[ome-users] making JPEG-XR work with CZIs

[Josh Moore]

On Mon, Feb 29, 2016 at 4:54 PM, Grothausmann, Roman Dr.
<grothausmann.roman at mh-hannover.de> wrote:
> Dear mailing list members,

Hi Roman,


> Curtis pointed out in this post
>
> https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;33157c9b.1409
>
> that there is an ongoing effort to support JPEG-XR.

The ticket Curtis referenced, 8493, was unfortunately closed
“NEEDFUNDING”. No current effort is being put into JPEG-XR.


> Investigating the parent tags this contribution should already be in
> bftools (and fiji). However, when I try to open a CZI-file with such
> content I still get:
>
> Checking file format [Zeiss CZI]
> Initializing reader
> ZeissCZIReader initializing test.czi
> Exception in thread "main" loci.formats.UnsupportedCompressionException:
> JPEG-XR not yet supported

Correct, this is the current state of affairs.


> So I had a look at
> https://github.com/openmicroscopy/bioformats/blob/master/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java#L2948
>
> where an UnsupportedCompressionException is still issued.
>
> Is there a reason JPEG-XR is not yet supported by the ZeissCZIReader or
> was it merely forgotten after JPEG-XR got merged into bioformats?

The ome.jxr classes were the initial effort from PR 1014 that Curtis
mentioned back in 2014. You can read more about the cost of trying to
implement JPEG-XR in
http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-September/005616.html
. We followed up with a blog post this year:
http://blog.openmicroscopy.org/file-formats/community/2016/01/06/format-support/


> I gave it a quick try to replace the UnsupportedCompressionException with:
>
> https://github.com/romangrothausmann/bioformats/commit/625ab357a2d20dbd81c00dd2c151d00910921096
>
> but I can't get
>
> import ome.jxr.*;
>
> to work with ant and I'm lost in finding the right build.xml to extend the
> classpath for ZeissCZIReader.java.
>
> Running javac by hand and using ant just to pack the *.class I get bfconvert

…

Sorry for leaving those classes where they could lead to confusion.
We’ll deprecate them in all upcoming versions.


> Any help or hints how to use bfconvert to process CZIs with JPEG-XR are
> very appreciated.

Our best suggestion for the moment is spelled out under “What you can
do” on the blog post. Comments/suggestions welcome.

> Roman


All the best,
The OME Team