[ome-users] error opening stitched *.lsm using Bio-formats

[Kai Schleicher]

Dear OME team,

I have come across a couple of user images 
<https://filesender.switch.ch/filesender/?vid=04329d13-fe8b-93c9-b234-000076047e49> 
which don't import properly into OMERO as they are not read by the 
Bio-formats, see quoted error message below:

> loci.formats.FormatException: Unmatched UUID: 
> urn:uuid:faa8d48e-8cd2-414a-a041-1a9bc24e8cec
>     at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:616)
>     at loci.formats.FormatReader.setId(FormatReader.java:1397)
>     at 
> loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)
>     at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)
>     at loci.plugins.in.Importer.showDialogs(Importer.java:140)
>     at loci.plugins.in.Importer.run(Importer.java:76)
>     at loci.plugins.LociImporter.run(LociImporter.java:78)
>     at ij.IJ.runUserPlugIn(IJ.java:217)
>     at ij.IJ.runPlugIn(IJ.java:181)
>     at ij.Executer.runCommand(Executer.java:137)
>     at ij.Executer.run(Executer.java:66)
>     at ij.IJ.run(IJ.java:297)
>     at ij.IJ.run(IJ.java:272)
>     at ij.macro.Functions.doRun(Functions.java:603)
>     at ij.macro.Functions.doFunction(Functions.java:96)
>     at ij.macro.Interpreter.doStatement(Interpreter.java:230)
>     at ij.macro.Interpreter.doStatements(Interpreter.java:218)
>     at ij.macro.Interpreter.run(Interpreter.java:115)
>     at ij.macro.Interpreter.run(Interpreter.java:85)
>     at ij.macro.MacroRunner.run(MacroRunner.java:139)
>     at java.lang.Thread.run(Thread.java:745)
It's unfortunately unclear how the images came about, but apparently 
these are several tiles imaged on a LSM700, later on stitched using the 
grid/collection stitcher in FIJI and finally saved in one file per 
channel (two, in this case)

The individual channel images open fine with the normal file -> open 
from FIJI.

When opening the image in FIJI and checking the info (ctrl-i) I did 
actually find the "unmatched" 
urn:uuid:faa8d48e-8cd2-414a-a041-1a9bc24e8cec in the ome-xml metadata block.

Is there maybe something else missing, i.e is the set of images not 
complete?

Thanks for your help and cheers,
Kai

-- 
>>Please note my NEW PHONE NUMBERS: +41 61 207 57 31 (direct) +41 61 207 22 50 (central)<<
Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel |
Phone: +41 61 207 57 31 (direct) +41 61 207 22 50 (central) | kai.schleicher at unibas.ch | www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch

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