Hi <div>I am still struggling with the import of Andor tif files as a screen. I have been reading up on the OME specifications for screens and have created am OME-XML header file that passes validation:</div><div><br></div>
<div><br></div><div><div><?xml version="1.0" encoding="UTF-8"?></div><div><OME xmlns="<a href="http://www.openmicroscopy.org/Schemas/OME/2011-06">http://www.openmicroscopy.org/Schemas/OME/2011-06</a>" xmlns:xsi="<a href="http://www.w3.org/2001/XMLSchema-instance">http://www.w3.org/2001/XMLSchema-instance</a>" xmlns:ROI="<a href="http://www.openmicroscopy.org/Schemas/ROI/2011-06">http://www.openmicroscopy.org/Schemas/ROI/2011-06</a>" xmlns:SA="<a href="http://www.openmicroscopy.org/Schemas/SA/2011-06">http://www.openmicroscopy.org/Schemas/SA/2011-06</a>" xmlns:SPW="<a href="http://www.openmicroscopy.org/Schemas/SPW/2011-06">http://www.openmicroscopy.org/Schemas/SPW/2011-06</a>" xmlns:Bin="<a href="http://www.openmicroscopy.org/Schemas/BinaryFile/2011-06">http://www.openmicroscopy.org/Schemas/BinaryFile/2011-06</a>" xsi:schemaLocation="<a href="http://www.openmicroscopy.org/Schemas/OME/2011-06">http://www.openmicroscopy.org/Schemas/OME/2011-06</a> <a href="http://www.openmicroscopy.org/Schemas/OME/2011-06/ome.xsd">http://www.openmicroscopy.org/Schemas/OME/2011-06/ome.xsd</a>" UUID="urn:uuid:0895d30c-6c56-11e1-8ce6-0021e9fffeca"></div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span><SPW:Plate ID="Plate:0"></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><SPW:Description>Plate 1 description.</SPW:Description></div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span><SPW:ScreenRef ID="Screen:1"/></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><SPW:Well ID="Well:1.1.1" Column="1" Row="1"></div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span><SPW:WellSample ID="WellSample:1.1.1.1" Index="1"></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><SPW:ImageRef ID="Image:0"/></div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span></SPW:WellSample></div><div><span class="Apple-tab-span" style="white-space:pre"> </span></SPW:Well></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><SPW:PlateAcquisition xmlns="<a href="http://www.openmicroscopy.org/Schemas/SPW/2010-06">http://www.openmicroscopy.org/Schemas/SPW/2010-06</a>" ID="PlateAcquisition:Plate:1:ScreenAcquisition:1" StartTime="2010-02-23T12:49:30" EndTime="2010-02-23T12:50:30"></div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span><SPW:WellSampleRef ID="WellSample:1.1.1.1"/></div><div><span class="Apple-tab-span" style="white-space:pre"> </span></SPW:PlateAcquisition></div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span></SPW:Plate></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><SPW:Screen ID="Screen:102" ProtocolDescription="" ProtocolIdentifier="" ReagentSetDescription="" ReagentSetIdentifier="" Name="new004" Type=""></div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span><SPW:Description/></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><SPW:PlateRef ID="Plate:0"/></div><div><span class="Apple-tab-span" style="white-space:pre"> </span></SPW:Screen></div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span><Image ID="Image:0" Name="9 images screen test _take1_Field001.tif"></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><AcquiredDate>2010-02-23T12:51:30</AcquiredDate></div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span><Pixels DimensionOrder="XYZCT" ID="Pixels:2:0" SizeX="512" SizeY="512" PhysicalSizeX="0.4" PhysicalSizeY="0.4" PhysicalSizeZ="1.0" Type="uint16" SizeC="2" SizeT="1" SizeZ="1" TimeIncrement="1.0"></div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span><Channel Color="-16776961" ID="urn:lsid:export.openmicroscopy.org:Channel:f25a632d-6bdd-4dd4-a07f-1d2c3dc129a2_90451:265926" SamplesPerPixel="1"></div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span><LightPath/></div><div><span class="Apple-tab-span" style="white-space:pre"> </span></Channel></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><Channel Color="16711935" ID="urn:lsid:export.openmicroscopy.org:Channel:f25a632d-6bdd-4dd4-a07f-1d2c3dc129a2_90452:265926" SamplesPerPixel="1"></div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span><LightPath/></div><div><span class="Apple-tab-span" style="white-space:pre"> </span></Channel></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"></div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span><UUID FileName="__omero_export__356461883636658620.ome.tiff">urn:uuid:0895d30c-6c56-11e1-8ce6-0021e9fffeca</UUID></div><div><span class="Apple-tab-span" style="white-space:pre"> </span></TiffData></div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span><TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="1" PlaneCount="1"></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><UUID FileName="__omero_export__356461883636658620.ome.tiff">urn:uuid:0895d30c-6c56-11e1-8ce6-0021e9fffeca</UUID></div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span></TiffData></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><Plane DeltaT="0.592" PositionX="54900.0" PositionY="22000.0" PositionZ="49.99" TheC="1" TheT="0" TheZ="0"/></div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span><Plane DeltaT="0.0" PositionX="54900.0" PositionY="22000.0" PositionZ="49.99" TheC="0" TheT="0" TheZ="0"/></div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span></Pixels></div><div><span class="Apple-tab-span" style="white-space:pre"> </span></Image></div><div></OME></div></div><div><br></div><div>
<br></div><div>So I have a screen, that has a plate, a well. the well has a wellsample. And for the plate I have an acquisition. In the well sample I have defined a single image for now what does contain 2 channels.</div>
<div><br></div><div>I can import the image alright but the image is not part of a screen, even when I tell the importer to make it part of a screen. I also tried to import one of the OME-XML sample files:</div><div><br></div>
<div><a href="http://trac.openmicroscopy.org.uk/ome/browser/ome.git/components/specification/Samples/OmeFiles/2010-06/6x4y1z1t1c8b-swatch-1s1p4w2ws.ome-v2010-06.ome.tiff">http://trac.openmicroscopy.org.uk/ome/browser/ome.git/components/specification/Samples/OmeFiles/2010-06/6x4y1z1t1c8b-swatch-1s1p4w2ws.ome-v2010-06.ome.tiff</a><br>
</div><div><br></div><div>Here there are 2 screens with several wells. If I import that file I can see the image but as with my example the images (12 altogether) are not part of a screen.</div><div><br></div><div>Any advice on how to improve my OME-XML code would be greatly appreciated.</div>
<div><br></div><div>Cheers Juergen</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div>-- <br><font><font color="#333333"><b>Dr. Juergen Helmers</b></font><br>
<i>Chief Developer</i> | webnow | <font color="#3366ff"><a href="http://www.web-now.de/" target="_blank">http://www.web-now.de</a></font><br>
<b>email:</b><a href="mailto:juergen.helmers@gmail.com" target="_blank">juergen.helmers@gmail.com</a> | <b>tel:</b>+49 30
37301306 | <b>skype:</b> helmerj </font><br>
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