I cannot open lif files from the SP8 confocal in Fiji

[Judit Pampalona]

Hello all,

I would be very grateful if someone can help me with this issue. When I try
to open a lif file obtained from an SP8 confocal by dragging the file to
the fiji barr, it appears the following message :

"File is not in a supported format, a reader plugin is not available, or it
was not found"

When I try to import the very same file using the File<import<Bioformats ,
viewing as Hyperstack, it opens a log window with the following text:

loci.formats.FormatException: Invalid Memory Block: found magic bytes 0,
expected 112
    at loci.formats.in.LIFReader.initFile(LIFReader.java:412)
    at loci.formats.FormatReader.setId(FormatReader.java:1183)
    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:202)
    at ij.IJ.runPlugIn(IJ.java:166)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at ij.Command.runPlugIn(Command.java:148)
    at ij.Command.runCommand(Command.java:97)
    at ij.Executer.run(Executer.java:64)
    at java.lang.Thread.run(Thread.java:662)



Then I tried to update the LOCI plugins (the three options) and it says
every time that there is an error when trying to install them.

My version of Fiji is v1.49i, do you know how to solve this?


Thanks in advance,

Judit

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[Dr Bertrand Vernay]

Good morning

Here is quick work around until Bioformat is fixed.

1- open the file in LAS AF lite
2- Save as lif with a new file name
3- Fiji can now open the old lif file version

If you export the file as lif from the sp8 Fiji will also open it as a stack and you can recreate the hyperstack manually or use a macro to automate the task.

Bertrand

On October 15, 2014 11:23:21 AM GMT+01:00, Judit Pampalona <[hidden email]> wrote:

>Hello all,
>
>I would be very grateful if someone can help me with this issue. When I
>try
>to open a lif file obtained from an SP8 confocal by dragging the file
>to
>the fiji barr, it appears the following message :
>
>"File is not in a supported format, a reader plugin is not available,
>or it
>was not found"
>
>When I try to import the very same file using the
>File<import<Bioformats ,
>viewing as Hyperstack, it opens a log window with the following text:
>
>loci.formats.FormatException: Invalid Memory Block: found magic bytes
>0,
>expected 112
>    at loci.formats.in.LIFReader.initFile(LIFReader.java:412)
>    at loci.formats.FormatReader.setId(FormatReader.java:1183)
>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:202)
>    at ij.IJ.runPlugIn(IJ.java:166)
>    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>    at
>sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>    at
>sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>    at java.lang.reflect.Method.invoke(Method.java:597)
>    at ij.Command.runPlugIn(Command.java:148)
>    at ij.Command.runCommand(Command.java:97)
>    at ij.Executer.run(Executer.java:64)
>    at java.lang.Thread.run(Thread.java:662)
>
>
>
>Then I tried to update the LOCI plugins (the three options) and it says
>every time that there is an error when trying to install them.
>
>My version of Fiji is v1.49i, do you know how to solve this?
>
>
>Thanks in advance,
>
>Judit
>
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>ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Nikolay Kladt]

Hi Judit,

This is a known problem, see:
http://www.openmicroscopy.org/community/viewtopic.php?f=13&t=7581&p=14588&hilit=leica#p14588

Best,
Niko

On Wed, Oct 15, 2014 at 12:23 PM, Judit Pampalona <
[hidden email]> wrote:

> Hello all,
>
> I would be very grateful if someone can help me with this issue. When I try
> to open a lif file obtained from an SP8 confocal by dragging the file to
> the fiji barr, it appears the following message :
>
> "File is not in a supported format, a reader plugin is not available, or it
> was not found"
>
> When I try to import the very same file using the File<import<Bioformats ,
> viewing as Hyperstack, it opens a log window with the following text:
>
> loci.formats.FormatException: Invalid Memory Block: found magic bytes 0,
> expected 112
>     at loci.formats.in.LIFReader.initFile(LIFReader.java:412)
>     at loci.formats.FormatReader.setId(FormatReader.java:1183)
>     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:202)
>     at ij.IJ.runPlugIn(IJ.java:166)
>     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>     at
>
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>     at
>
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>     at java.lang.reflect.Method.invoke(Method.java:597)
>     at ij.Command.runPlugIn(Command.java:148)
>     at ij.Command.runCommand(Command.java:97)
>     at ij.Executer.run(Executer.java:64)
>     at java.lang.Thread.run(Thread.java:662)
>
>
>
> Then I tried to update the LOCI plugins (the three options) and it says
> every time that there is an error when trying to install them.
>
> My version of Fiji is v1.49i, do you know how to solve this?
>
>
> Thanks in advance,
>
> Judit
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Dr. Nikolay Kladt
Image and Data Analyst, CECAD Imaging Facility
[hidden email]
++49 221 478 84028
https://www.linkedin.com/in/kladtn

CECAD Cologne - Excellent in Aging Research
Universität zu Köln
Joseph-Stelzmann Str. 26
50931 Cologne

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