http://imagej.273.s1.nabble.com/Import-Zeiss-CZI-Data-into-ImageJ-tp5009482p5009487.html
There is a .czi to .tif (or .bigtif) converter for Axio Scan files. See
> Hi Trevor,
>
> > loci.formats.UnsupportedCompressionException: JPEG-XR not yet supported
>
> Bio-Formats does not yet support CZI files compressed using JPEG-XR
> compression.
>
> However, there is an issue tracking the need for it:
>
https://trac.openmicroscopy.org.uk/ome/ticket/8493>
> And better, there is an initial implementation under review:
>
https://github.com/openmicroscopy/bioformats/pull/1014>
> But it looks like there are some obstacles to including it, and/or missing
> functionality, so I do not know the ultimate timeline for inclusion into
> Bio-Formats.
>
> Regards,
> Curtis
>
>
> On Wed, Sep 3, 2014 at 11:59 AM, 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>