[ome-users] Histology data in JPEG XR format
Melissa Linkert
melissa at glencoesoftware.com
Wed Sep 3 20:44:40 BST 2014
Hi Trevor,
> I've been able to get my JPEG-XR files converted into TIFF files using
> software obtained from this site:
> http://hcbi.fas.harvard.edu/resources_software
>
> However, when I attempt to open the TIFF files in ImageJ, I get the error
> message:
>
> loci.formats.MissingLibraryException: Java Advanced Imaging (JAI) is
> required to read some TIFF files. Please install JAI from
> https://jai.dev.java.net/
Would you be willing to upload one of the files to
http://qa.openmicroscopy.org.uk/qa/upload? Without seeing the file,
it's going to be difficult for us to diagnose why Bio-Formats cannot
open it.
If you prefer not send a file (or don't want to wait for a fix), then
you might also try using Zeiss' freely available Zen Lite:
http://www.zeiss.com/microscopy/en_us/products/microscopy-software/zen-lite.html#downloads
which should allow you to save the original .czi files without
compression or export to TIFF (both of which should then be openable in
ImageJ).
Finally, we are working on support for JPEG-XR compressed images within
.czi files, as described on the OME issue tracking system:
https://trac.openmicroscopy.org.uk/ome/ticket/8493
If you would like to be automatically notified of updates to that
ticket, please let us know.
Regards,
-Melissa
On Wed, Sep 03, 2014 at 06:15:07PM -0600, Trevor Steve wrote:
> Hi All,
>
> As a follow-up with this issue:
>
> I've been able to get my JPEG-XR files converted into TIFF files using
> software obtained from this site:
> http://hcbi.fas.harvard.edu/resources_software
>
> However, when I attempt to open the TIFF files in ImageJ, I get the error
> message:
>
> loci.formats.MissingLibraryException: Java Advanced Imaging (JAI) is
> required to read some TIFF files. Please install JAI from
> https://jai.dev.java.net/
>
> This error message persisted despite installing the JAI Image I/O Tools
> into my imageJ plugins from the bio-formats downloads page at
> http://downloads.openmicroscopy.org/bio-formats/5.0.4/ I tried the 5.04,
> Latest Build, and Daily Builds. I'm not sure if maybe "plugins" is not the
> best place for me to put the JAI image tool... if anyone can suggest this
> should be placed somewhere else, that would be helpful information.
>
> Interestingly, when I attempt to open the same TIFF file in Fiji, I get a
> different error message:
>
> loci.formats.FormatException: loci.common.ReflectException: Cannot execute
> method: decodeAsRenderedImage
> at
> loci.formats.in.TiffJAIReader.openBufferedImage(TiffJAIReader.java:198)
> at loci.formats.in.TiffJAIReader.initFile(TiffJAIReader.java:158)
> at loci.formats.FormatReader.setId(FormatReader.java:1317)
> at loci.formats.DelegateReader.setId(DelegateReader.java:261)
> 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:202)
> at ij.IJ.runPlugIn(IJ.java:166)
> at ij.Executer.runCommand(Executer.java:131)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:662)
> Caused by: loci.common.ReflectException: Cannot execute method:
> decodeAsRenderedImage
> at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:320)
> at
> loci.formats.in.TiffJAIReader.openBufferedImage(TiffJAIReader.java:193)
> ... 13 more
> Caused by: java.lang.reflect.InvocationTargetException
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:315)
> ... 14 more
> Caused by: java.io.IOException: Illegal page requested from a TIFF file.
> at
> com.sun.media.jai.codecimpl.TIFFImageDecoder.decodeAsRenderedImage(TIFFImageDecoder.java:110)
> ... 19 more
>
> The dialog box for the error says:
>
> File is not in a supported format, a reader plugin is not available, or it
> was not found.
>
> at loci.plugins.in.Importer.showDialogs(Importer.java:141)
>
> So I'm not sure where to go from here with the data.....
>
> If anyone has any suggestions as to how I can open my data, this would be
> much appreciated.
>
> Thanks,
>
> Trevor
>
>
> On Wed, Sep 3, 2014 at 1:00 PM, Dmitry Fedorov <fedorov at ece.ucsb.edu> wrote:
>
> > Hi Trevor,
> >
> > Note that you need to read a CZI file compressed with JPEG-XR and not a
> > standard JPEG-XR file. OpenSlide project is actively working on adding
> > support for JPEG-XR compressed CZI files into its library. Once added
> > viewer and databases using openslide will be able to operate on those
> > images.
> >
> > Cheers,
> > dmitry
> >
> >
> > On Wed, Sep 3, 2014 at 11:27 AM, Trevor Steve <tsteve at ualberta.ca> wrote:
> >
> >> Hi All,
> >>
> >> I am trying to work with CZI files compressed using JPEG-XR compression.
> >> I am wondering if anyone has any experience working with such files from
> >> the following perspectives... considering that my research goal is to make
> >> measurements of histological structures from the images
> >>
> >> 1. Using ImageJ: I understand that the Bio-Formats plugin currently
> >> does not support JPEG-XR compressed files. Progress has been made, but it
> >> does not look like a solution has been found. Any advice on how progress
> >> could be made here would be appreciated.
> >>
> >> https://github.com/openmicroscopy/bioformats/pull/1014
> >>
> >> 2. Converting JPEG-XR files to a format used by ImageJ. The programs I
> >> am familiar with for converting images do not have functionality to allow
> >> conversion between JPEG-XR to analyzable formats such as TIFF.
> >>
> >> http://www.bioimage.ucsb.edu/BioImage Convert
> >>
> >> If anyone knows of a program which can convert JPEG-XR files, this would
> >> be much appreciated.
> >>
> >> 3. Programs that can work with JPEG-XR files and measure length of
> >> histological structures. I know that some programs such as Photoshop and
> >> GIMP can open JPEG-XR files, but are much less useful for my research
> >> application. If anyone knows of a program which is similar to ImageJ (easy
> >> to measure histological areas, volumes, lengths) but can open JPEG-XR, this
> >> would also be useful.
> >>
> >> Thanks,
> >>
> >> Trevor
> >>
> >>
> >>
> >> --
> >> Trevor Steve, MD
> >>
> >> Neurology Resident (PGY-7)
> >> PhD Student, Department of Medicine
> >> University of Alberta
> >>
> >> _______________________________________________
> >> ome-users mailing list
> >> ome-users at lists.openmicroscopy.org.uk
> >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >>
> >>
> >
> >
> > --
> > __________________________________
> >
> > Dmitry Fedorov Levit <dima at dimin.net>
> > Web: http://www.dimin.net/
> > __________________________________
> >
> > Center for Bio-Image Informatics:
> > <http://www.bioimage.ucsb.edu/>
> >
> > Vision Research Lab, Electrical and Computer Engineering:
> > <http://vision.ece.ucsb.edu/>
> >
> > University of California, Santa Barbara
> > _________________________________
> >
>
>
>
> --
> Trevor Steve, MD
>
> Neurology Resident (PGY-7)
> PhD Student, Department of Medicine
> University of Alberta
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
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