Open Microscopy Environment

Hi,
This is on OMERO 5.0.8. Many hours after importing a mixture of 240 TIFFS and JPGs (all 2200 by 6000 pixels in size), the thumbnail panel shows the "clock" for many of the images:


and for many of them, the "Pyramid being generated" message shows when opening them in full view. Is there a way to make that process quicker? The system is pretty lightly loaded so it's not busy doing something else.

Thanks,
- Damir

Hi Damir,

the issue you describe here looks very similar to the one from this forum thread.

Are you importing single tile TIFF files? If so, performance improvements for the pyramid generation have been included in OMERO 5.1.0 and you may want to test this import workflow on a development 5.1.0 server. You might also want to increase the number of pixeldata threads in the server configuration and check if this speeds up the pyramid generation process.

Best regards,
Sebastien

Hi Sebastien,

Yes, you are right that there are many similarities with the earlier thread. Apologies that I hadn't looked at that first. I'll look carefully at the suggestions in there and in your reply here for my 5.0.8 server.

I just tried the import of (yes, indeed these are all single-tile TIFFs and single-tile JPGs) on my new server running OMERO 5.1.0 and the pyramid creation is definitely much much faster so that's great for when all my servers are upgraded to 5.1

One glitch that remains in 5.1 is the following: even though the pyramids are generated and the thumbnails are as well, the thumbnail display in the web client still shows many clocks even if I refresh the display using the OMERO refresh button. However, when I refresh the webpage using the browser refresh, all the thumbnails will show up. I guess this has something to do with the browser caching things or is there something else in play?

Thanks,
- Damir

Hi Damir

It could also be the thumbnail version check in place i.e. the version is checked after for example changing the rendering settings so an update is started.
We will have to investigate.

Thanks for your feedback

Jmarie

Hi Jmarie,

I've reported this problem (Browser not refreshing thumbnails by using the webclient builtin refresh button) before in this thread (this thread mainly talks about the pixel generation problem also described in this thread, but also mentions the second problem):
viewtopic.php?f=4&t=7593

I believe at the time Will Moore actually looked into this specific issue, also created a Trac ticket for it. But I cannot retrieve it anymore.

I think the issue is that going from no thumbnail to the first thumbnail does not actually increase the version, and thus not the URL.

Thanks,

Paul

Hi All,

Paul is correct (see ticket at http://trac.openmicroscopy.org/ome/ticket/12538). When you refresh the tree in web, it does now check to see if there is a new version of the thumbnail and if so then the browser will load it. The problem now is the fact that there are no new thumbnails automatically generated (and no change in thumb version number) when pyramid generation completes.
Therefore, web does not know to request a new thumbnail (see discussion on ticket).

Currently the ticket is scheduled for 5.1.1, so hopefully this will be fixed soon.

Regards,

Will.

Just an update - thumbnails refresh in web during pyramid generation should now be fixed for 5.1.1. See post at viewtopic.php?f=6&t=7747&p=15690#p15690

Regards,

Will.