[ome-users] Problem displaying OME.Tiff exports from zeiss Zen blue

[Kai Schleicher]

Hi Damir and Sebastien,

Thanks for your replys! I tested the files again with OMERO 5.2.2 and can confirm that it works. Concerning the script I am sure it would be great to have. In case Niko or I will have one we'll of course let you know.

Thanks and cheers,
Kai

From: Damir Sudar [mailto:dsudar at lbl.gov]
Sent: Dienstag, 8. März 2016 18:35
To: OME User Support List
Subject: Re: [ome-users] Problem displaying OME.Tiff exports from zeiss Zen blue

Hi Kai,

As Sebastien mentions, I have the exact same problem. Sebastien provided guidance how to write a script to delete the broken pyramid files that block new ones from being generated and as soon as my current grant is out the door, I'll look at writing such a script. But in case you do it sooner than me, please let us all know. No doubt there are others with the same issue.

Note that pyramid generation for those very large Axioscan/ZEN-generated OME-TIFFs takes a fairly long time, even on a powerful server. But I can attest that it does work on 5.2.2.

Cheers,
- Damir
On 3/8/2016 3:00 AM, Sebastien Besson (Staff) wrote:
Hi Kai,

thanks for reporting this issue. Looking at the images, they were imported back into February
using OMERO 5.2.1 / Bio-Formats 5.1.6. The pyramid generation was broken with exactly the
same stack trace than the one reported by Damir in a forum thread [1] and fixed in Bio-Formats
5.1.8.

There are a different answers to your email:

- re-importing the same image into an OMERO 5.2.2 instance e.g. the demo server should work
  out-of-the-box and the pyramid should be properly generated
- in a production environment, deleting the stale pyramid files using the command suggested
  in the thread linked above should also work without forcing a new import
- from our side, we have created a card to improve the behavior illustrated by this use case both
  server-side during pyramid generation and client-side e.g. via scripts [2]

Best,
Sebastien

[1] https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=7907
[2] https://trello.com/c/TM1Si3UN/38-pyramids

On 7 Mar 2016, at 14:01, Kai Schleicher <kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch>> wrote:

Hi,

I recorded images in the czi format on the Zeiss Axioscan Slidescanner and exported them via Zen Blue to OME-TIFFs.

These OME-Tiffs open correctly in FIJI using the latest Bioformats.

However, they fail to open after being imported into OMERO.

Import to is handled without error but the images cannot be displayed in the viewer. The also do not have a preview, instead the "watch"-icon is shown.

I am using the latest version of OMERO (your demo server) and this client: OMERO.insight-5.2.2-ice35-b17-win.

The images in question have the ID 203547 and 203548.

Thanks for your help and cheers,
Kai

--
Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel
Phone: +41 61 267 22 50 | kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch> | www.biozentrum.unibas.ch<http://www.biozentrum.unibas.ch/> | www.microscopynetwork.unibas.ch<http://www.microscopynetwork.unibas.ch/>

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Damir Sudar - Staff Scientist

Lawrence Berkeley Natl Laboratory / MBIB

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