[ome-users] importing HCS data as a screen

Wed Mar 14 01:06:44 GMT 2012

Hi Jürgen,

> 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:
*snip*
> 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.

Interesting.  I can definitely duplicate the problem with the sample
OME-TIFF file linked above, but I cannot duplicate the problem using
your own OME-XML (imported against both 4.3.3 and the latest development
server).

Just to be sure: which client are you using to import the file?  I
tested with OMERO.insight, but if you are using something else then I will
re-test.  Also (maybe a stupid question), but have you tried
explicitly refreshing the tree in Insight?  Especially if you import
from Insight, it's possible to have screens missing from the tree until
the refresh button is clicked.

We'll certainly fix what is wrong with the sample OME-TIFF (likely the
fact that all of the Plate/Screen/WellSample/Image linkages are missing),
but as far as I can see your own files should import correctly.

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

Your OME-XML looks pretty good.  I'd suggest changing the "ID"
attribute on ScreenRef so that it matches the "ID" of one of the
Screens defined (should be "Screen:102" in this case), as Bio-Formats
will issue warnings otherwise; this shouldn't prevent the file from
importing correctly though.  You might also change the "xmlns" on
PlateAcquisition so that it points to the 2011-06 schema (like all of
the other "xmlns" attributes).

Regards,
-Melissa

On Mon, Mar 12, 2012 at 05:55:47PM +0200, Juergen Helmers wrote:
> 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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