project:1234~/np~
...:Project:1234

Invalid - Old 

urn:lsid:omewibble:Project:1123
Project:1234

Valid - New 

urn:lsid:ome.wibble:Project:1123
urn:lsid:a.ww12312541___---ww.d.d.b:Project:c
Project:1234

Invalid - New 

a.b:Project:c
uurn:lsid:a.b:Project:c
rn:lsid:a.b:Project:c
urn:lid:a.b:Project:c
urn:lsid:ome.wi~%#bble:Project:1123
~np~^.^:Project:1234~/np~
...:Project:1234
urn:lsid:omewibble:Project:1123

This enforces two forms, the LSID form of urn:lsid:[domain-name]:Project:[uniqueID] and a shorter form to be used for internal only references Project:[uniqueID]. The uniqueID can be any non-whitespace characters. The regex parser in XSD is slightly non standard and assumes that the pattern is always meant to start at the beginning of the line and finish at the end of the line, this means that ^ and $ are not necessary. The domain-name is any standard character (including unicode) with dash and dot. It must contain at least one dot. by Andrew

Correct capitalisation of PixelType enumeration

Old 

    <xsd:attribute name="PixelType" use="required">
        <xsd:simpleType>
            <xsd:restriction base="PixelTypes">
                <xsd:enumeration value = "int8"/>
                <xsd:enumeration value = "int16"/>
                <xsd:enumeration value = "int32"/>
                <xsd:enumeration value = "Uint8"/>
                <xsd:enumeration value = "Uint16"/>
                <xsd:enumeration value = "Uint32"/>
                <xsd:enumeration value = "float"/>
            </xsd:restriction>
        </xsd:simpleType>

New 

    <xsd:attribute name="PixelType" use="required">
        <xsd:simpleType>
            <xsd:restriction base="PixelTypes">
                <xsd:enumeration value = "int8"/>
                <xsd:enumeration value = "int16"/>
                <xsd:enumeration value = "int32"/>
                <xsd:enumeration value = "uint8"/>
                <xsd:enumeration value = "uint16"/>
                <xsd:enumeration value = "uint32"/>
                <xsd:enumeration value = "float"/>
            </xsd:restriction>
        </xsd:simpleType>

by Chris

Add TiffData block

Add support for OME-XML TIFF information

Old 

    <xsd:element name="Pixels">
...
        <xsd:complexType>
            <xsd:sequence>
                <xsd:element ref="Bin:BinData" maxOccurs="unbounded"/>
                <xsd:element ref="Plane" minOccurs="0" maxOccurs="unbounded"/>
            </xsd:sequence>
...
        </xsd:complexType>
    </xsd:element>

New 

    <xsd:element name="Pixels">
...
        <xsd:complexType>
            <xsd:sequence>
                <xsd:choice maxOccurs="unbounded">
                    <xsd:element ref="Bin:BinData"/>
                    <xsd:element ref="TiffData"/>
                </xsd:choice>
                <xsd:element ref="Plane" minOccurs="0" maxOccurs="unbounded"/>
            </xsd:sequence>
...
        </xsd:complexType>
    </xsd:element>
...
    <xsd:element name="TiffData">
        <xsd:annotation>
            <xsd:documentation>
            </xsd:documentation>
        </xsd:annotation>
        <xsd:complexType>
            <xsd:attribute name="IFD" type="xsd:integer" default="0">
                <xsd:annotation>
                    <xsd:documentation>
                        Gives the IFD(s) for which this element is applicable. Indexed from 0. 
                        Default is 0 (the first IFD).
                    </xsd:documentation>
                </xsd:annotation>
            </xsd:attribute>
            <xsd:attribute name="FirstZ" type="xsd:integer" default="0">
                <xsd:annotation>
                    <xsd:documentation>
                        Gives the Z position of the image plane at the specified IFD. Indexed from 0. 
                        Default is 0 (the first Z position).
                    </xsd:documentation>
                </xsd:annotation>
            </xsd:attribute>
            <xsd:attribute name="FirstT" type="xsd:integer" default="0">
                <xsd:annotation>
                    <xsd:documentation>
                        Gives the T position of the image plane at the specified IFD. Indexed from 0.
                        Default is 0 (the first T position).
                    </xsd:documentation>
                </xsd:annotation>
            </xsd:attribute>
            <xsd:attribute name="FirstC" type="xsd:integer" default="0">
                <xsd:annotation>
                    <xsd:documentation>
                        Gives the C position of the image plane at the specified IFD. Indexed from 0. 
                        Default is 0 (the first C position).
                    </xsd:documentation>
                </xsd:annotation>
            </xsd:attribute>
            <xsd:attribute name="NumPlanes" type="xsd:integer">
                <xsd:annotation>
                    <xsd:documentation>
                        Gives the number of IFDs affected. Dimension order of IFDs is given by the enclosing
                        Pixels element's DimensionOrder attribute. Default is the number of IFDs in the TIFF
                        file, unless an IFD is specified, in which case the default is 1.
                    </xsd:documentation>
                </xsd:annotation>
            </xsd:attribute>
        </xsd:complexType>
    </xsd:element>

by Andrew

Other Information

Minimum OME-XML file specification

 <?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:/Users/andrew/Work/SVN/OME/src/xml/workingcopy/ome.xsd">
     <ome:Image ID="Image:a" Name="Name92" DefaultPixels="Pixels:b">
         <ome:CreationDate>2006-05-04T18:13:51.0Z</ome:CreationDate>
         <ome:Pixels ID="Pixels:a" 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>

This is the updated version that matches the new regex. by Andrew

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