[ome-users] convert .lif file with bfconvert

Sun Jun 1 07:19:08 BST 2014

Hi Mark,

I just tried "File > Import > Bio-Formats" and it works as well.
If I select one of the files produced with ...%s.ome.tiff in the first
open dialog box and then Hyperstack in the "Bio-Formats Import
Options", I can open any of the series files.
If I separate on of these files into another directory and try to open
it the same way, Fiji crashes.
I can also open the file containing all the series, but made some
coffee in between.
So far I've used "File > Open". Sorry. "File > Open" also works for
the separated file, in case this matters, but shows them in gray and
plane by plane (no channell selection).

Thanks,
Michael

On 1 June 2014 03:08, Mark Hiner <hiner at wisc.edu> wrote:
> 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 I can check next week to see if I was using an outdated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
>> >> >
>> >> >
>> >> >
>> >
>> >
>
>