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PerkinElmer support for older Ultraview RS

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Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.

PerkinElmer support for older Ultraview RS

Postby hroque » Tue Feb 21, 2012 5:53 pm

Hi all,

While trying to upload to OMERO a movie from our PerkinElmer UltraView RS I realize that Bioformats doesn't seem to support this older version of PerkinElmer files.
Is this a backward compatibility issue or just a norm that backwards compatibility is not maintained in newer versions of Bioformats?
Is it possible to allow Bioformats to read these older versions of PerkinElmer files?

Cheers,
Helio Roque
hroque
 
Posts: 36
Joined: Thu Nov 04, 2010 6:20 pm

Re: PerkinElmer support for older Ultraview RS

Postby mlinkert » Tue Feb 21, 2012 6:18 pm

Hi Helio,

While trying to upload to OMERO a movie from our PerkinElmer UltraView RS I realize that Bioformats doesn't seem to support this older version of PerkinElmer files.
Is this a backward compatibility issue or just a norm that backwards compatibility is not maintained in newer versions of Bioformats?
Is it possible to allow Bioformats to read these older versions of PerkinElmer files?


We'd be happy to fix this problem, but we really need more information in order to do so. What is the exact error message that you see? Are you using the latest version of OMERO (4.3.4)? Are you able to send one of the datasets that does not import?

If you are able to send a dataset and need somewhere to put it, please let me know and I will send you our SFTP server details privately.

Regards,
-Melissa
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Re: PerkinElmer support for older Ultraview RS

Postby hroque » Tue Feb 21, 2012 8:05 pm

Thanks for the fast reply,

here is the error msg:

Code: Select all
java.lang.ArrayIndexOutOfBoundsException
   at java.lang.System.arraycopy(Native Method)
   at loci.formats.in.PerkinElmerReader.removeExtraFiles(PerkinElmerReader.java:731)
   at loci.formats.in.PerkinElmerReader.initFile(PerkinElmerReader.java:554)
   at loci.formats.FormatReader.setId(FormatReader.java:1072)
   at loci.formats.ImageReader.setId(ImageReader.java:677)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
   at loci.formats.ChannelFiller.setId(ChannelFiller.java:249)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
   at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:257)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
   at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:312)
   at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:488)
   at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6402)
   at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1228)
   at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
   at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
   at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:111)
   at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
   at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
   at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
   at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
   at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
   at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
   at java.lang.Thread.run(Thread.java:680)

   at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6447)
   at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1228)
   at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
   at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
   at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:111)
   at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
   at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
   at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
   at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
   at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
   at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
   at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.ArrayIndexOutOfBoundsException
   at java.lang.System.arraycopy(Native Method)
   at loci.formats.in.PerkinElmerReader.removeExtraFiles(PerkinElmerReader.java:731)
   at loci.formats.in.PerkinElmerReader.initFile(PerkinElmerReader.java:554)
   at loci.formats.FormatReader.setId(FormatReader.java:1072)
   at loci.formats.ImageReader.setId(ImageReader.java:677)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
   at loci.formats.ChannelFiller.setId(ChannelFiller.java:249)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
   at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:257)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
   at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:312)
   at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:488)
   at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6402)
   ... 11 more


I'll be happy to send a dataset for you to have a look at but indeed it is too big to attach.

Cheers,
Helio
hroque
 
Posts: 36
Joined: Thu Nov 04, 2010 6:20 pm

Re: PerkinElmer support for older Ultraview RS

Postby mlinkert » Wed Feb 22, 2012 1:52 am

Hi Helio,

here is the error msg:

Code: Select all
java.lang.ArrayIndexOutOfBoundsException
   at java.lang.System.arraycopy(Native Method)
   at loci.formats.in.PerkinElmerReader.removeExtraFiles(PerkinElmerReader.java:731)
   at loci.formats.in.PerkinElmerReader.initFile(PerkinElmerReader.java:554)
   at loci.formats.FormatReader.setId(FormatReader.java:1072)
   at loci.formats.ImageReader.setId(ImageReader.java:677)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
   at loci.formats.ChannelFiller.setId(ChannelFiller.java:249)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
   at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:257)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
   at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:312)
   at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:488)
   at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6402)
   at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1228)
   at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
   at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
   at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:111)
   at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
   at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
   at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
   at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
   at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
   at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
   at java.lang.Thread.run(Thread.java:680)

   at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6447)
   at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1228)
   at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
   at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
   at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:111)
   at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
   at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
   at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
   at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
   at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
   at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
   at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.ArrayIndexOutOfBoundsException
   at java.lang.System.arraycopy(Native Method)
   at loci.formats.in.PerkinElmerReader.removeExtraFiles(PerkinElmerReader.java:731)
   at loci.formats.in.PerkinElmerReader.initFile(PerkinElmerReader.java:554)
   at loci.formats.FormatReader.setId(FormatReader.java:1072)
   at loci.formats.ImageReader.setId(ImageReader.java:677)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
   at loci.formats.ChannelFiller.setId(ChannelFiller.java:249)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
   at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:257)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
   at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:312)
   at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:488)
   at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6402)
   ... 11 more



Fantastic, thank you.

I'll be happy to send a dataset for you to have a look at but indeed it is too big to attach.


I've just sent you a private message with our SFTP server information.

Regards,
-Melissa
User avatar
mlinkert
Team Member
 
Posts: 353
Joined: Fri May 29, 2009 2:12 pm
Location: Southwest Wisconsin

Re: PerkinElmer support for older Ultraview RS

Postby mlinkert » Sat Feb 25, 2012 1:12 am

Hi Helio,

Thank you very much for sending a dataset.

We have now implemented a fix:

https://github.com/melissalinkert/biofo ... fb2cab46af

The next release of OMERO will contain this fix.

Regards,
-Melissa
User avatar
mlinkert
Team Member
 
Posts: 353
Joined: Fri May 29, 2009 2:12 pm
Location: Southwest Wisconsin

Re: PerkinElmer support for older Ultraview RS

Postby hroque » Wed Feb 29, 2012 6:17 pm

Thanks for the fix.

The daily built plugin does already work on Fiji, but is it possible to have a daily built from the OMERO server?

Thanks,
Helio
hroque
 
Posts: 36
Joined: Thu Nov 04, 2010 6:20 pm

Re: PerkinElmer support for older Ultraview RS

Postby mlinkert » Tue Mar 06, 2012 4:15 pm

Hi Helio,

The daily built plugin does already work on Fiji, but is it possible to have a daily built from the OMERO server?


Unfortunately, no - we don't produce daily builds of OMERO, given the fact that as a whole it is much, much more complex than Bio-Formats.

The best thing to do is to wait until the next stable version is available (it's won't be terribly long now).

Regards,
-Melissa
User avatar
mlinkert
Team Member
 
Posts: 353
Joined: Fri May 29, 2009 2:12 pm
Location: Southwest Wisconsin

Re: PerkinElmer support for older Ultraview RS

Postby hroque » Wed Sep 12, 2012 10:16 am

Hi again,

Once again we are having problems with uploading Perkin Elmer files to OMERO.
Single stacks work fine but movies always fail.

Here is the error that we get

Code: Select all
java.lang.ArrayIndexOutOfBoundsException: 6698
   at loci.formats.in.PerkinElmerReader.initFile(PerkinElmerReader.java:385)
   at loci.formats.FormatReader.setId(FormatReader.java:1105)
   at loci.formats.ImageReader.setId(ImageReader.java:695)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
   at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
   at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
   at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:310)
   at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:486)
   at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6335)
   at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1248)
   at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
   at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
   at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:110)
   at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
   at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
   at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
   at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
   at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
   at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
   at java.lang.Thread.run(Thread.java:680)


Unfortunately this is becoming a really impossibility. These files are our main source of data and if we're not able to upload it becomes very problematic!

Thanks
Helio
hroque
 
Posts: 36
Joined: Thu Nov 04, 2010 6:20 pm

Re: PerkinElmer support for older Ultraview RS

Postby mlinkert » Thu Sep 13, 2012 12:24 am

Hi Helio,

This is the same as the problem recently reported to OMERO.qa, correct? If so, that has now been turned into a ticket:

http://trac.openmicroscopy.org.uk/ome/ticket/9600

...and we should have this fixed in time for the 4.4.4 release of Bio-Formats/OMERO. As noted in the ticket, the problem seems to be that some of the image files in the dataset contain just one Z section and timepoint, while some of the files contain all of the Z sections for their timepoint. We're currently expecting that all of the files will contain a single Z section and timepoint.

Regards,
-Melissa
User avatar
mlinkert
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Posts: 353
Joined: Fri May 29, 2009 2:12 pm
Location: Southwest Wisconsin

Re: PerkinElmer support for older Ultraview RS

Postby hroque » Thu Sep 13, 2012 7:43 am

Hi Melissa,

Yes it is indeed the same problem.
Glad to hear a solution is on its way!
And if it can come on the next release BioFormats/OMERO that would even be greater!! :)

Thanks,
Helio
hroque
 
Posts: 36
Joined: Thu Nov 04, 2010 6:20 pm


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