[ome-users] Fwd: MATLAB bfopen image series metadata issue

[Roger Leigh]

Dear Thurston,

I've taken a look at the image you uploaded, in particular looking at
the OME-XML metadata with "showinf -nopix -omexml".  Rather than using
the global or series metadata, you could try using these
MetadataRetrieve calls directly:

   getPlanePositionX(image, plane)
   getPlanePositionY(image, plane)

Where image is the image number, and plane is the plane number; since
all your images have only one z/c/t, the plane number will always be
zero.  This, for example, is the metadata for the first image:

    <Image ID="Image:0" Name="56_E11_R3D.dv">
       <AcquisitionDate>2013-07-25T09:43:30</AcquisitionDate>
       <InstrumentRef ID="Instrument:0"/>
       <ObjectiveSettings ID="Objective:10109"/>
       <Pixels DimensionOrder="XYZCT" ID="Pixels:0"
PhysicalSizeX="0.6456999778747559" PhysicalSizeY="0.6456999778747559"
PhysicalSizeZ="0.20000000298023224" SizeC="1" SizeT="1" SizeX="1024"
SizeY="1024" SizeZ="1" Type="uint16">
          <Channel ID="Channel:0:0" NDFilter="0.009999999776482582"
SamplesPerPixel="1">
             <LightPath/>
          </Channel>
          <MetadataOnly/>
          <Plane DeltaT="0.0" ExposureTime="1.500000071246177E-4"
PositionX="7815.39013671875" PositionY="-15843.3984375"
PositionZ="-111.29199981689453" TheC="0" TheT="0" TheZ="0"/>
       </Pixels>

You can see the position information (PositionX/PositionY) in the
<Plane> element, and the getPlanePosition[XY] calls will retrieve this
information for you.


Regards,
Roger

On 24/07/2013 21:13, Sebastien Besson wrote:
> Hi Thurston,
>
> thanks for uploading your data.
> I am on leave until August 5 but I am forwarding your email to the
> relevant people who will follow up on this thread.
>
> Cheers,
> Sebastien
>
> Begin forwarded message:
>
>> *From: *Thurston Herricks <Thurston.Herricks at systemsbiology.org
>> <mailto:Thurston.Herricks at systemsbiology.org>>
>> *Subject: **Re: [ome-users] MATLAB bfopen image series metadata issue*
>> *Date: *24 July 2013 17:10:35 GMT+01:00
>> *To: *Sebastien Besson <s.besson at dundee.ac.uk
>> <mailto:s.besson at dundee.ac.uk>>
>>
>> Hello Dr Besson,
>> I have uploaded a deltavision DV file'56_E11_R3D.dv' to the open
>> microscopy server.  This is an example of the file that is giving me
>> trouble.  The file should have 25 images stored in it that are to be
>> stiched together.  Unfortunatly the meta data for each series is
>> identical so that I cannot get the stage XY positions of the
>> individual images in the series.
>> When I utilize the following commands r.getMetadataGlobal() I get all
>> of the metadata but it is jumbled.  Then when I try to use the
>> r.setSeries(index) and r.getSeriesMetadata, the meta data is identical
>> for all series and it shouldn't be.
>> If there is anything else I can try or if you need more information
>> please let me know.
>> Thanks for your time.
>> -Thurston
>>
>>
>> On Wed, Jul 24, 2013 at 3:09 AM, Sebastien Besson
>> <s.besson at dundee.ac.uk <mailto:s.besson at dundee.ac.uk>> wrote:
>>
>>     Hi Thurston,
>>
>>     given a reader r, the way to retrieve the global metadata is:
>>
>>     r.getGlobalMetadata()
>>
>>     and the way to retrieve metadata per-series is:
>>
>>     r.setSeries(iSeries)
>>     r.getSeriesMetadata()
>>
>>     I just tested bfopen() on a file where series metadata are
>>     expected to be different.
>>     The function output resulted on non-identical hash tables.
>>
>>     Note however the way the series metadata is constructed is
>>     reader-specific.
>>     In the current implementation of the DeltaVision reader, all
>>     series metadata are identical by construction.
>>
>>     If this is not the case and you are expecting different metadata
>>     per series, could you upload a sample file to:
>>     http://qa.openmicroscopy.org.uk/qa/upload/
>>
>>     Cheers,
>>     Sebastien
>>
>>     On 24 Jul 2013, at 00:27, Thurston Herricks wrote:
>>
>>>     Hello,
>>>     I am using bfopen to load image sets from a deltavision
>>>     microscope into MATLAB.  I am currently using MATLAB R2013a.
>>>     An issue has cropped up when multiple image series are in a
>>>     single file.  In bfopen.m line 212, when r.getSeriesMetadata is
>>>     called only the metadata from the last series is writen to the
>>>     results.  When r.setSeries( index ) is changed, the metadata
>>>     retrieved for rgetSeriesMetadata is identical for all indicies.
>>>     Is there another method for retrieving image meta data?
>>>     Thanks
>>>     Thurston Herricks

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096