[ome-users] [Software Feedback] Leica LASAF 3 format crashes Bioformats in FIJI

[Curtis Rueden]

Hi Sam,

Sorry for the delay in reply; I got busy with the ImageJ 2.0.0-beta4
release. In the future, to avoid such delays, please CC the OME-users list.

I tested your file with the latest trunk build of Bio-Formats, and it seems
to be working now. The fix will be included in the forthcoming 4.4.4
release of Bio-Formats; we will update Fiji accordingly as soon as 4.4.4 is
ready.

Regards,
Curtis


On Wed, Sep 5, 2012 at 4:20 PM, Sam Johnson <sam.johnson at duke.edu> wrote:

> Thanks Curtis.  I had updated FIJI and Bioformats but not luck.  I'm using
> win32.  It gets to the import options but on clicking ok I get
>
> java.lang.NullPointerException
> at loci.formats.in.LIFReader.translateDetectors(LIFReader.java:1106)
>  at loci.formats.in.LIFReader.translateMetadata(LIFReader.java:958)
> at loci.formats.in.LIFReader.initMetadata(LIFReader.java:485)
>  at loci.formats.in.LIFReader.initFile(LIFReader.java:431)
> at loci.formats.FormatReader.setId(FormatReader.java:1178)
>  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:185)
>  at ij.IJ.runPlugIn(IJ.java:152)
> at ij.IJ.runPlugIn(IJ.java:141)
> at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:375)
>  at HandleExtraFileTypes.run(HandleExtraFileTypes.java:53)
> at ij.IJ.runUserPlugIn(IJ.java:185)
>  at ij.IJ.runPlugIn(IJ.java:152)
> at ij.IJ.runPlugIn(IJ.java:141)
> at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:413)
>  at ij.io.Opener.openImage(Opener.java:288)
> at ij.io.Opener.openImage(Opener.java:309)
>  at ij.io.Opener.open(Opener.java:138)
> at ij.io.Opener.openAndAddToRecent(Opener.java:224)
>  at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
> at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
>  at java.lang.Thread.run(Thread.java:662)
>
> I attach a small example file
>
> Many thanks
>
> Sam
>
> On Wed, Sep 5, 2012 at 3:53 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:
>
>> Hi Sam,
>>
>>
>>> We had the new leica SP8 system in for demo last week.  I believe they
>>> have changed the file format slightly for LASAF3 and I can't open any of
>>> the data in FIJI.  I can give you an example file if you don't have one.
>>
>>
>> Can you please update your Fiji to the latest (Help > Update Fiji) and
>> try again?
>>
>> If you still have trouble, you can send us a sample non-working file
>> using Help > Upload Sample Image.
>>
>> Thanks,
>> Curtis
>>
>>
>> On Wed, Sep 5, 2012 at 10:05 AM, <sam.johnson at duke.edu> wrote:
>>
>>> Sam Johnson sent a message using the contact form at
>>> http://loci.wisc.edu/contact.
>>>
>>> Hello
>>>
>>> We had the new leica SP8 system in for demo last week.  I believe they
>>> have changed the file format slightly for LASAF3 and I can't open any of
>>> the data in FIJI.  I can give you an example file if you don't have one.
>>>
>>> Thanks for your wonderful plugin
>>>
>>> Cheers
>>>
>>> Sam
>>>
>>
>>
>
>
> --
> Sam Johnson, PhD
> Director, Light Microscopy Core Facility
> Duke University and Duke University Medical Center
> 4215 French Family Science Center, Science Drive
> Box 90338
> Durham, NC 27708
> USA
>
> sam.johnson at duke.edu
> Tel. (919) 613-8216
> Fax. (919) 613-8177
> http://microscopy.duke.edu
>
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