Open Microscopy Environment

Hi all

is it possible to update bioformats for an existing omero installation. The Bioformats version included with omero has a nasty bug that prevents the reading of certain Zeiss tiff files from Supra's and NVisions. This bug is fixed in the new release of bioformats but this is not included in the omero server yet.

Is there a simple way to install the new bioformats libraries into an existing omero server installation to get this functionality.

thanks

Gregor

Dear Gregor,

There isn't yet a supported way to plug a newer Bio-Formats into an older OMERO and Bio-Formats 5.2 releases will not work in OMERO 5.2 anyway because of some API/model changes. We do plan to address the first point but that is still work in progress I am afraid. We are also working on OMERO 5.3 which will use the latest Bio-Formats 5.2.

We may release another Bio-Formats in the 5.1 line that includes the fix you need. Also, if you are feeling especially enterprising then it may well be possible to backport just the relevant reader fix from Bio-Formats 5.2 to Bio-Formats 5.1 and replace the relevant JARs in your OMERO installation but we do not provide step-by-step instructions for this nor could we provide much reassurance that OMERO would continue to work properly thereafter.

Sorry I don't have good news here for you for the short term; safest and surest would be to just wait for OMERO 5.3 and upgrade to that, but that is some weeks out yet as we want to finish polishing and testing the new features well to make sure that everything is solid.

Cheers,

Mark