Re: Import Zeiss CZI Data into ImageJ

Posted by Trevor Steve on
URL: http://imagej.273.s1.nabble.com/Import-Zeiss-CZI-Data-into-ImageJ-tp5009482p5009484.html

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