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Import Zeiss CZI Data into ImageJ

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Trevor Steve

Import Zeiss CZI Data into ImageJ

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

Douglas Richardson

Re: Import Zeiss CZI Data into ImageJ

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

ctrueden

Re: Import Zeiss CZI Data into ImageJ

In reply to this post by Trevor Steve

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:

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Trevor Steve

Re: Import Zeiss CZI Data into ImageJ

In reply to this post by Douglas Richardson

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

ctrueden

Re: Import Zeiss CZI Data into ImageJ

Hi Trevor,

> 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.

The best place to ask Bio-Formats questions is on the ome-users mailing
list:

http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/

Regards,
Curtis

On Wed, Sep 3, 2014 at 12:27 PM, Trevor Steve <[hidden email]> wrote:

> 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
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Douglas Richardson

Re: Import Zeiss CZI Data into ImageJ

In reply to this post by ctrueden

Hi Trevor,

There is a .czi to .tif (or .bigtif) converter for Axio Scan files. See
our website: http://hcbi.fas.harvard.edu/resources_software

Hope this helps!

-Doug

On Wed, Sep 3, 2014 at 1:21 PM, Curtis Rueden <[hidden email]> wrote:

> 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
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html