Open Microscopy Environment

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

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

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

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

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

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

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

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

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

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