We're Hiring!

CZI and JPEG XR

Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats
Please note:
Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.

CZI and JPEG XR

Postby Gebhard » Wed Oct 12, 2016 1:05 pm

Hi,

we recently got a Zeiss AxioScan slide-scanner, which produces some quite large files (3-5 GB) in the CZI format. These files use the JPEG-XR coding, which seems to be problematic for omero. When importing, we always get a "unknown format" error. Is this a problem with our system, or a general problem?

Exporting to other formats is not really an option for us for various reasons (Zeiss-software crashes, we need multiple versions of our images, loss of information when down-scaling, >3channel images,...)

Any help would be really great!


Best,
Gebhard
Gebhard
 
Posts: 18
Joined: Fri Jul 01, 2016 7:20 am

Re: CZI and JPEG XR

Postby mtbc » Thu Oct 13, 2016 8:00 am

While Bio-Formats does not yet support JPEG-XR compression, it is now being worked on thanks to ZEISS and Glencoe Software. The announcement is available at https://www.openmicroscopy.org/site/new ... io-formats and you can read further background to this kind of collaboration with industrial partners at http://blog.openmicroscopy.org/file-for ... tnerships/

In short: it's a general problem, but a solution is in progress! It may well be a few months yet before we are able to release a version of OMERO that can handle these files but at that time we will of course announce in the usual way and mention JPEG-XR support in "what's new" as many users await it.

Cheers,
Mark
User avatar
mtbc
Team Member
 
Posts: 282
Joined: Tue Oct 23, 2012 10:59 am
Location: Dundee, Scotland

Re: CZI and JPEG XR

Postby Gebhard » Mon Oct 17, 2016 10:40 am

Thanks, this sounds really good!

Best,
Gebhard
Gebhard
 
Posts: 18
Joined: Fri Jul 01, 2016 7:20 am


Return to User Discussion [Legacy]

Who is online

Users browsing this forum: No registered users and 0 guests