[ome-devel] ScanR

josh.moore at gmx.de josh.moore at gmx.de
Tue Nov 3 17:27:25 GMT 2009 

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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