[ome-users] Histology data in JPEG XR format

[Dmitry Fedorov]

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
>
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>
>


-- 
__________________________________

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
_________________________________
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