Open Microscopy Environment

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

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

Thanks, this sounds really good!

Best,
Gebhard