Open Microscopy Environment

Hi there!

I'm currently experimenting with the demo server as may eventually implement our own OMERO server for our school. However, about two days ago I am suddenly unable to upload or delete anything. When uploading it gets stuck at "importing metadata" and stays there all the way. For deleting it is always in process does not complete.

Anyone else having issues with the Demo Server like this?

Thanks!

Hi Shaun,

we certainly have seen high CPU usages on the demo server. Our initial investigation seemed to highlight performance issues related to the Zeiss CZI reader in Bio-Formats.

So far we have not been able to pinpoint the cause, this might be an issue that has been addressed in a more recent version of Bio-Formats not yet used in OMERO or a completely new issue. In the meantime, we have restarted the demo server so the service should be back to normal. Although please be aware that the issues you have been seeing with the CZI files might still be present. We will update the card linked above with information about the investigation as soon as possible.

Best,
Sebastien

Dear Sebastien,

Thank you for your help and your reply. Have also noted the issues. Will keep them in mind while experimenting with the server and may consider other formats eventually I guess.

Thanks again for your help

Regards
Shaun

HI Shaun,

some update on this thread. While investigating the events, it turns out the main issue is related to the opening of certain CZI files that you tried to import on the server and Bio-Formats hanging at initialization. These locked threads eventually led to the server becoming unresponsive until we restarted it.

From our testing, it seems this particular issue has been fixed in a more recent release of Bio-Formats. We will keep monitoring the threads and update the post as soon as the demo server is upgrade to the upcoming OMERO version which will include a more recent Bio-Formats where this issue is fixed.

Best,
Sebastien

Hi Shaun,

quick update on this, the latest release of OMERO 5.3.4 was deployed on the demo server. This includes Bio-Formats 5.5.3 which should fix for the hanging threads issue reported above.

If you try to re-import some of the files that were previously failing into the demo server, I would expect the imports to complete.

Best,
Sébastien