[ome-devel] ScanR

josh.moore at gmx.de josh.moore at gmx.de
Mon Nov 2 19:08:41 GMT 2009 

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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