http://imagej.273.s1.nabble.com/Import-Zeiss-CZI-Data-into-ImageJ-tp5009482p5009486.html
> 2. Work is in progress to allow decompression of JPEG XR for use in
> If this is the case... any additional advice/expertise to help me
> Hi Douglas,
>
> The data were acquired by a collaborator in another country. I will email
> him to find out these details, but for now I am assuming that the data were
> acquired on a Zeiss AxioScan, and that the JPEG XR compression was turned
> on. So it is most likely that the data is JPEG XR compressed.
>
> Assuming this is the problem, it looks like:
>
> 1. Others have had trouble reading JPEG XR with Java
>
http://forums.zeiss.com/microscopy/community/showthread.php?t=1158>
> and
>
> 2. Work is in progress to allow decompression of JPEG XR for use in
> Bio-Formats
>
https://github.com/openmicroscopy/bioformats/pull/1014>
> If this is the case... any additional advice/expertise to help me advance
> this work would be much appreciated.
>
> Thanks,
>
> Trevor
>
>
> On Wed, Sep 3, 2014 at 11:17 AM, Douglas Richardson <
>
[hidden email]
> > wrote:
>
> > Hi Trevor,
> >
> > Was the data acquired on a Zeiss AxioScan? In the scan settings window
> did
> > you have JPEGXR compression turned on? If so, even though the file
> > extension is .CZI, the data is actually JPEGXR compressed.
> >
> >
> > On Wed, Sep 3, 2014 at 12:59 PM, Trevor Steve <
[hidden email]>
> wrote:
> >
> > > Hi all,
> > >
> > > I have histology images in the Zeiss CZI data format which I am trying
> to
> > > import into ImageJ.
> > >
> > > I have installed the Bio-Formats plugin and am using the Bio-Formats
> > > Importer to load the images.
> > >
> > > When I run the import for the raw histology images, ImageJ gives the
> > > following:
> > >
> > > loci.formats.UnsupportedCompressionException: JPEG-XR not yet supported
> > > at
> > >
> > >
> >
> loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:2822)
> > > at
> > >
> > >
> >
> loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:2794)
> > > at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:561)
> > > at loci.formats.FormatReader.setId(FormatReader.java:1317)
> > > at
> > loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)
> > > at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
> > > at loci.plugins.in.Importer.showDialogs(Importer.java:141)
> > > at loci.plugins.in.Importer.run(Importer.java:79)
> > > at loci.plugins.LociImporter.run(LociImporter.java:81)
> > > at ij.IJ.runUserPlugIn(IJ.java:199)
> > > at ij.IJ.runPlugIn(IJ.java:163)
> > > at ij.Executer.runCommand(Executer.java:131)
> > > at ij.Executer.run(Executer.java:64)
> > > at java.lang.Thread.run(Thread.java:619)
> > >
> > >
> > > I am not sure if I am making an error in the import settings, as the
> data
> > > should not be JPEG-XR, but rather CZI.
> > >
> > > Would gratefully appreciate any advice on this matter and how I can
> move
> > > forward with importing my data.
> > >
> > > Thanks,
> > >
> > > Trevor
> > >
> > >
> > >
> > > --
> > > Trevor Steve, MD
> > >
> > > Neurology Resident (PGY-7)
> > > PhD Student, Department of Medicine
> > > University of Alberta
> > >
> > > --
> > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> > >
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
> >
>
>
> --
> Trevor Steve, MD
>
> Neurology Resident (PGY-7)
> PhD Student, Department of Medicine
> University of Alberta
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>