revisiting viewing large czi slides in Omero

[daveko]

So i previously had some issues opening very large (2gb+) files. It would only show a placeholder icon for the thumbnail, and the viewer would take forever to open the image (and ultimately hang).

After some time has passed, i've been revisiting this problem. This time I'm using the 5.2.1 virtual appliance, and running on a pretty powerful desktop machine.

I've alotted 8 cores/16 threads to the VM, as well as 50gb of RAM.

I've changed the JVM settings to the following:

Code: Select all

blitz=-Xmx5000m -XX:MaxPermSize=3g -XX:+IgnoreUnrecognizedVMOptions # Settings({'max_system_memory': '50000', 'system_memory': '50000', 'percent': '10', 'perm_gen': '3g', 'strategy': 'percent'})
indexer=-Xmx5000m -XX:MaxPermSize=3g -XX:+IgnoreUnrecognizedVMOptions # Settings({'max_system_memory': '50000', 'system_memory': '50000', 'percent': '10', 'perm_gen': '3g', 'strategy': 'percent'})
pixeldata=-Xmx30000m -XX:MaxPermSize=3g -XX:+IgnoreUnrecognizedVMOptions # Settings({'max_system_memory': '50000', 'system_memory': '50000', 'percent': '60', 'perm_gen': '3g', 'strategy': 'percent'})
repository=-Xmx5000m -XX:MaxPermSize=3g -XX:+IgnoreUnrecognizedVMOptions # Settings({'max_system_memory': '50000', 'system_memory': '50000', 'percent': '10', 'perm_gen': '3g', 'strategy': 'percent'})

I've uploaded my logfiles to the QA upload if that helps. (ticket 17655)

thanks very much in advance.

[mlinkert]

Thank you for reporting this problem, and for sending log files. We suspect that this was fixed in Bio-Formats 5.4.0, in which case upgrading to the forthcoming OMERO 5.3.0 should allow the files to open.

In the meantime, if you are willing to send one of the .czi files, we would certainly be happy to test locally to verify that Bio-Formats 5.4.0/OMERO 5.3.0 will fix it. Instructions for sending large files to the OME team are being sent by private message.

[mlinkert]

My apologies for the delay in following up on this, and thank you for uploading the problematic file.

With OMERO 5.3.0, the file imports in under 3 minutes, and Insight/web show a valid thumbnail immediately after import. The image viewer takes a few seconds to load initially, but the image is otherwise available immediately after import. There is no placeholder or clock icon, so no need to wait for OMERO to generate a pyramid file.

If upgrading to OMERO 5.3.0 and re-importing does not solve the problem on your server, please let us know and we'll investigate further.