[ome-users] converting lif files to ome-tiff

Tue Aug 19 19:52:44 BST 2014

Hi all,

I have some problems converting my .lif files to ome-tiff.
I have converted my .lif files originating from a "CLSM Leica SP 8"
with bfconvert of Bio-Formats 5.0.3.
Trying to make it reproducible I took the file "ko-A.ome.tiff" which
can be found here:
"https://www.dropbox.com/sh/t2z0f4jttcnfh8s/AADq21HNR7EwH1JFxskhXXhea"
  in the ome-tiff-files folder.

Below you can find the output of bfconvert, xmlvalid and
SCIFIOTestDriver itkSCIFIOImageIOTest with the -a flag.
The output of tiffcomment you can find as attachment.
itkSCIFIOImageIOTest in this example crashes trying to read the third series.

I'm actually trying to iterate over all series, reading and processing
them using itk.
With some other files I was successful.
With yet some other files my program crashed quite randomly after
reading some series.

Thanks a lot in advance
Michael Meuli

michael at mmeuli:~/bioimage/ome/bftools-5.0.3$ ./bfconvert
/home/michael/Dropbox/bactelize_data_20131209/lif-files/ko-A.lif
/home/michael/bioimage/ome/data/5.0.3/ko-A.ome.tiff
/home/michael/Dropbox/bactelize_data_20131209/lif-files/ko-A.lif
LIFReader initializing
/home/michael/Dropbox/bactelize_data_20131209/lif-files/ko-A.lif
Reading header
Finding image offsets
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Unknown Immersion value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
[Leica Image File Format] ->
/home/michael/bioimage/ome/data/5.0.3/ko-A.ome.tiff [OME-TIFF]
Series 0: converted 15/186 planes (8%)
Series 0: converted 44/186 planes (23%)
Series 0: converted 74/186 planes (39%)
Series 0: converted 105/186 planes (56%)
Series 0: converted 135/186 planes (72%)
Series 0: converted 164/186 planes (88%)
Series 0: converted 186/186 planes (100%)
......
Series 11: converted 30/126 planes (23%)
Series 11: converted 60/126 planes (47%)
Series 11: converted 90/126 planes (71%)
Series 11: converted 120/126 planes (95%)
Series 11: converted 126/126 planes (100%)
[done]
119.187s elapsed (9.487353+32.9513ms per plane, 3466ms overhead)

michael at mmeuli:~/bioimage/ome/bftools-5.0.3$ ./xmlvalid
/home/michael/bioimage/ome/data/5.0.3/ko-A.ome.tiff
Parsing schema path
http://www.openmicroscopy.org/Schemas/OME/2013-06/ome.xsd
Validating /home/michael/bioimage/ome/data/5.0.3/ko-A.ome.tiff
cvc-complex-type.2.4.a: Invalid content was found starting with
element 'MetadataOnly'. One of
'{"http://www.openmicroscopy.org/Schemas/OME/2013-06":TiffData,
"http://www.openmicroscopy.org/Schemas/OME/2013-06":Plane,
"http://www.openmicroscopy.org/Schemas/SA/2013-06":AnnotationRef}' is
expected.
cvc-complex-type.2.4.a: Invalid content was found starting with
element 'MetadataOnly'. One of
'{"http://www.openmicroscopy.org/Schemas/OME/2013-06":TiffData,
"http://www.openmicroscopy.org/Schemas/OME/2013-06":Plane,
"http://www.openmicroscopy.org/Schemas/SA/2013-06":AnnotationRef}' is
expected.
cvc-complex-type.2.4.a: Invalid content was found starting with
element 'MetadataOnly'. One of
'{"http://www.openmicroscopy.org/Schemas/OME/2013-06":TiffData,
"http://www.openmicroscopy.org/Schemas/OME/2013-06":Plane,
"http://www.openmicroscopy.org/Schemas/SA/2013-06":AnnotationRef}' is
expected.
cvc-complex-type.2.4.a: Invalid content was found starting with
element 'MetadataOnly'. One of
'{"http://www.openmicroscopy.org/Schemas/OME/2013-06":TiffData,
"http://www.openmicroscopy.org/Schemas/OME/2013-06":Plane,
"http://www.openmicroscopy.org/Schemas/SA/2013-06":AnnotationRef}' is
expected.
cvc-complex-type.2.4.a: Invalid content was found starting with
element 'MetadataOnly'. One of
'{"http://www.openmicroscopy.org/Schemas/OME/2013-06":TiffData,
"http://www.openmicroscopy.org/Schemas/OME/2013-06":Plane,
"http://www.openmicroscopy.org/Schemas/SA/2013-06":AnnotationRef}' is
expected.
cvc-complex-type.2.4.a: Invalid content was found starting with
element 'MetadataOnly'. One of
'{"http://www.openmicroscopy.org/Schemas/OME/2013-06":TiffData,
"http://www.openmicroscopy.org/Schemas/OME/2013-06":Plane,
"http://www.openmicroscopy.org/Schemas/SA/2013-06":AnnotationRef}' is
expected.
cvc-complex-type.2.4.a: Invalid content was found starting with
element 'MetadataOnly'. One of
'{"http://www.openmicroscopy.org/Schemas/OME/2013-06":TiffData,
"http://www.openmicroscopy.org/Schemas/OME/2013-06":Plane,
"http://www.openmicroscopy.org/Schemas/SA/2013-06":AnnotationRef}' is
expected.
cvc-complex-type.2.4.a: Invalid content was found starting with
element 'MetadataOnly'. One of
'{"http://www.openmicroscopy.org/Schemas/OME/2013-06":TiffData,
"http://www.openmicroscopy.org/Schemas/OME/2013-06":Plane,
"http://www.openmicroscopy.org/Schemas/SA/2013-06":AnnotationRef}' is
expected.
cvc-complex-type.2.4.a: Invalid content was found starting with
element 'MetadataOnly'. One of
'{"http://www.openmicroscopy.org/Schemas/OME/2013-06":TiffData,
"http://www.openmicroscopy.org/Schemas/OME/2013-06":Plane,
"http://www.openmicroscopy.org/Schemas/SA/2013-06":AnnotationRef}' is
expected.
cvc-complex-type.2.4.a: Invalid content was found starting with
element 'MetadataOnly'. One of
'{"http://www.openmicroscopy.org/Schemas/OME/2013-06":TiffData,
"http://www.openmicroscopy.org/Schemas/OME/2013-06":Plane,
"http://www.openmicroscopy.org/Schemas/SA/2013-06":AnnotationRef}' is
expected.
cvc-complex-type.2.4.a: Invalid content was found starting with
element 'MetadataOnly'. One of
'{"http://www.openmicroscopy.org/Schemas/OME/2013-06":TiffData,
"http://www.openmicroscopy.org/Schemas/OME/2013-06":Plane,
"http://www.openmicroscopy.org/Schemas/SA/2013-06":AnnotationRef}' is
expected.
cvc-complex-type.2.4.a: Invalid content was found starting with
element 'MetadataOnly'. One of
'{"http://www.openmicroscopy.org/Schemas/OME/2013-06":TiffData,
"http://www.openmicroscopy.org/Schemas/OME/2013-06":Plane,
"http://www.openmicroscopy.org/Schemas/SA/2013-06":AnnotationRef}' is
expected.
Error validating document: 12 errors found

michael at mmeuli:~/bioimage/itk/itk-4.6.0/gcc64rel/bin$
./SCIFIOTestDriver itkSCIFIOImageIOTest
/home/michael/bioimage/ome/data/5.0.3/ko-A.ome.tiff
/home/michael/bactelize_out_20131209/ko-A.ome.tiff -w -a -d 5
reader->GetUseStreaming(): 1
done checking streaming usage

itk::ExceptionObject (0x27976a0)
Location: "unknown"
File: /home/michael/bioimage/itk/itk-4.6.0/gcc64rel/Modules/Remote/SCIFIO/src/itkSCIFIOImageIO.cxx
Line: 899
Description: itk::ERROR: SCIFIOImageIO(0x25bf990): SCIFIOImageIO:
'SCIFIOITKBridge read' exited abnormally. Exception in thread "main"
java.lang.IllegalArgumentException: Invalid Z index: 60/60
at loci.formats.FormatTools.getIndex(FormatTools.java:328)
at loci.formats.FormatTools.getIndex(FormatTools.java:289)
at loci.formats.FormatReader.getIndex(FormatReader.java:979)
at loci.formats.ImageReader.getIndex(ImageReader.java:476)
at loci.formats.ReaderWrapper.getIndex(ReaderWrapper.java:403)
at loci.scifio.itk.SCIFIOITKBridge.read(SCIFIOITKBridge.java:426)
at loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:150)
at loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:108)
at loci.scifio.itk.SCIFIOITKBridge.waitForInput(SCIFIOITKBridge.java:83)
at loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:161)
at loci.scifio.itk.SCIFIOITKBridge.main(SCIFIOITKBridge.java:693)
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