[ITK] convert .lif file with bfconvert

Mark Hiner hiner at wisc.edu
Wed Jun 4 07:59:24 EDT 2014 

Hi Michael,

This worked for me as well. Thanks a lot.
>

I'm glad we got it working too!

Could you give me a hint on how to get the single channells out of
> "itk::Image< unsigned short, 5 >"?
>

I spend most of my time in Java-land, so I'm not as familiar with the ITK
API as I'd like to be. It does sound like the ExtractImageFilter
<http://www.itk.org/Doxygen/html/classitk_1_1ExtractImageFilter.html> could
do what you want by collapsing the image along the channel axis. Maybe
someone else on this list can provide a code example, or a better solution?

Thanks,
Mark


On Tue, Jun 3, 2014 at 1:56 AM, Michael Meuli <michael.meuli at gmail.com>
wrote:

> Hi Mark
>
> > export JAVA_FLAGS=-Xmx3400m
> > /SCIFIOTestDriver itkSCIFIOImageIOTest
> bfconvert_output/output_series_0.ome.tiff test.ome.tiff -w -d 5
>
> This worked for me as well. Thanks a lot.
> So I can convert my multi-channell-z-series images contained in my
> .lif files with bfconvert into ome.tiff and read these with itk thanks
> to the SCIFIO module.
> If I see this correctly this reads the image into an object of type
> "itk::Image< unsigned short, 5 >".
> I was trying to read it into "itk::Image< <itk::Vector<unsigned short,
> 3>>, 3 >" and to use VectorIndexSelectionCastImageFilter
> to get to the single channells.
> Could you give me a hint on how to get the single channells out of
> "itk::Image< unsigned short, 5 >"?
>
> Thanks,
> Michael
>
>
>
> On 2 June 2014 15:27, Mark Hiner <hiner at wisc.edu> wrote:
> > Hi Michael,
> >
> >
> >> So far I've used "File > Open". Sorry.
> >
> >
> > No need to apologize! This is a common misunderstanding. When you use
> "File
> >> Open", your .ome.tiff gets picked up by the ImageJ TIFF reader instead
> of
> > Bio-Formats. So that's why metadata is missing. This is actually
> something
> > we're improving with the ImageJ2 release this week: "File > Open" will be
> > able to work with Bio-Formats automatically.
> >
> >
> >> I just tried "File > Import > Bio-Formats" and it works as well.
> >
> >
> > This made me suspect that there was something going wrong on my end. I
> > should have asked which version of Bio-Formats you were using bfconvert
> > from.. I was using it from v5.0.1. I updated to v5.0.2 this morning and
> > tried bfconvert, and now my output .ome.tiffs open just fine in Fiji's
> > Bio-Formats Importer. So I'm sorry for any misguidance there.
> >
> > Anyway, as for the itkSCIFIOImageIO use, I was still getting
> > OutOfMemoryErrors. So you'll want to increase the amount of memory Java
> can
> > use. By default, the ImageIO creates a JVM with 256m. You can override
> this
> > by setting a "JAVA_FLAGS" environment variable. Once I went over 3g, I
> was
> > actually able to convert your data appropriately, finally! To increase
> > available memory, I used the command:
> >
> > export JAVA_FLAGS=-Xmx3400m
> >
> > Also! I forgot there were some important considerations with other flags
> to
> > use with the itkSCIFIOImageIO:
> >
> > use "-d 5". I know your data is 3D + channels, but as an .ome.tiff it
> will
> > be considered 5D by the imageio and the wrong dimensions could get
> truncated
> > if you set -d less than 5.
> > If necessary, set pixel type with "-t". The default is unsigned short (an
> > ITK pixel type, which is equivalent to Bio-Formats's uint16). Your data
> is
> > uint16 so there's no need to use this flag, just wanted you to be aware
> of
> > it.
> >
> > So, the command that worked for me was:
> >
> > /SCIFIOTestDriver itkSCIFIOImageIOTest
> > bfconvert_output/output_series_0.ome.tiff test.ome.tiff -w -d 5
> >
> > Let me know if you have any more problems,
> >
> > Mark
> >
> >
> >
> > On Sun, Jun 1, 2014 at 1:19 AM, Michael Meuli <michael.meuli at gmail.com>
> > wrote:
> >>
> >> 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
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >
> >> >> >
> >> >
> >> >
> >
> >
>
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