[ome-devel] ScanR

Rubén Muñoz ruben.munoz at embl.de
Tue Nov 3 17:34:12 GMT 2009 

Hi Josh, I try it right away,
Regardless of the immediate result, we are grateful for your prompt
support and amazing reliability.
Ruben

On Tue, 3 Nov 2009 18:27:25 +0100, 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
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