Open Microscopy Environment

Hi all
I am wondering which version of BioFormats is used in
OMERO v4.4.4 and v4.4.5 ?

We have observed that certain nd2 files cannot be loaded in our
Omero system but can be loaded into our test system with Omero 4.4.5.

Thanks for your feedback.

Best
Alex

Hi Alex,

OMERO and Bio-Formats are released at the same time, so OMERO 4.4.4 uses Bio-Formats 4.4.4 and OMERO 4.4.5 uses Bio-Formats 4.4.5.

-Melissa

Hi Melissa hi all

Thanks for your comment.
We updated to OMERO 4.4.5 but unfortunately still have
issues with nd2 files and also certain tiff files.

It could be related to our installation since we could load the files
into a training system recently.

Could you give us a hint where we should look (log files etc) to get more
ideas on where the issue is with the failed import?

Would it help to provide you with the files?
Thanks.

Best
Alex

Hi again,

I just wanted to provide some more feedback what OMERO tells us:

When opening the nd2 image by clicking on 'Launch Viewer' you get
- Error instantiating pixel buffer: <path to Pixel data>/4285_pyramid

So the whole import and conversion did not succeed correctly using BioFormats 4.4.5.

Since we have been able to import such a file on the training OMERO server running OMERO 4.4.5, I'm wondering what we can do to fix this issue.

Thanks a lot for any suggestion.

Cheers
Alex

If I understand correctly, the files did import into your OMERO 4.4.5 installation, but when you go to view them in Insight (or Web?) you see an error message. Is that correct?

If the same files did import and are viewable with a different 4.4.5 server, then I would guess that the problem is not Bio-Formats, but rather something in the server configuration. Could you please attach the server and/or Insight logs (whichever you have access to)?

Hi Melissa
Thanks again for your feedback.
I tried again this evening - after around 45 min the nd2 file has been successfully imported. So I do not know what was wrong this morning...

The only thing I still see is that the web client of OMERO 4.4.5 has some issues with displaying the nd2 filem insight works fine though.
In the web client some of the tiles are not displayed at all.


Cheers
Alex

Hi Alex,

I'm wondering whether this is a bug in the web image viewer or a performance or rendering issue on the server. What browser are you using? Do you see the same thing if you try a different browser?

Could you try to show a 'console' for the browser to see if there are any error messages? I'm not sure how to do this for IE9 but for Firefox, you can add the "Firebug" plugin http://getfirebug.com/, then run it and look under the 'Console' tab. This should tell you if you're getting errors retrieving the tiles.

You can also look in the server web logs /var/logs/OMEROweb.log to see if there's any errors there.

Many thanks,

Will.