Open Microscopy Environment

Posted: **Mon Sep 19, 2016 9:06 am**

Hi,
We have a fusion-fx machine from Labtec. When I send images (tif images) to our Omero server(5.2.0) via importer I got a message : missing library to detect the file.
I can open this image in Fiji with out any problem.
However, when I try to open the same image with bio-formats plugin (5.2.2) in Fiji I got this messages :

loci.formats.FormatException: loci.common.ReflectException: Cannot execute method: decodeAsRenderedImage
at loci.formats.in.TiffJAIReader.openBufferedImage(TiffJAIReader.java:196)
at loci.formats.in.TiffJAIReader.initFile(TiffJAIReader.java:156)
at loci.formats.FormatReader.setId(FormatReader.java:1401)
at loci.formats.DelegateReader.setId(DelegateReader.java:300)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)
Caused by: loci.common.ReflectException: Cannot execute method: decodeAsRenderedImage
at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:316)
at loci.formats.in.TiffJAIReader.openBufferedImage(TiffJAIReader.java:191)
... 13 more
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:311)
... 14 more
Caused by: java.io.EOFException
at com.sun.media.jai.codec.SeekableStream.readFully(SeekableStream.java:329)
at com.sun.media.jai.codec.SeekableStream.readFully(SeekableStream.java:306)
at com.sun.media.jai.codec.SeekableStream.readUnsignedIntLE(SeekableStream.java:708)
at com.sun.media.jai.codec.TIFFDirectory.readUnsignedInt(TIFFDirectory.java:524)
at com.sun.media.jai.codec.TIFFDirectory.initialize(TIFFDirectory.java:289)
at com.sun.media.jai.codec.TIFFDirectory.<init>(TIFFDirectory.java:125)
at com.sun.media.jai.codecimpl.TIFFImage.<init>(TIFFImage.java:318)
at com.sun.media.jai.codecimpl.TIFFImageDecoder.decodeAsRenderedImage(TIFFImageDecoder.java:112)
... 19 more

Philippe

Posted: **Tue Sep 20, 2016 11:05 am**

Hi Philippe,

to troubleshoot more on this issue, would it be possible to upload or share some sample TIFF images exhibiting the problem. It is possible the error you encounter while importing OMERO has the same root as the one you saw with Fiji.

On the Fiji front, I assume the successful file opening was performed using the regular Fiji > Open menu or was it with an earlier version of Bio-Formats? In the meantime, have you tried disabling the JAI option (BIo-Formats Plugins Configuration > Tagged Image File Formats) for the TIFF reader to see if it helps for this particular file?

Best,
Sebastien

Posted: **Fri Sep 23, 2016 8:47 am**

sbesson wrote:Hi Philippe,

to troubleshoot more on this issue, would it be possible to upload or share some sample TIFF images exhibiting the problem. It is possible the error you encounter while importing OMERO has the same root as the one you saw with Fiji.

On the Fiji front, I assume the successful file opening was performed using the regular Fiji > Open menu or was it with an earlier version of Bio-Formats? In the meantime, have you tried disabling the JAI option (BIo-Formats Plugins Configuration > Tagged Image File Formats) for the TIFF reader to see if it helps for this particular file?

Best,
Sebastien

Hi Sebastien,
Disabling JAI option works fine with Fiji. In fact Fusion Fx have two types of format one with specific metadata that we would conserve and an other without meta data. The first format hang Bio-format if we don't disable the JAI option. However, how can we do to transfert this type of file with omero import ?

Thanks
Philippe

Posted: **Mon Sep 26, 2016 1:54 pm**

Hi Philippe,

Judging by the error messages the Omero upload issue might well be separate to the Fiji JAI option problem.

If you would be able to upload a sample file that would allow us to further test and investigate what is going wrong:
https://www.openmicroscopy.org/qa2/qa/upload/

With Thanks,
David Gault

Posted: **Thu Sep 29, 2016 7:50 am**

dgault wrote:Hi Philippe,

Judging by the error messages the Omero upload issue might well be separate to the Fiji JAI option problem.

If you would be able to upload a sample file that would allow us to further test and investigate what is going wrong:
https://www.openmicroscopy.org/qa2/qa/upload/

With Thanks,
David Gault

Hi David,
I posted an example on your server.

Philippe

Posted: **Thu Sep 29, 2016 4:12 pm**

Hi Philippe,

Thank you for providing a sample file. I was able to test it this afternoon and am seeing another separate issue while reading the file as well as those reported earlier in this thread. I will do some further investigation tomorrow and keep you up to date with what I discover.

David

Posted: **Fri Sep 30, 2016 2:16 pm**

Hi Philippe,

I have opened one code PR for an exception discovered while testing the file you uploaded. https://github.com/openmicroscopy/bioformats/pull/2592

However after removing this error I was not able to reproduce the same error which you encountered with Omero. Would you be able to paste the exact error message and any available stack trace that you are seeing with this error?

David

Posted: **Mon Oct 03, 2016 3:25 pm**

dgault wrote:Hi Philippe,

I have opened one code PR for an exception discovered while testing the file you uploaded. https://github.com/openmicroscopy/bioformats/pull/2592

However after removing this error I was not able to reproduce the same error which you encountered with Omero. Would you be able to paste the exact error message and any available stack trace that you are seeing with this error?

David

Hi David,

The OMERO importer (5.2.0) exception message is :

java.lang.ArrayIndexOutOfBoundsException: 0
at loci.formats.in.BaseTiffReader.getImageCreationDate(BaseTiffReader.java:523)
at loci.formats.in.BaseTiffReader.initMetadataStore(BaseTiffReader.java:429)
at loci.formats.in.TiffReader.initMetadataStore(TiffReader.java:229)
at loci.formats.in.BaseTiffReader.initMetadata(BaseTiffReader.java:99)
at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:577)
at loci.formats.FormatReader.setId(FormatReader.java:1426)
at loci.formats.DelegateReader.setId(DelegateReader.java:290)
at loci.formats.ImageReader.setId(ImageReader.java:835)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:289)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at loci.formats.Memoizer.setId(Memoizer.java:650)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:410)
at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:566)
at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:367)
at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:5989)
at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1035)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:73)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:48)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:97)
at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
at java.lang.Thread.run(Unknown Source)

at org.openmicroscopy.shoola.env.data.util.StatusLabel.update(StatusLabel.java:671)
at ome.formats.importer.ImportCandidates.safeUpdate(ImportCandidates.java:526)
at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:461)
at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:566)
at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:367)
at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:5989)
at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1035)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:73)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:48)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:97)
at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 0
at loci.formats.in.BaseTiffReader.getImageCreationDate(BaseTiffReader.java:523)
at loci.formats.in.BaseTiffReader.initMetadataStore(BaseTiffReader.java:429)
at loci.formats.in.TiffReader.initMetadataStore(TiffReader.java:229)
at loci.formats.in.BaseTiffReader.initMetadata(BaseTiffReader.java:99)
at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:577)
at loci.formats.FormatReader.setId(FormatReader.java:1426)
at loci.formats.DelegateReader.setId(DelegateReader.java:290)
at loci.formats.ImageReader.setId(ImageReader.java:835)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:289)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at loci.formats.Memoizer.setId(Memoizer.java:650)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:410)
... 16 more

Philippe

Posted: **Mon Oct 03, 2016 6:10 pm**

Thanks Philippe,

This is indeed the same error that we were able to reproduce. A fix for this will be included as part of the next Bio-Formats 5.2.3 release.

David Gault

Open Microscopy Environment

Image from Fusion-fx

Image from Fusion-fx

Re: Image from Fusion-fx

Re: Image from Fusion-fx

Re: Image from Fusion-fx

Re: Image from Fusion-fx

Re: Image from Fusion-fx

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Re: Image from Fusion-fx

Re: Image from Fusion-fx