[ome-users] importing HCS data as a screen

Mon Mar 26 18:20:28 BST 2012

Hi Jürgen,

My apologies for taking so long to reply.

> I have the latest stable release of Omero running, so that would be 4.3.4
> and I did try insight and importer from the latest client package which is
> 4.3.3.
> I have hit that reload button many times and also very hard but the images
> do not show up anywhere but in the the images history tab under "today"
> having no association with a screen or a project, even I told the importer
> to make them part of an existing screen or project.

I tested again just now with OMERO.server 4.3.4, OMERO.insight 4.3.3, and the
attached OME-TIFF file (which is just your original XML with two planes of
artificial data that match the specified dimensions).

Importing this file into Insight with the location set to "Screen" does
work for me, and the attached screenshot shows what I see under the
screens tab (be sure to double-click on the plate acquisition as
highlighted).

If you import the attached OME-TIFF file in that fashion, do you see the
same problem?  If not (and the same exact workflow does not work with
your files), then it might be time to send one of the actual OME-TIFF
datasets so that we can debug more thoroughly.  I'm sorry to not have
anything more conclusive at this point.

Regards,
-Melissa

On Wed, Mar 14, 2012 at 10:24:37AM +0200, Juergen Helmers wrote:
> On Wed, Mar 14, 2012 at 3:06 AM, Melissa Linkert <
> melissa at glencoesoftware.com> wrote:
> 
> > Hi Jürgen,
> >
> 
> Hi Melissa!
> 
> >
> > 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.
> >
> >
> I have the latest stable release of Omero running, so that would be 4.3.4
> and I did try insight and importer from the latest client package which is
> 4.3.3.
> I have hit that reload button many times and also very hard but the images
> do not show up anywhere but in the the images history tab under "today"
> having no association with a screen or a project, even I told the importer
> to make them part of an existing screen or project.
> 
> 
> > 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.
> >
> 
> Weird...
> 
> >
> > > 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).
> >
> >
> Thanks for the advice. Will do all those changes. If now only they would
> import as instructed... Is there any log file I could inspect as to find
> out what goes wrong during import?
> 
> Thanks for you help!!!
> 
> Cheers Juergen
> 
> 
> > 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
> >
> > > _______________________________________________
> > > ome-users mailing list
> > > ome-users at lists.openmicroscopy.org.uk
> > > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> >

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