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Fiji+Bio-Formats: how to open a MOV file?

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Rodrigo Gonçalves
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Fiji+Bio-Formats: how to open a MOV file?

Rodrigo Gonçalves
Hello, I need to open a MOV file in Fiji.
- When I try "Open" from main menu, it takes me to Bio-Formats importer. When selecting OK using the default options, I get the "File is not in a supported format, a reader plugin is not available, or it was not found" message.

- When I try Import -> BioFormat I get (using exactly the same import options as above) the "Sorry, there was a problem during import" message and the text at the end of this email is logged.

Aside from this apparent inconsistency in Bio-Formats behavior, the 2nd case seems to be a Java-related error (see transcript below): Apparently I need to use Java32 with Fiji instead of the one apparently installed in my system (*), is that correct?

* Linux Mint on a 64bit processor
What would you suggest in this case? Maybe I can download Java32 and start Fiji using a different Java installation? How?Or, alternatively, could you guide me to open it using Bio-Formats Import Options using my current setup?
Thanks!!Rodrigo
_______________________________loci.formats.MissingLibraryException: QuickTime for Java is not supported with a 64-bit JVM. Please invoke the 32-bit JVM (-d32) to utilize QTJava functionality.
    at loci.formats.gui.LegacyQTTools.checkQTLibrary(LegacyQTTools.java:336)
    at loci.formats.in.LegacyQTReader.initFile(LegacyQTReader.java:142)
    at loci.formats.FormatReader.setId(FormatReader.java:1426)
    at loci.formats.DelegateReader.setId(DelegateReader.java:298)
    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)


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ctrueden
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Re: Fiji+Bio-Formats: how to open a MOV file?

ctrueden
Hi Rodrigo,

> I need to open a MOV file in Fiji.

It sounds like your MOV file uses a codec which Bio-Formats does not
support. And you cannot use the QTJ approach (ImageJ's default approach)
because QTJ is not available for Linux.

Try turning on the FFMPEG update site, and opening the movie using File >
Import > Movie (FFMPEG)...

For further details, see:
http://imagej.net/QuickTime

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Tue, Aug 16, 2016 at 4:30 PM, Rodrigo Gonçalves <
[hidden email]> wrote:

> Hello, I need to open a MOV file in Fiji.
> - When I try "Open" from main menu, it takes me to Bio-Formats importer.
> When selecting OK using the default options, I get the "File is not in a
> supported format, a reader plugin is not available, or it was not found"
> message.
>
> - When I try Import -> BioFormat I get (using exactly the same import
> options as above) the "Sorry, there was a problem during import" message
> and the text at the end of this email is logged.
>
> Aside from this apparent inconsistency in Bio-Formats behavior, the 2nd
> case seems to be a Java-related error (see transcript below): Apparently I
> need to use Java32 with Fiji instead of the one apparently installed in my
> system (*), is that correct?
>
> * Linux Mint on a 64bit processor
> What would you suggest in this case? Maybe I can download Java32 and start
> Fiji using a different Java installation? How?Or, alternatively, could you
> guide me to open it using Bio-Formats Import Options using my current setup?
> Thanks!!Rodrigo
> _______________________________loci.formats.MissingLibraryException:
> QuickTime for Java is not supported with a 64-bit JVM. Please invoke the
> 32-bit JVM (-d32) to utilize QTJava functionality.
>     at loci.formats.gui.LegacyQTTools.checkQTLibrary(
> LegacyQTTools.java:336)
>     at loci.formats.in.LegacyQTReader.initFile(LegacyQTReader.java:142)
>     at loci.formats.FormatReader.setId(FormatReader.java:1426)
>     at loci.formats.DelegateReader.setId(DelegateReader.java:298)
>     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)
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Rodrigo Gonçalves
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Re: Fiji+Bio-Formats: how to open a MOV file?

Rodrigo Gonçalves
Yes! It works!Thanks!!

________________________

      From: Curtis Rueden <[hidden email]>
 To: [hidden email]
 Sent: Wednesday, 17 August 2016, 16:47
 Subject: Re: Fiji+Bio-Formats: how to open a MOV file?
   
Hi Rodrigo,

> I need to open a MOV file in Fiji.

It sounds like your MOV file uses a codec which Bio-Formats does not
support. And you cannot use the QTJ approach (ImageJ's default approach)
because QTJ is not available for Linux.

Try turning on the FFMPEG update site, and opening the movie using File >
Import > Movie (FFMPEG)...

For further details, see:
http://imagej.net/QuickTime

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Tue, Aug 16, 2016 at 4:30 PM, Rodrigo Gonçalves <
[hidden email]> wrote:

> Hello, I need to open a MOV file in Fiji.
> - When I try "Open" from main menu, it takes me to Bio-Formats importer.
> When selecting OK using the default options, I get the "File is not in a
> supported format, a reader plugin is not available, or it was not found"
> message.
>
> - When I try Import -> BioFormat I get (using exactly the same import
> options as above) the "Sorry, there was a problem during import" message
> and the text at the end of this email is logged.
>
> Aside from this apparent inconsistency in Bio-Formats behavior, the 2nd
> case seems to be a Java-related error (see transcript below): Apparently I
> need to use Java32 with Fiji instead of the one apparently installed in my
> system (*), is that correct?
>
> * Linux Mint on a 64bit processor
> What would you suggest in this case? Maybe I can download Java32 and start
> Fiji using a different Java installation? How?Or, alternatively, could you
> guide me to open it using Bio-Formats Import Options using my current setup?
> Thanks!!Rodrigo
> _______________________________loci.formats.MissingLibraryException:
> QuickTime for Java is not supported with a 64-bit JVM. Please invoke the
> 32-bit JVM (-d32) to utilize QTJava functionality.
>    at loci.formats.gui.LegacyQTTools.checkQTLibrary(
> LegacyQTTools.java:336)
>    at loci.formats.in.LegacyQTReader.initFile(LegacyQTReader.java:142)
>    at loci.formats.FormatReader.setId(FormatReader.java:1426)
>    at loci.formats.DelegateReader.setId(DelegateReader.java:298)
>    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)
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html


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