[ome-devel] ScanR

Rubén Muñoz ruben.munoz at embl.de
Tue Nov 3 17:54:57 GMT 2009 

Hello Josh and Melissa,
It worked like a charm.
Got the plate with the correct layout and the expected  
multidimensional images all imported.

We are going for the 1TB performance test now.

Best,

--
Rubén Muñoz
European Molecular Biology Laboratory



On Nov 3, 2009, at 6:27 PM, josh.moore at gmx.de wrote:

>
> Hi Ruben,
>
> thanks to Melissa:
>
>  https://skyking.microscopy.wisc.edu/trac/java/changeset/5661
>
> the latest build seems to be populating ScanR plates:
>
>  http://hudson.openmicroscopy.org.uk/job/LOCI-Beta4.1/23/
>
> Let us know how it works for you.
>
> ~Josh.
>
> Rubén Muñoz writes:
>> I do get the 'screen' dialog. I can add a new one and at the end I  
>> get
>> the screen symbol to the left followed by (0) because is empty. The
>> images are in the database however.
>>
>>
>> --
>> Rubén Muñoz
>> European Molecular Biology Laboratory
>>
>>
>>
>> On Nov 2, 2009, at 8:08 PM, josh.moore at gmx.de wrote:
>>
>>>
>>> Ruben,
>>>
>>> Do you also not get a screen when clicking on the directory for
>>> import? My guess is that the OMERO.importer detection of a screen is
>>> causing the problem.
>>>
>>> ~J.
>>>
>>> Rubén Muñoz writes:
>>>> Hi Josh, forgive my fuzzy bug report.
>>>>
>>>> With the new ScanR importer I am getting an empty screen(0) but all
>>>> the images appear in the "today" list. They seem OK but not grouped
>>>> in rows and columns under the new screen.
>>>>
>>>> No error message or exception so far.
>>>>
>>>> Is this a OMERO o bioformats issue?
>>>>
>>>> El 02/11/2009, a las 19:41, "Josh Moore" <josh at glencoesoftware.com>
>>>> escribió:
>>>>
>>>>>
>>>>> Does this mean you can get things up and running now, Ruben? Or  
>>>>> are
>>>>> there any other blockers?
>>>>>
>>>>> ~J.
>>>>>
>>>>> Rubén Muñoz writes:
>>>>>> Hi Melissa,
>>>>>> while now the bfconvert always generates an output file. Ive been
>>>>>> testing to directly import the folder into OMERO.importer. For
>>>>>> that:
>>>>>>
>>>>>> - Replaced the bio-formats.jar into the importer folder
>>>>>> - Inserted 'Scanr' and 'Companion/Scanr' new records in the Omero
>>>>>> Posgres DB at table 'formats'.
>>>>>>
>>>>>> The result is:
>>>>>>
>>>>>> - Was promoted for Screening name and Proceeded with 'Add to
>>>>>> queue'.
>>>>>> - Import process ended without Errors.
>>>>>> - Screen in Omero appears empty at the end of the smooth process
>>>>>> (no
>>>>>> wells in the screen).
>>>>>> - At recent images some of the images 'could not be displayed
>>>>>> because
>>>>>> are invalid images'
>>>>>>
>>>>>> I believe that youre very near to the Scanr importer, and wish to
>>>>>> provide you with more detailed test. But as a hint I tried to
>>>>>> convert
>>>>>> our current Data Set to OME.tif with bfconvert and then to  
>>>>>> OME.tif
>>>>>> again with OME.tif. Didnt work for me.
>>>>>>
>>>>>> Is the order of the images in the output the correct? The sizes  
>>>>>> of
>>>>>> the
>>>>>> Data Set and output file do correspond. Also the Dimensions are
>>>>>> well
>>>>>> taken (Ive checked). Only the Timepoint aré calculated based on  
>>>>>> the
>>>>>> other dimensions and the number of files...
>>>>>>
>>>>>> My sincere gratitude,
>>>>>> Ruben
>>>>>>
>>>>>> El 30/10/2009, a las 17:17, Melissa Linkert
>>>>>> <melissa at glencoesoftware.com> escribió:
>>>>>>
>>>>>>> Hi Ruben,
>>>>>>>
>>>>>>>> I believe you use -bigtiff flag but Im getting trouble with the
>>>>>>>> big
>>>>>>>> datasets. Can you see if I miss something:
>>>>>>>>
>>>>>>>> ./bfconvert -bigtiff
>>>>>>>> /Users/gonzales/Images/161009test2/151009_001/data/--W00001--
>>>>>>>> P00001--Z00000--T00000--Cherry.tif test.ome.tif
>>>>>>>
>>>>>>> This is the correct command; however, there was a bug that  
>>>>>>> caused
>>>>>>> the
>>>>>>> '-bigtiff' flag to be ignored.  This command should work as
>>>>>>> expected
>>>>>>> if you update to the latest trunk build of Bio-Formats.
>>>>>>>
>>>>>>>> While you improve the ScanR,  Josh suggested that we provide  
>>>>>>>> you
>>>>>>>> Leica
>>>>>>>> "ome.tif" that are not really compliant. If theres place in the
>>>>>>>> FTP
>>>>>>>> I do it
>>>>>>>> right away with name Leica.tar.bz2
>>>>>>>
>>>>>>> Feel free to upload, unless Leica.tar.bz2 is larger than 6 GB.
>>>>>>>
>>>>>>> Regards,
>>>>>>> -Melissa
>>>>>>>
>>>>>>> On Thu, Oct 29, 2009 at 4:47 PM, Rubén Muñoz <ruben.munoz at embl.d
>>>>>>> e> w
>>>>>>> rote:
>>>>>>>> On Oct 29, 2009, at 5:12 PM, Melissa Linkert wrote:
>>>>>>>>
>>>>>>>>> Hi Ruben,
>>>>>>>>
>>>>>>>> Hi Melissa,
>>>>>>>>
>>>>>>>>>
>>>>>>>>> I'm moving this discussion to the ome-devel list, as it may be
>>>>>>>>> of
>>>>>>>>> interest to others.
>>>>>>>>>
>>>>>>>>>> Please consider my ScanrReader.java as possible help.
>>>>>>>>>
>>>>>>>>> Thank you very much for the patch.  I've committed a modified
>>>>>>>>> version
>>>>>>>>> of it to the LOCI SVN repository; you can view the changes  
>>>>>>>>> here:
>>>>>>>>
>>>>>>>> Thats so kind of you, glad to hear that.
>>>>>>>>
>>>>>>>>>
>>>>>>>>> https://skyking.microscopy.wisc.edu/trac/java/changeset/5652
>>>>>>>>
>>>>>>>> I believe you use -bigtiff flag but Im getting trouble with the
>>>>>>>> big
>>>>>>>> datasets. Can you see if I miss something:
>>>>>>>>
>>>>>>>> ./bfconvert -bigtiff
>>>>>>>> /Users/gonzales/Images/161009test2/151009_001/data/--W00001--
>>>>>>>> P00001--Z00000--T00000--Cherry.tif
>>>>>>>> test.ome.tif
>>>>>>>> /Users/gonzales/Images/161009test2/151009_001/data/--W00001--
>>>>>>>> P00001--Z00000--T00000--Cherry.tif
>>>>>>>> [Olympus ScanR] -> test.ome.tif [OME-TIFF]
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>>>>>>>> ......................................................Exception
>>>>>>>> in
>>>>>>>> thread "main" loci.formats.FormatException: File is too large;
>>>>>>>> call
>>>>>>>> setBigTiff(true)
>>>>>>>>     at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:
>>>>>>>> 188)
>>>>>>>>     at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:
>>>>>>>> 223)
>>>>>>>>     at loci.formats.out.OMETiffWriter.saveBytes
>>>>>>>> (OMETiffWriter.java:193)
>>>>>>>>     at loci.formats.ImageWriter.saveBytes(ImageWriter.java:185)
>>>>>>>>     at
>>>>>>>> loci.formats.tools.ImageConverter.testConvert
>>>>>>>> (ImageConverter.java:
>>>>>>>> 228)
>>>>>>>>     at loci.formats.tools.ImageConverter.main
>>>>>>>> (ImageConverter.java:253)
>>>>>>>>
>>>>>>>>>
>>>>>>>>> The only major difference between the committed changes and  
>>>>>>>>> your
>>>>>>>>> patch
>>>>>>>>> is that the committed changes do not have hard-coded well,
>>>>>>>>> position,
>>>>>>>>> Z, T, and channel counts.  The number of wells is currently
>>>>>>>>> being
>>>>>>>>> calculated from the well names in the "well selection table +
>>>>>>>>> cDNA"
>>>>>>>>> table.  The number of channels (core[0].sizeC) is equivalent  
>>>>>>>>> to
>>>>>>>>> the
>>>>>>>>> number of channels defined in experiment_description.xml that
>>>>>>>>> have
>>>>>>>>> the
>>>>>>>>> "idle" flag set to 0.
>>>>>>>>
>>>>>>>> So the information was there, just awaiting for someone to find
>>>>>>>> the
>>>>>>>> way to
>>>>>>>> read it.
>>>>>>>>
>>>>>>>>>
>>>>>>>>> The latest revision of ScanrReader does correctly detect the
>>>>>>>>> dimensions for all of the datasets that I have.  If you  
>>>>>>>>> continue
>>>>>>>>> to
>>>>>>>>> experience problems, though, please let me know.
>>>>>>>>>
>>>>>>>>
>>>>>>>> While you improve the ScanR,  Josh suggested that we provide  
>>>>>>>> you
>>>>>>>> Leica
>>>>>>>> "ome.tif" that are not really compliant. If theres place in the
>>>>>>>> FTP
>>>>>>>> I do it
>>>>>>>> right away with name Leica.tar.bz2
>>>>>>>>
>>>>>>>>> Regards,
>>>>>>>>> -Melissa
>>>>>>>>
>>>>>>>> Regards,
>>>>>>>>
>>>>>>>> Ruben
>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Fri, Oct 23, 2009 at 5:53 PM, Rubén Muñoz  
>>>>>>>>> <ruben.munoz at embl.d
>>>>>>>>> e> wrote:
>>>>>>>>>>
>>>>>>>>>> Hi Melissa, thanks for your reply.
>>>>>>>>>>
>>>>>>>>>> I'd be happy to fix this, but first would like to clarify
>>>>>>>>>> that an
>>>>>>>>>> assumption is correct.
>>>>>>>>>>
>>>>>>>>>> core[0].sizeC (the number of channels) is taken from a block
>>>>>>>>>> like
>>>>>>>>>> this:
>>>>>>>>>>
>>>>>>>>>> <Name>multiple_channel_typedef</Name>
>>>>>>>>>> <Dimsize>3</Dimsize>
>>>>>>>>>>
>>>>>>>>>> Yes, but not all the channels are finally used.
>>>>>>>>>> While the experiment_descriptor.xml reads:
>>>>>>>>>> <Name>multiple_channel_typedef</Name>
>>>>>>>>>> <Dimsize>12</Dimsize>
>>>>>>>>>> The directory only has two channel Cherry and eGFP.
>>>>>>>>>>
>>>>>>>>>> My understanding is that Dimsize is used in multiple places,
>>>>>>>>>> and
>>>>>>>>>> its
>>>>>>>>>> usage is determined by the value in in the "Name" element.   
>>>>>>>>>> Is
>>>>>>>>>> this
>>>>>>>>>> correct?  If so, do you know what the correct Name values are
>>>>>>>>>> for
>>>>>>>>>> channels and positions?
>>>>>>>>>>
>>>>>>>>>> That's how it should be...
>>>>>>>>>> ... but the new set only gets converted for me when I fix all
>>>>>>>>>> the
>>>>>>>>>> next
>>>>>>>>>> values:
>>>>>>>>>> wellColumns = 2;
>>>>>>>>>> wellRows = 3;
>>>>>>>>>> core[0].sizeC = 2;
>>>>>>>>>> core[0].sizeT = 6;
>>>>>>>>>> core[0].sizeZ = 3;
>>>>>>>>>> Im sorry to do that now but a colleague is going to offer me
>>>>>>>>>> details
>>>>>>>>>> about
>>>>>>>>>> experiment_descriptor.xml.
>>>>>>>>>> Additionally I introduced some code to handle different
>>>>>>>>>> positions
>>>>>>>>>> in a
>>>>>>>>>> well,
>>>>>>>>>> P00001, P00002 and so on.
>>>>>>>>>> Please consider my ScanrReader.java as possible help. It is
>>>>>>>>>> working well
>>>>>>>>>> for
>>>>>>>>>> the set and generates an OME.TIF with 1.7G that imports to
>>>>>>>>>> OMERO
>>>>>>>>>> and
>>>>>>>>>> displays Z, T, and C data in the correct way
>>>>>>>>>> .
>>>>>>>>>> Regards,
>>>>>>>>>> Ruben
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> <ScanrReader.java>
>>>>>>>>
>>>>>>>>
>>>>>> _______________________________________________
>>>>>> ome-devel mailing list
>>>>>> ome-devel at lists.openmicroscopy.org.uk
>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>>>> _______________________________________________
>>>> ome-devel mailing list
>>>> ome-devel at lists.openmicroscopy.org.uk
>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel

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