Open Microscopy Environment

When we import Zeiss Supra images into OMERO 5.1 they import without errors but show as blank (all black) both as thumbnails and in the viewer. If we download them from OMERO again the images display correctly using other image viewing software.

Could you please confirm the exact version of OMERO that you're using (both server and client)? 5.1.4 is the latest in the 5.1 line; 5.2.0 is the absolute latest version.

If you're using an older version, I would suggest upgrading to at least 5.1.4. You might also try checking the rendering options in the OMERO client, to see if reducing the maximum value fixes the image display. Instructions for doing this in the web client are in point 6 of http://help.openmicroscopy.org/web-client.html; instructions for Insight are in http://help.openmicroscopy.org/viewing- ... #rendering.

If that doesn't work, then it would be very helpful if you could send an example file to http://qa.openmicroscopy.org.uk/qa/upload/ so that we can duplicate the problem.

Hi,

this was using the OMERO plugin for ImageJ connecting to a OMERO server v. 5.1.2. Changing the rendering settings doesn't seem to have helped unfortunately. We'll aim to upgrade to v. 5.1.4 ASAP and in the meantime i've uploaded a sample image (Zeiss_supra_SEM.tif) to your QA link.

Thanks for your help,

Matt.

Hi,

Thank you for submitting your files.
We tested the import locally on both OMERO 5.2.0 and 5.1.4 servers, and in both cases we were able to import the '.czi' file without any issues. The resultant image post import was not blank and we were able to view the data in both cases. So a simple upgrade to OMERO 5.1.4 or OMERO 5.2.0 should solve your issue.

Please let us know if this does not solve your issue.

Best,
Balaji

Hi Balaji,

thanks for looking at this. The problem in this instance was opening tif files from a Zeiss Supra in OMERO 5.1.2. We've since upgraded to v 5.2.0 but i'm still experiencing the same blank display problem with the Zeiss_supra_SEM.tif image that I uploaded.

Thanks,

Matt.

Hi,

Thank you for the update.
I had initially concentrated on the .czi file alone.

On retesting,
We were able to reproduce the bug locally on the ".tiff" file,
and I have filed a ticket on this regard,
https://trac.openmicroscopy.org/ome/ticket/13119#ticket

and will get looked into, at the earliest.

Best,
Balaji

Hi,

It looks like this ticket is closed but we're still experiencing the bug in OMERO 5.2.7. Is it working for you? Would it help if I upload the images again?

Many thanks,

Matt.

HI Matt,

the ticket has been closed since the bug has been fixed as part of Bio-Formats 5.2.0 which was released in August 2016. However, since this version also includes model changes, the version of Bio-Formats used by OMERO 5.2.7 is still Bio-Formats 5.1.x.

The bug fix should be included as part of the next major release of OMERO 5.3.0 scheduled for the end of March.

Best,
Sebastien