[ome-users] importing HCS data as a screen

[Juergen Helmers]

Hi
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:


<?xml version="1.0" encoding="UTF-8"?>
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2011-06" xmlns:xsi="
http://www.w3.org/2001/XMLSchema-instance" xmlns:ROI="
http://www.openmicroscopy.org/Schemas/ROI/2011-06" xmlns:SA="
http://www.openmicroscopy.org/Schemas/SA/2011-06" xmlns:SPW="
http://www.openmicroscopy.org/Schemas/SPW/2011-06" xmlns:Bin="
http://www.openmicroscopy.org/Schemas/BinaryFile/2011-06"
xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2011-06
http://www.openmicroscopy.org/Schemas/OME/2011-06/ome.xsd"
UUID="urn:uuid:0895d30c-6c56-11e1-8ce6-0021e9fffeca">
 <SPW:Plate ID="Plate:0">
<SPW:Description>Plate 1 description.</SPW:Description>
 <SPW:ScreenRef ID="Screen:1"/>
<SPW:Well ID="Well:1.1.1" Column="1" Row="1">
 <SPW:WellSample ID="WellSample:1.1.1.1" Index="1">
<SPW:ImageRef ID="Image:0"/>
 </SPW:WellSample>
</SPW:Well>
<SPW:PlateAcquisition xmlns="
http://www.openmicroscopy.org/Schemas/SPW/2010-06"
ID="PlateAcquisition:Plate:1:ScreenAcquisition:1"
StartTime="2010-02-23T12:49:30" EndTime="2010-02-23T12:50:30">
 <SPW:WellSampleRef ID="WellSample:1.1.1.1"/>
</SPW:PlateAcquisition>
 </SPW:Plate>
<SPW:Screen ID="Screen:102" ProtocolDescription="" ProtocolIdentifier=""
ReagentSetDescription="" ReagentSetIdentifier="" Name="new004" Type="">
 <SPW:Description/>
<SPW:PlateRef ID="Plate:0"/>
</SPW:Screen>
 <Image ID="Image:0" Name="9 images screen test _take1_Field001.tif">
<AcquiredDate>2010-02-23T12:51:30</AcquiredDate>
 <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">
 <Channel Color="-16776961"
ID="urn:lsid:export.openmicroscopy.org:Channel:f25a632d-6bdd-4dd4-a07f-1d2c3dc129a2_90451:265926"
SamplesPerPixel="1">
 <LightPath/>
</Channel>
<Channel Color="16711935"
ID="urn:lsid:export.openmicroscopy.org:Channel:f25a632d-6bdd-4dd4-a07f-1d2c3dc129a2_90452:265926"
SamplesPerPixel="1">
 <LightPath/>
</Channel>
<TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1">
 <UUID
FileName="__omero_export__356461883636658620.ome.tiff">urn:uuid:0895d30c-6c56-11e1-8ce6-0021e9fffeca</UUID>
</TiffData>
 <TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="1" PlaneCount="1">
<UUID
FileName="__omero_export__356461883636658620.ome.tiff">urn:uuid:0895d30c-6c56-11e1-8ce6-0021e9fffeca</UUID>
 </TiffData>
<Plane DeltaT="0.592" PositionX="54900.0" PositionY="22000.0"
PositionZ="49.99" TheC="1" TheT="0" TheZ="0"/>
 <Plane DeltaT="0.0" PositionX="54900.0" PositionY="22000.0"
PositionZ="49.99" TheC="0" TheT="0" TheZ="0"/>
 </Pixels>
</Image>
</OME>


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.

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:

http://trac.openmicroscopy.org.uk/ome/browser/ome.git/components/specification/Samples/OmeFiles/2010-06/6x4y1z1t1c8b-swatch-1s1p4w2ws.ome-v2010-06.ome.tiff

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.

Any advice on how to improve my OME-XML code would be greatly appreciated.

Cheers Juergen





-- 
*Dr. Juergen Helmers*
*Chief Developer* | webnow | http://www.web-now.de
*email:*juergen.helmers at gmail.com | *tel:*+49 30 37301306 | *skype:*helmerj
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