Re: Problem opening Leica SP1 .lei file

Posted by ctrueden on Jun 30, 2008; 4:52pm
URL: http://imagej.273.s1.nabble.com/Problem-opening-Leica-SP1-lei-file-tp3695642p3695644.html

Hi Matija,

It looks like you found a bug in Bio-Formats. First, please try the
latest trunk build, available for download from the Bio-Formats web
site at http://www.loci.wisc.edu/ome/formats-download.html. If you
still experience this error with the latest version, and would be able
to provide a sample dataset demonstrating the problem, it would be
extremely helpful to us for debugging. Files less than 15 MB can be
sent as to me directly as email attachments, or if you need a place to
put larger files you can use our FTP server -- just let us know and
I'll send you the connection details off-list.

Thanks,
Curtis

On Sun, Jun 29, 2008 at 5:49 PM, matijac
<[hidden email]> wrote:

> I have almost exactly the same problem. I am trying to open an image stack
> made on a Leica SP1 confocal microscope. I have ImageJ v1.40g running on
> Windows XP. I have installed the latest HAndleExtraFileTypes.class plugin.
> When opening the .lei file, I get an error saying that the accompanying txt
> file could not be found. However, the path to the .txt file in the error
> message is incorrect. It has the format C:\pathNAME.txt . The backslash
> behind the directory name and the .txt file name (NAME) is missing. I copied
> the .txt file to one directory lower and renamed it to fit the error message
> and tried again. I then got a different error message -"Plugin or class not
> found
> Leica_TIFF_sequence". I double checked that my
> HAndleExtraFileTypes.class was up to date, then I found this forum online. I
> installed the Bio-Formats plug-in and tried again. I got the following error
> message:
>
> java.lang.ArrayIndexOutOfBoundsException: 0
>       at loci.formats.in.LeicaReader.initFile(LeicaReader.java:491)
>       at loci.formats.FormatReader.setId(FormatReader.java:633)
>       at loci.formats.FormatHandler.setId(FormatHandler.java:134)
>       at loci.plugins.Importer.run(Importer.java:145)
>       at loci.plugins.LociImporter.run(LociImporter.java:74)
>       at ij.IJ.runUserPlugIn(IJ.java:158)
>       at ij.IJ.runPlugIn(IJ.java:124)
>       at ij.IJ.runPlugIn(IJ.java:113)
>       at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:253)
>       at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
>       at ij.IJ.runUserPlugIn(IJ.java:158)
>       at ij.IJ.runPlugIn(IJ.java:124)
>       at ij.IJ.runPlugIn(IJ.java:113)
>       at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:304)
>       at ij.io.Opener.openImage(Opener.java:233)
>       at ij.io.Opener.openImage(Opener.java:249)
>       at ij.io.Opener.open(Opener.java:116)
>       at ij.io.Opener.open(Opener.java:55)
>       at ij.plugin.Commands.run(Commands.java:23)
>       at ij.IJ.runPlugIn(IJ.java:131)
>       at ij.Executer.runCommand(Executer.java:104)
>       at ij.Executer.run(Executer.java:58)
>       at java.lang.Thread.run(Unknown Source)
>
>
> Needless to say, I am pretty much lost at this point.
>
> Any help would be greatly appreciated.
>
> Matija
>
>
> Michael Doube-3 wrote:
>>
>> Hi all
>>
>> I tried to open someone else's images taken on a Leica SP1 confocal
>> microscope by dragging and dropping the .lei file (which describes the
>> imaging session) onto ImageJ, but I got an error that the directory
>> couldn't be found - it looked as though the plugin was duplicating the
>> directory name string then confusing itself by looking for
>> ~/images/directory_1directory_1/ instead of just ~/images/directory_1/
>>
>> I don't have access to the images right now so can't give exact details
>> of the error message.  Can anyone else confirm this behaviour?
>>
>> This is ij 1.41e on 32-bit Ubuntu 8.04, using the IJ-bundled JRE.
>>
>> Mike
>>
>>
>
> --
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>