[ome-users] convert .lif file with bfconvert

Sun Jun 1 02:08:25 BST 2014

Hi Michael,

I can import the bfconvert output into Fiji with no problem.
>

I just wanted to confirm, you're using "File > Import > Bio-Formats" or the
Bio-Formats importer in Fiji, correct? It definitely didn't work for me
when I tried yesterday. I can check next week to see if I was using an
outdated Bio-Formats or something..

Thanks,
Mark

On Sat, May 31, 2014 at 7:52 AM, Michael Meuli <michael.meuli at gmail.com>
wrote:

> Hi Mark
>
> I can import the bfconvert output into Fiji with no problem.
> (If I do "./bfconvert /path/to/wt-dead-A.lif /path/to/output.ome.tiff" or
> "./bfconvert /path/to/wt-dead-A.lif /path/to/output_series_%s.ome.tiff"
> I can open the file(s) with Fiji.)
> If I open the .lif file with Fiji and export one series to ome.tiff I
> can read the output with ./SCIFIOTestDriver itkSCIFIOImageIOTest ...
> whereas I'm not able to read the output of bfconvert.
>
> Thanks a lot and best regards
> Michael
>
>
>
> On 30 May 2014 16:18, Mark Hiner <hinerm at gmail.com> wrote:
> > Hi Michael,
> >
> >> "./SCIFIOTestDriver
> itkSCIFIOImageIOTest/path/to/output_series_0.ome.tiff
> >> /path/to/scifio-test.ome.tiff"
> >
> > Just a reminder, since you're writing ome.tiff you should have a "-w"
> flag
> > at the end of this command. It sounds like you were using -w, just
> wanted to
> > clarify for anyone else reading this thread.
> >
> >> Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
> >
> >  There are two problems here. First, it seems that in SCIFIOImageIO the
> use
> > of Bio-Formats is overly aggressive in pulling in all the series, thus
> the
> > OutOfMemoryError. If you physically isolate a single series (e.g. delete
> or
> > move to another directory series 1-19) the application will run, but we
> get
> > another exception (at least on my end):
> >
> > ./SCIFIOTestDriver itkSCIFIOImageIOTest output_series_0.ome.tiff
> > scifio-test.ome.tiff -w
> >
> > reader->GetUseStreaming(): 1
> > done checking streaming usage
> > ITK test driver caught an ITK exception:
> >
> > itk::ExceptionObject (0x7ff8838b6ae8)
> > Location: "unknown"
> > File:
> >
> /Users/mhiner/loci/ITK/build/Modules/Remote/SCIFIO/src/itkSCIFIOImageIO.cxx
> > Line: 180
> > Description: itk::ERROR: SCIFIOImageIO(0x7ff8838b4f00): SCIFIOImageIO
> exited
> > abnormally. Creating new reader for output_series_0.ome.tiff
> >
> > log4j:WARN No appenders could be found for logger
> > (loci.common.services.ServiceFactory).
> > log4j:WARN Please initialize the log4j system properly.
> > log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
> > more info.
> > Exception in thread "main" loci.formats.FormatException: Unmatched UUID:
> > urn:uuid:b72fe97b-02c9-4029-a876-ca2bae46cbac
> >     at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:456)
> >
> >     at loci.formats.FormatReader.setId(FormatReader.java:1244)
> >     at loci.formats.ImageReader.setId(ImageReader.java:727)
> >     at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
> >     at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
> >     at
> > loci.scifio.itk.SCIFIOITKBridge.createReader(SCIFIOITKBridge.java:617)
> >     at
> > loci.scifio.itk.SCIFIOITKBridge.readImageInfo(SCIFIOITKBridge.java:268)
> >     at
> > loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:133)
> >
> >     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:163)
> >     at loci.scifio.itk.SCIFIOITKBridge.main(SCIFIOITKBridge.java:688)
> >
> > I also get this exception when importing with Bio-Formats into Fiji.
> >
> > As a side note, there are flags for itkSCIFIOImageIOTest that, in theory,
> > should help the out of memory side:
> >
> > "-s <n1, n2>" should limit the series read.
> > "-v <n>" should divide the data into divisions, which might mitigate the
> > risk of OutOfMemoryErrors.
> >
> > But neither of these will help the UUID exception. Also, I still got
> > OutOfMemoryErrors with these, so it was still trying to initialize using
> all
> > the series. So I created a new issue in the SCIFIO-ImageIO tracker.
> >
> > Anyway, try importing the bfconvert output into Fiji with Bio-Formats and
> > let me know if you don't get the UUID exception. If you do, then I think
> the
> > bfconvert output is just invalid..
> >
> > Regards,
> > Mark
> >
> >
> > On Thu, May 29, 2014 at 12:17 PM, Michael Meuli <michael.meuli at gmail.com
> >
> > wrote:
> >>
> >> Hi Mark,
> >>
> >> Thanks for the quick response. I can see I was using
> >> itkSCIFIOImageIOTest the wrong way and it doesn't make sense to use it
> >> like this.
> >> If I use the -w flag I get an error in all cases but at the moment I
> >> don't care as my aim now is to read ome.tiff files with itk.
> >> I've written a small program (mainly by copy paste from examples /
> >> https://github.com/michaelmeuli/bactelize) which so far reads the
> >> multi-channel-z-series.ome.tif file, does a maximum intensity
> >> projection of one channel and writes a 2D image and it seems to work
> >> with the multi-channel-z-series.ome.tif but not with the files
> >> converted with bfconvert.
> >>
> >> Expressed with itkSCIFIOImageIOTest:
> >> "./SCIFIOTestDriver itkSCIFIOImageIOTest
> >> /path/to/multi-channel-z-series.ome.tif /path/to/scifio-test.ome.tiff"
> >> doesn't give an error and seems to produce a tiff file of the first
> >> z-plane, but
> >> "./SCIFIOTestDriver itkSCIFIOImageIOTest
> >> /path/to/output_series_0.ome.tiff /path/to/scifio-test.ome.tiff" gives
> >> an error:
> >>
> >> reader->GetUseStreaming(): 1
> >> done checking streaming usage
> >> ITK test driver caught an ITK exception:
> >>
> >> itk::ExceptionObject (0x2f87680)
> >> Location: "unknown"
> >> File:
> >>
> /home/michael/Colocalization/ITK-Release-build/Modules/Remote/SCIFIO/src/itkSCIFIOImageIO.cxx
> >> Line: 180
> >> Description: itk::ERROR: SCIFIOImageIO(0x2f78970): SCIFIOImageIO
> >> exited abnormally. Creating new reader for
> >>
> >>
> /home/michael/bioimage/ome/data/wt-dead-A-ome-tiff/output_series_0.ome.tiff
> >> log4j:WARN No appenders could be found for logger
> >> (loci.common.services.ServiceFactory).
> >> log4j:WARN Please initialize the log4j system properly.
> >> log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig
> >> for more info.
> >> Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
> >> at java.nio.HeapByteBuffer.<init>(HeapByteBuffer.java:39)
> >> at java.nio.ByteBuffer.allocate(ByteBuffer.java:312)
> >> at
> >>
> loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:132)
> >> at
> >>
> loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:118)
> >> at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:532)
> >> at loci.common.NIOFileHandle.seek(NIOFileHandle.java:254)
> >> at
> >>
> loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:140)
> >> at loci.formats.tiff.TiffParser.getIFDOffsets(TiffParser.java:308)
> >> at loci.formats.tiff.TiffParser.getIFDs(TiffParser.java:226)
> >> at
> loci.formats.in.MinimalTiffReader.initFile(MinimalTiffReader.java:426)
> >> at loci.formats.FormatReader.setId(FormatReader.java:1244)
> >> at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:704)
> >> at loci.formats.FormatReader.setId(FormatReader.java:1244)
> >> at loci.formats.ImageReader.setId(ImageReader.java:727)
> >> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
> >> at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
> >> at
> loci.scifio.itk.SCIFIOITKBridge.createReader(SCIFIOITKBridge.java:622)
> >> at
> loci.scifio.itk.SCIFIOITKBridge.readImageInfo(SCIFIOITKBridge.java:266)
> >> at
> >> loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:131)
> >> 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)
> >>
> >> Best regards
> >> Michael Meuli
> >>
> >>
> >>
> >> On 29 May 2014 17:41, Mark Hiner <hiner at wisc.edu> wrote:
> >> > Hi Michael,
> >> >
> >> >
> >> >> The problem is that ./SCIFIOTestDriver itkSCIFIOImageIOTest
> >> >> /path/to/output_series_0.ome.tiff /path/to/scifiotest.ome.tiff
> >> >> (and my little program) throws an exception.
> >> > ...
> >> >
> >> >> How do I use bfconvert the correct way for my case?
> >> >
> >> > You used bfconvert correctly to convert your dataset. Just so it's
> >> > clear, if
> >> > your goal was to produce an OME-TIFF:
> >> >
> >> >> /SCIFIOTestDriver itkSCIFIOImageIOTest
> >> >> /path/to/output_series_0.ome.tiff
> >> >> /path/to/scifiotest.ome.tiff
> >> >
> >> > would be unnecessary, as you already have the OME-TIFF output from
> >> > bfconvert. The itkSCIFIOImageIOTest is an analogous tool to bfconvert
> >> > written in the Bio-Formats C++ framework. (although comparing the
> >> > outputs of
> >> > the itkSCIFIOImageIOTest conversion would be a good way to check for
> >> > errors
> >> > in the conversion process)
> >> >
> >> > That said, I believe your conversion failed because the output was
> >> > picked up
> >> > by the ITK TIFF ImageIO, which I believe only supports 3D data. The
> >> > itkSCIFIOImageIOTest utility does basically no automation - you have
> to
> >> > tell
> >> > it exactly how to run, and because the SCIFIOImageIO is an external
> >> > module
> >> > it is not prioritized by the ITK format detection framework over
> >> > internal
> >> > modules (I'm not sure it's part of the automatic detection framework
> at
> >> > all,
> >> > actually). So you need to force the use of the SCIFIOImageIO for
> >> > writing.
> >> >
> >> > If you run:
> >> >
> >> >  /SCIFIOTestDriver itkSCIFIOImageIOTest
> >> >
> >> > with no arguments from the command line, it will print the usage +
> >> > available
> >> > flags. The flag you wanted here is "-w"  to write with the
> SCIFIOImageIO
> >> > (which will use Bio-Formats, and thus the OME-TIFF writer).
> >> >
> >> > So the final syntax is:
> >> >
> >> > /SCIFIOTestDriver itkSCIFIOImageIOTest
> /path/to/output_series_0.ome.tiff
> >> > /path/to/scifiotest.ome.tiff -w
> >> >
> >> > which worked for me locally.
> >> >
> >> > Let me know if you have any other questions or issues!
> >> >
> >> > Regards,
> >> > Mark
> >> >
> >> > On Thu, May 29, 2014 at 4:40 AM, Michael Meuli <
> michael.meuli at gmail.com>
> >> > wrote:
> >> >>
> >> >> ./SCIFIOTestDriver itkSCIFIOImageIOTest
> >> >> /path/to/output_series_0.ome.tiff /path/to/scifiotest.ome.tiff
> >> >
> >> >
> >> >
> >
> >
>
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