Long... long loading time for Multi-channel Pyramid ome.tif file

Hi Omero team,

I found it takes such a long time for the OMERO to processs the multiple-channel pyramid ome.tiff after they are uploaded in OMERO. Also for visualize them once they are processed.
But for other types of pyramid tiff like .mrxs or .ziss they are much better.

I am wondering if this is a problem of how I constructing the pyramid tiff or it is a problem of the pyramid ome.tiff format itself.

Here is how I construct the pyramid ome.tif.
Stitch the tiles in each channel and write it as a pyramid tiff, use bfconvert tools to convert a multi-channel tiff into one single ome-tiff.

Thanks in advance for the help!

Best regards,
John

Hi @John_Xu, generally it sounds like you are constructing it ok. Do you have the bfconvert command you are using?

If you are able to send us either the original files or the converted file then I can take a look to see if there is anything wrong with the structure of it. https://www.openmicroscopy.org/qa2/qa/upload/

Hi @dgault,

Thanks for the help!
Sorry, I didn’t make it clear. It is not the constructing takes a long time. It is the background process after uploading (constructing the Pixeldata maybe) takes a long time.

2020-01-29 23:29:15,852 ERROR [  ome.services.pixeldata.PixelDataThread] (1-thread-5) ExceptionException!
ome.conditions.SessionTimeoutException: Session (started=2020-01-29 23:04:54.69, hits=15, last access=2020-01-29 23:04:54.781) exceeded timeToIdle (600000) by 861045 ms
	at ome.services.sessions.state.SessionCache.getDataNullOrThrowOnTimeout(SessionCache.java:470) ~[omero-server.jar:5.5.4]
	at ome.services.sessions.state.SessionCache.getSessionContext(SessionCache.java:368) ~[omero-server.jar:5.5.4]
	at ome.services.sessions.state.SessionCache.getSessionContext(SessionCache.java:353) ~[omero-server.jar:5.5.4]
	at ome.security.basic.CurrentDetails.login(CurrentDetails.java:164) ~[omero-server.jar:5.5.4]
	at ome.services.util.Executor$Impl.execute(Executor.java:439) ~[omero-server.jar:5.5.4]
	at ome.services.util.Executor$Impl.execute(Executor.java:392) ~[omero-server.jar:5.5.4]
	at ome.services.pixeldata.PixelDataThread.go(PixelDataThread.java:302) ~[omero-server.jar:5.5.4]
	at ome.services.pixeldata.PixelDataThread.access$000(PixelDataThread.java:51) ~[omero-server.jar:5.5.4]
	at ome.services.pixeldata.PixelDataThread$1.call(PixelDataThread.java:250) ~[omero-server.jar:5.5.4]
	at java.util.concurrent.FutureTask.run(FutureTask.java:266) ~[na:1.8.0_232]
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) ~[na:1.8.0_232]
	at java.util.concurrent.FutureTask.run(FutureTask.java:266) ~[na:1.8.0_232]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) ~[na:1.8.0_232]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) ~[na:1.8.0_232]
	at java.lang.Thread.run(Thread.java:748) ~[na:1.8.0_232]
2020-01-29 23:29:15,854 ERROR [  ome.services.pixeldata.PixelDataThread] (1-thread-5) ExceptionException!
ome.conditions.SessionTimeoutException: Session (started=2020-01-29 23:04:54.69, hits=15, last access=2020-01-29 23:04:54.781) exceeded timeToIdle (600000) by 861046 ms
	at ome.services.sessions.state.SessionCache.getDataNullOrThrowOnTimeout(SessionCache.java:470) ~[omero-server.jar:5.5.4]
	at ome.services.sessions.state.SessionCache.getSessionContext(SessionCache.java:368) ~[omero-server.jar:5.5.4]
	at ome.services.sessions.state.SessionCache.getSessionContext(SessionCache.java:353) ~[omero-server.jar:5.5.4]
	at ome.security.basic.CurrentDetails.login(CurrentDetails.java:164) ~[omero-server.jar:5.5.4]
	at ome.services.util.Executor$Impl.execute(Executor.java:439) ~[omero-server.jar:5.5.4]
	at ome.services.util.Executor$Impl.execute(Executor.java:392) ~[omero-server.jar:5.5.4]
	at ome.services.pixeldata.PixelDataThread.go(PixelDataThread.java:302) ~[omero-server.jar:5.5.4]
	at ome.services.pixeldata.PixelDataThread.access$000(PixelDataThread.java:51) ~[omero-server.jar:5.5.4]
	at ome.services.pixeldata.PixelDataThread$1.call(PixelDataThread.java:250) ~[omero-server.jar:5.5.4]
	at java.util.concurrent.FutureTask.run(FutureTask.java:266) ~[na:1.8.0_232]
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) ~[na:1.8.0_232]
	at java.util.concurrent.FutureTask.run(FutureTask.java:266) ~[na:1.8.0_232]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) ~[na:1.8.0_232]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) ~[na:1.8.0_232]
	at java.lang.Thread.run(Thread.java:748) ~[na:1.8.0_232]

Best regards,
John Xu

Thats ok, i understood, I just want to make sure that the structure of the file looks correct first to identify if that is what is causing the slowness or it is for another reason. If I can see the converted file or recreate it myself then I check that there is any some odd behaviour going on. There is no reason the OME TIFF should perform any worse than other files with similar settings.