Compliant HCS specification

OME compliant HCS file specification. This was developed in conjunction with the June 2010 release of the OME-XML Model and has been updated to the June 2016 release.

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 a file should contain to be useful while conforming to the spirit of the OME projects aims.

This sample structure is based on Sample One in the OME Compliant File Specification (see Compliant file specification):

<?xml version="1.0" encoding="UTF-8"?>
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06"
     xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
     xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06
                         http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">

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

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

  <!-- Screen is not required -->

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

Alternative valid forms:

• would have a TiffData block instead of the BinData block (this would be used in the header of an OME-TIFF file)
• would have a MetadataOnly block instead of the BinData block (this would be used as a companion to one or more BinaryOnly OME-TIFF files)

Note

A units system was added in January 2015. This sample assumes the default unit for each value is used.