[ome-devel] Leica OME.TIF data uploaded

[Rubén Muñoz]

Hello all,

One of the problems below has been solved. A incorrect tag was found  
in the ome.tif, and immediately reported to the microscope vendor, who  
confirmed the problem.

<Pixels ID="Pixels:0" DimensionOrder="XYZCT" PixelType="uint8"
BigEndian="false" SizeX="512" SizeY="512" SizeZ="1" SizeC="1" SizeT="1"
PhysicalSizeX="0.481471031904221" PhysicalSizeY="0.481471031904221"
PhysicalSizeZ="NaN" TimeIncrement="0">

Setting PhysicalSizeZ="0.0" where PhysicalSizeZ="Nan" permitted that  
he files import and display. The database doesnt import  
multidimensional information however, only individual images as  
datasheet.

Best regards,

Ruben

On Tue, 10 Nov 2009 12:00:02 +0000,
ome-devel-request at lists.openmicroscopy.org.uk wrote:
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>   1. Leica OME.TIF data uploaded (Rub?n Mu?oz)
>   2. Re: Leica OME.TIF data uploaded (Rub?n Mu?oz)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 10 Nov 2009 10:27:52 +0100
> From: Rub?n Mu?oz <ruben.munoz at embl.de>
> To: Melissa Linkert <melissa at glencoesoftware.com>
> Cc: ome-devel at lists.openmicroscopy.org.uk
> Subject: [ome-devel] Leica OME.TIF data uploaded
> Message-ID: <AADD230A-04CD-49AE-BE77-BCA1818A8005 at embl.de>
> Content-Type: text/plain; charset=iso-8859-1; format=flowed; delsp=yes
>
> Hi Melissa,
>
> I thank you again for having the ScanR fully operational.
>
> The file  experiment--2009_10_27_15_43_34.zip recently uploaded
> contains one new Leica acquisition.
> We will get you more complex data if you consider so, but our main
> concern is that this dataset (which is ome.tif compliant), when
> imported looks completelly blank into OMERO.web and OMERO.insight. 3
> channels, all at maximum values.
>
> Is there a format conversion problem? I tried bfconvert to other
> formats with the same result (white mages).
>
> We did verify that the experiment does contain cell information. And
> that these are valid acquisitions.
>
> Best regards,
>
> --
> Rub?n Mu?oz
> European Molecular Biology Laboratory
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 10 Nov 2009 10:32:20 +0100
> From: Rub?n Mu?oz <ruben.munoz at embl.de>
> To: Melissa Linkert <melissa at glencoesoftware.com>
> Cc: ome-devel at lists.openmicroscopy.org.uk
> Subject: Re: [ome-devel] Leica OME.TIF data uploaded
> Message-ID: <6155F463-57DE-4B65-8AD5-CED9FD780DBC at embl.de>
> Content-Type: text/plain; charset=iso-8859-1; format=flowed; delsp=yes
>
> Melissa,
>
> I have to add a comment on my last post: the thumbnailing of the
> images does work, because we can see the cells in the image browser.
>
> --
> Rub?n Mu?oz
> European Molecular Biology Laboratory
>
>
>
> On Nov 10, 2009, at 10:27 AM, Rub?n Mu?oz wrote:
>
>> Hi Melissa,
>>
>> I thank you again for having the ScanR fully operational.
>>
>> The file  experiment--2009_10_27_15_43_34.zip recently uploaded
>> contains one new Leica acquisition.
>> We will get you more complex data if you consider so, but our main
>> concern is that this dataset (which is ome.tif compliant), when
>> imported looks completelly blank into OMERO.web and OMERO.insight. 3
>> channels, all at maximum values.
>>
>> Is there a format conversion problem? I tried bfconvert to other
>> formats with the same result (white mages).
>>
>> We did verify that the experiment does contain cell information. And
>> that these are valid acquisitions.
>>
>> Best regards,
>>
>> --
>> Rub?n Mu?oz
>> European Molecular Biology Laboratory
>>
>>
>>
>
>
>
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> End of ome-devel Digest, Vol 68, Issue 6
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