Re: I cannot open lif files from the SP8 confocal in Fiji

Posted by Dr Bertrand Vernay on Oct 15, 2014; 10:45am
URL: http://imagej.273.s1.nabble.com/I-cannot-open-lif-files-from-the-SP8-confocal-in-Fiji-tp5010050p5010051.html

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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