Compliant HCS Specification

A compliant specification for HCS OME files has been defined. This is not the minimum required for the display of an image, that is the Minimum Specification. This is the information we feel a file should contain to provide a useful file conforming to the spirit of the OME projects aims.

A sample of the structure. This is based on Sample One in the OME Compliant File Specification (see Compliant Specification).

<?xml version="1.0" encoding="UTF-8"?>
<OME:OME xmlns:ROI="http://www.openmicroscopy.org/Schemas/ROI/2010-06"
    xmlns:OME="http://www.openmicroscopy.org/Schemas/OME/2010-06"
    xmlns:BIN="http://www.openmicroscopy.org/Schemas/BinaryFile/2010-06"
    xmlns:SPW="http://www.openmicroscopy.org/Schemas/SPW/2010-06"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2010-06 
    http://www.openmicroscopy.org/Schemas/OME/2010-06/ome.xsd">     

<SPW:Plate 
        ID="Plate:1" 
        Name="Control Plate" 
        ColumnNamingConvention="letter" 
        RowNamingConvention="number" 
        Columns="12" 
        Rows="8"
        >
        <SPW:Description></SPW:Description>

        <!-- repeat SPW:Well for # of wells in the plate that contain images -->
        <SPW:Well ID="Well:1" Column="0" Row="0">
            <!-- repeat SPW:WellSample for # of images taken in the well -->
            <SPW:WellSample ID="WellSample:1" Index="0">
                <!-- 
                    if there is an image associated with this SPW:WellSample
                    it is linked using an SPW:ImageRef
                -->
                <SPW:ImageRef ID="Image:0"/>
            </SPW:WellSample>
        </SPW:Well>
    </SPW:Plate>
    <!-- plus one more Plate for each Plate in this set -->

    <!-- SPW:Screen is not required -->

    <!-- The OME:Image element follows the structure for the OME Compliant File Specification -->
    <OME:Image ID="Image:0" Name="Series 1">
        <OME:AcquiredDate>2008-02-06T13:43:19</OME:AcquiredDate>
        <OME:Description>An example OME compliant file, based on Olympus.oib</OME:Description>
        <OME:Pixels DimensionOrder="XYCZT" ID="Pixels:0" 
                    PhysicalSizeX="0.207" PhysicalSizeY="0.207" PhysicalSizeZ="0.0" 
                    SizeC="3" SizeT="16" SizeX="1024" SizeY="1024" SizeZ="1"
            TimeIncrement="120.1302" Type="uint16">
            <OME:Channel EmissionWavelength="523" ExcitationWavelength="488" ID="Channel:0:0"
                IlluminationType="Epifluorescence" Name="CH1" SamplesPerPixel="1"
                PinholeSize="103.5" AcquisitionMode="LaserScanningConfocalMicroscopy"/>
            <OME:Channel EmissionWavelength="578" ExcitationWavelength="561" ID="Channel:0:1"
                IlluminationType="Epifluorescence" Name="CH3" SamplesPerPixel="1"
                PinholeSize="127.24" AcquisitionMode="LaserScanningConfocalMicroscopy"/>
            <OME:Channel ExcitationWavelength="488" ID="Channel:0:2" 
                IlluminationType="Transmitted"
                ContrastMethod="DIC" Name="TD1" SamplesPerPixel="1"  
                AcquisitionMode="LaserScanningConfocalMicroscopy"/>
            <BIN:BinData BigEndian="false" Length="0"/>
        </OME:Pixels>
    </OME:Image>
</OME:OME>

The data in this sample is nonsense.

An alternative valid forms:

• Would have a ome:TiffData block instead of the bf:BinData block. This would be used in the header of an OME-TIFF file.
• Would have a ome:MetadataOnly block instead of the bf:BinData block. This would ONLY be acceptable if the image data of the file CANNOT, for technical reasons, be represented in an OME file.