[ome-users] OMERO pyramid creation

[Sebastien Besson (Staff)]

Hi Kai,

thanks for the update. I could also confirm the error while reimporting your image into the
OMERO server.

The issue is actually a bug associated with the reading of the CZI file. Luckily this bug has
been  fixed and released in the most recent Bio-Formats version as you could confirm by
opening the file using Fiji.

This version is not yet included in the latest release of OMERO but the import of the file into
one of our development server went through without errors. So I expect your problem to be
fixed with the imminent release of OMERO 5.3.3.

Answering one of your initial questions, if Bio-Formats reads pyramidal subresolutions available
within the file, OMERO should not recalculate pyramids. In this case, the client message was slightly
misleading as the issue is rather at the file import level.

Best,
Sebastien

On 16 Jun 2017, at 13:02, Kai Schleicher <kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch>> wrote:


Hi,

I have an update to this: while there was no error during upload, I received an error during processing "failed to read pixels" for one of the images (example image ID 576<https://demo.openmicroscopy.org/webclient/?show=image-576> , see attached error log)

thanks for your help and cheers,
Kai



On 06/16/2017 11:45 AM, Kai Schleicher wrote:

Hi,

first, even though its already a bit in the past: Thanks for the great OME meeting! I was happy to meet everyone and see all the new and amazing things to come :)

second, thanks for the freshly installed 5.3.2 OMERO demo server! For testing I have uploaded some jpegXR compressed multi-sceen BF and FL images of our AxioScan slidescanner (*czi), which uploaded with no issue (dataset ID 17<https://demo.openmicroscopy.org/webclient/?show=dataset-17>, example image ID 576<https://demo.openmicroscopy.org/webclient/?show=image-576> ).

I noticed however that the OMERO sever spends some time calculating a pyramid for my images.

Since these images already contained pyramids that where calculated by Zen after acquisition, do you think it would be possible to skip pyramid creation on the OMERO server side and use the ones provided in the czi instead?

While I could confirm that FIJI/Bio-formats recognises the pyramids in those images, I don't really know if they are on the same zoom-level that OMERO expects/ likes to use.

Let me know if you wish to have the example images uploaded somewhere else other than your demo server :)

Thanks and cheers,
Kai

--
>>Please note my NEW PHONE NUMBERS: +41 61 207 57 31 (direct) +41 61 207 22 50 (central)<<
Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel |
Phone: +41 61 207 57 31 (direct) +41 61 207 22 50 (central) | 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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