.lif files on Imagej error

[Lebistes]

Hello, I downloaded to my pc a .lif file from a Leika microscope.
The I downloaded the plugin LOCI, moved the file in the Imagej plugin folder, restart Imagej and open the file.
This is the error that I receive:
ImageJ 1.48e; Java 1.6.0_20 [64-bit]; Windows 7 6.1; 42MB of 3500MB (1%)
 
java.lang.IllegalArgumentException: 0 must not be null and positive.
        at ome.xml.model.primitives.PositiveInteger.<init>(PositiveInteger.java:56)
        at loci.formats.in.LIFReader.initMetadata(LIFReader.java:566)
        at loci.formats.in.LIFReader.initFile(LIFReader.java:446)
        at loci.formats.FormatReader.setId(FormatReader.java:1244)
        at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
        at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
        at loci.plugins.in.Importer.showDialogs(Importer.java:141)
        at loci.plugins.in.Importer.run(Importer.java:79)
        at loci.plugins.LociImporter.run(LociImporter.java:81)
        at ij.IJ.runUserPlugIn(IJ.java:196)
        at ij.IJ.runPlugIn(IJ.java:160)
        at ij.IJ.runPlugIn(IJ.java:149)
        at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:258)
        at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
        at ij.IJ.runUserPlugIn(IJ.java:196)
        at ij.IJ.runPlugIn(IJ.java:160)
        at ij.IJ.runPlugIn(IJ.java:149)
        at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:453)
        at ij.io.Opener.openImage(Opener.java:310)
        at ij.io.Opener.openImage(Opener.java:333)
        at ij.io.Opener.open(Opener.java:143)
        at ij.io.Opener.openAndAddToRecent(Opener.java:246)
        at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
        at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
        at java.lang.Thread.run(Thread.java:619)

May you help me to solve the problem?
Thanks

Fabio Valenti

[Melissa Linkert-2]

Hi Fabio,

> Hello, I downloaded to my pc a .lif file from a Leika microscope.
> The I downloaded the plugin LOCI, moved the file in the Imagej plugin
> folder, restart Imagej and open the file.
> This is the error that I receive:
> ImageJ 1.48e; Java 1.6.0_20 [64-bit]; Windows 7 6.1; 42MB of 3500MB (1%)

Which version of Bio-Formats are you using?  "Help > About Plugins >
LOCI Plugins" should tell you; if the version number is something other
than 4.4.9, then I would recommend trying the 4.4.9 version from here:

http://downloads.openmicroscopy.org/bio-formats/4.4.9/

If you see that error with the 4.4.9 version, then it would be helpful
if you could send a file that shows the problem.  If needed, feel free to upload
the file to:

http://qa.openmicroscopy.org.uk/qa/upload/

Regards,
-Melissa

On Mon, Oct 28, 2013 at 07:39:23AM -0700, Lebistes wrote:

> Hello, I downloaded to my pc a .lif file from a Leika microscope.
> The I downloaded the plugin LOCI, moved the file in the Imagej plugin
> folder, restart Imagej and open the file.
> This is the error that I receive:
> ImageJ 1.48e; Java 1.6.0_20 [64-bit]; Windows 7 6.1; 42MB of 3500MB (1%)
>  
> java.lang.IllegalArgumentException: 0 must not be null and positive.
>         at
> ome.xml.model.primitives.PositiveInteger.<init>(PositiveInteger.java:56)
>         at loci.formats.in.LIFReader.initMetadata(LIFReader.java:566)
>         at loci.formats.in.LIFReader.initFile(LIFReader.java:446)
>         at loci.formats.FormatReader.setId(FormatReader.java:1244)
>         at
> loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
>         at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
>         at loci.plugins.in.Importer.showDialogs(Importer.java:141)
>         at loci.plugins.in.Importer.run(Importer.java:79)
>         at loci.plugins.LociImporter.run(LociImporter.java:81)
>         at ij.IJ.runUserPlugIn(IJ.java:196)
>         at ij.IJ.runPlugIn(IJ.java:160)
>         at ij.IJ.runPlugIn(IJ.java:149)
>         at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:258)
>         at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
>         at ij.IJ.runUserPlugIn(IJ.java:196)
>         at ij.IJ.runPlugIn(IJ.java:160)
>         at ij.IJ.runPlugIn(IJ.java:149)
>         at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:453)
>         at ij.io.Opener.openImage(Opener.java:310)
>         at ij.io.Opener.openImage(Opener.java:333)
>         at ij.io.Opener.open(Opener.java:143)
>         at ij.io.Opener.openAndAddToRecent(Opener.java:246)
>         at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
>         at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
>         at java.lang.Thread.run(Thread.java:619)
>
> May you help me to solve the problem?
> Thanks
>
> Fabio Valenti
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/lif-files-on-Imagej-error-tp5005346.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Lebistes]

>Which version of Bio-Formats are you using?
I´m using the 4.4.9.
>If you see that error with the 4.4.9 version, then it would be helpful
>if you could send a file that shows the problem.  If needed, feel free to upload
>the file to:
>http://qa.openmicroscopy.org.uk/qa/upload/
I tried to upload it. I hope you received it.
Otherwise let me know
regards,

Fabio

[Melissa Linkert-2]

Hi Fabio,

> >Which version of Bio-Formats are you using?
> I´m using the 4.4.9.
> >If you see that error with the 4.4.9 version, then it would be helpful
> >if you could send a file that shows the problem.  If needed, feel free to
> upload
> >the file to:
> >http://qa.openmicroscopy.org.uk/qa/upload/
> I tried to upload it. I hope you received it.
> Otherwise let me know

Thank you for uploading an example file.  The file should open with the
trunk build of Bio-Formats, from:

http://hudson.openmicroscopy.org.uk/job/BIOFORMATS-trunk/lastSuccessfulBuild/artifact/artifacts/loci_tools.jar

The fix will also be included in the next stable release.

Regards,
-Melissa

On Tue, Oct 29, 2013 at 02:16:58AM -0700, Lebistes wrote:

> >Which version of Bio-Formats are you using?
> I´m using the 4.4.9.
> >If you see that error with the 4.4.9 version, then it would be helpful
> >if you could send a file that shows the problem.  If needed, feel free to
> upload
> >the file to:
> >http://qa.openmicroscopy.org.uk/qa/upload/
> I tried to upload it. I hope you received it.
> Otherwise let me know
> regards,
>
> Fabio
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/lif-files-on-Imagej-error-tp5005346p5005363.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Lebistes]

Hi, thanks for your answer.
Please explain me what to do.
So, previously I downloaded the plugin 4.4.9
Now you said me to download another version (trunk verion???? what does it mean???).
So I have to cancel the previous plugin and change it with the new one?
Thanks

Fabio

[ctrueden]

Hi Fabio,

> I have to cancel the previous plugin and change it with the new one?

Please use the Fiji distribution of ImageJ:
    http://fiji.sc/

Then enable the "Bio-Formats daily builds" update site as described here:
    http://fiji.sc/Bio-Formats#Daily_builds

It is much simpler than trying to download JAR files into the plain ImageJ
distribution.

Regards,
Curtis


On Wed, Oct 30, 2013 at 4:59 AM, Lebistes <[hidden email]> wrote:

> Hi, thanks for your answer.
> Please explain me what to do.
> So, previously I downloaded the plugin 4.4.9
> Now you said me to download another version (trunk verion???? what does it
> mean???).
> So I have to cancel the previous plugin and change it with the new one?
> Thanks
>
> Fabio
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/lif-files-on-Imagej-error-tp5005346p5005381.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Lebistes]

Hello,
thanks for your help.
I did it but I receive the same error with fiji, even after the update

[ctrueden]

Hi Fabio,

> I did it but I receive the same error with fiji, even after the update

Sorry for the long delay in reply. You can now easily use the
aforementioned "Bio-Formats trunk build" by enabling the "Bio-Formats 5"
update site (*not* "Bio-Formats 4"), according to the instructions at:

   http://fiji.sc/Bio-Formats#Daily_builds

Please let us know if you continue to have any trouble!

Regards,
Curtis


On Thu, Oct 31, 2013 at 5:20 AM, Lebistes <[hidden email]> wrote:

> Hello,
> thanks for your help.
> I did it but I receive the same error with fiji, even after the update
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/lif-files-on-Imagej-error-tp5005346p5005399.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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[Lebistes]

Hello,

thanks for your answer.

I tried the update, following all the steps from the website, and it do everything correctly.

But at the end, when I check the version of LOCI plugin, it tell me the old version, the 4.4.9 dev

So I don´t know what to do.

Regards,

Fabio

2013/12/4 Curtis Rueden [via ImageJ] <[hidden email]>

Hi Fabio,

> I did it but I receive the same error with fiji, even after the update

Sorry for the long delay in reply. You can now easily use the
aforementioned "Bio-Formats trunk build" by enabling the "Bio-Formats 5"
update site (*not* "Bio-Formats 4"), according to the instructions at:

   http://fiji.sc/Bio-Formats#Daily_builds

Please let us know if you continue to have any trouble!

Regards,
Curtis

On Thu, Oct 31, 2013 at 5:20 AM, Lebistes <[hidden email]> wrote:

> Hello,
> thanks for your help.
> I did it but I receive the same error with fiji, even after the update
>
>
>

> --
> View this message in context:

> http://imagej.1557.x6.nabble.com/lif-files-on-Imagej-error-tp5005346p5005399.html

> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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If you reply to this email, your message will be added to the discussion below:

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NAML

[ctrueden]

Hi Fabio,

> I tried the update, following all the steps from the website, and it
> do everything correctly.
> But at the end, when I check the version of LOCI plugin, it tell me
> the old version, the 4.4.9 dev
> So I don´t know what to do.

Apologies for the delay in reply. Have you made any progress on this issue?

Are you still unable to update from a fresh download of Fiji from fiji.sc,
followed by enabling the Bio-Formats-5 update site as described at
http://fiji.sc/Bio-Formats#Daily_builds ?

If so, what is your OS, and to which folder did you install Fiji?

Regards,
Curtis


On Thu, Dec 5, 2013 at 5:51 AM, Lebistes <[hidden email]> wrote:

> Hello,
> thanks for your answer.
> I tried the update, following all the steps from the website, and it do
> everything correctly.
> But at the end, when I check the version of LOCI plugin, it tell me the old
> version, the 4.4.9 dev
> So I don´t know what to do.
> Regards,
>
> Fabio
>
>
> 2013/12/4 Curtis Rueden [via ImageJ] <
> [hidden email]
> >
>
> > Hi Fabio,
> >
> > > I did it but I receive the same error with fiji, even after the update
> >
> > Sorry for the long delay in reply. You can now easily use the
> > aforementioned "Bio-Formats trunk build" by enabling the "Bio-Formats 5"
> > update site (*not* "Bio-Formats 4"), according to the instructions at:
> >
> >    http://fiji.sc/Bio-Formats#Daily_builds
> >
> > Please let us know if you continue to have any trouble!
> >
> > Regards,
> > Curtis
> >
> >
> > On Thu, Oct 31, 2013 at 5:20 AM, Lebistes <[hidden email]<
> http://user/SendEmail.jtp?type=node&node=5005809&i=0>>
> > wrote:
> >
> > > Hello,
> > > thanks for your help.
> > > I did it but I receive the same error with fiji, even after the update
> > >
> > >
> > >
> > > --
> > > View this message in context:
> > >
> >
> http://imagej.1557.x6.nabble.com/lif-files-on-Imagej-error-tp5005346p5005399.html
> >
> > > Sent from the ImageJ mailing list archive at Nabble.com.
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> > --
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> >
> >
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> >
> >
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> >  To unsubscribe from .lif files on Imagej error, click here<
> >
> > .
> > NAML<
> http://imagej.1557.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml
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> --
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>
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[Lebistes]

Hi Curtis,

luckily I solved the problem with a fresh download in a new folder and running it as administrator.

Thanks for your help.

Bests,

Fabio

2014/1/13 Curtis Rueden [via ImageJ] <[hidden email]>

Hi Fabio,

> I tried the update, following all the steps from the website, and it
> do everything correctly.
> But at the end, when I check the version of LOCI plugin, it tell me
> the old version, the 4.4.9 dev
> So I don´t know what to do.

Apologies for the delay in reply. Have you made any progress on this issue?

Are you still unable to update from a fresh download of Fiji from fiji.sc,
followed by enabling the Bio-Formats-5 update site as described at
http://fiji.sc/Bio-Formats#Daily_builds ?

If so, what is your OS, and to which folder did you install Fiji?

Regards,
Curtis

On Thu, Dec 5, 2013 at 5:51 AM, Lebistes <[hidden email]> wrote:

> Hello,

> thanks for your answer.

> I tried the update, following all the steps from the website, and it do
> everything correctly.
> But at the end, when I check the version of LOCI plugin, it tell me the old
> version, the 4.4.9 dev
> So I don´t know what to do.
> Regards,
>
> Fabio
>
>
> 2013/12/4 Curtis Rueden [via ImageJ] <

> [hidden email]

> >

>
> > Hi Fabio,
> >
> > > I did it but I receive the same error with fiji, even after the update
> >
> > Sorry for the long delay in reply. You can now easily use the
> > aforementioned "Bio-Formats trunk build" by enabling the "Bio-Formats 5"
> > update site (*not* "Bio-Formats 4"), according to the instructions at:
> >
> >    http://fiji.sc/Bio-Formats#Daily_builds
> >
> > Please let us know if you continue to have any trouble!
> >
> > Regards,
> > Curtis
> >
> >
> > On Thu, Oct 31, 2013 at 5:20 AM, Lebistes <[hidden email]<

> http://user/SendEmail.jtp?type=node&node=5005809&i=0>>

> > wrote:

> >
> > > Hello,
> > > thanks for your help.
> > > I did it but I receive the same error with fiji, even after the update
> > >
> > >
> > >
> > > --
> > > View this message in context:
> > >
> >
> http://imagej.1557.x6.nabble.com/lif-files-on-Imagej-error-tp5005346p5005399.html

> >

> > > Sent from the ImageJ mailing list archive at Nabble.com.
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
> >

> > ------------------------------

> >  If you reply to this email, your message will be added to the discussion
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> >  To unsubscribe from .lif files on Imagej error, click here<

>

>
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NAML

[VAM]

Hi,

I have a problem with Importing .lif files in Image J.
I downloaded the Bioformats package, but unfortunately each time I want to open a .lif file the following error occurs
loci.formats.FormatException: Invalid Memory Block: found magic bytes 0, expected 112
        at loci.formats.in.LIFReader.initFile(LIFReader.java:416)
        at loci.formats.FormatReader.setId(FormatReader.java:1317)
        at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)
        at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
        at loci.plugins.in.Importer.showDialogs(Importer.java:141)
        at loci.plugins.in.Importer.run(Importer.java:79)
        at loci.plugins.LociImporter.run(LociImporter.java:81)
        at ij.IJ.runUserPlugIn(IJ.java:202)
        at ij.IJ.runPlugIn(IJ.java:166)
        at ij.Executer.runCommand(Executer.java:131)
        at ij.Executer.run(Executer.java:64)
        at java.lang.Thread.run(Thread.java:662)

I have no idea what to do about this.

Does anyone have some suggestions?

Greetings,
Vicky