[ome-users] Big File questions

Wood, Christopher CJW at stowers.org
Thu Jul 7 21:32:06 BST 2011

Hi (again),

Our omero server (4.3) is experiencing some odd behavior that seems to be related to big images and importing/rendering them.

Some large tif images, around 2560x2160x100z,  where imported into a dataset - the pyramid/big image strategy is used. It takes a while to calculate the pyramids, but finishes and it seems fine.

When trying to view these afterword (a day later), if the dataset is clicked in Insight (on a client computer) and insight tries to show the thumbnails, the cpu on the server goes to 100% and the logs show lines like:
2011-07-07 11:14:17,675 INFO  [                 org.perf4j.TimingLogger] (l.Server-1) start[1310055257626] time[49] tag[omero.loadPixelsByImage]
2011-07-07 11:14:17,721 INFO  [                 org.perf4j.TimingLogger] (l.Server-1) start[1310055257675] time[46] tag[omero.loadRenderingSettingsByUser]
2011-07-07 11:14:17,744 INFO  [             ome.io.nio.FilePathResolver] (l.Server-1) Metadata only file, resulting path: /OMERO/Files/Dir-003/3311
2011-07-07 11:14:17,744 INFO  [                ome.io.nio.PixelsService] (l.Server-1) Using Pyramid BfPixelBuffer: /OMERO/Pixels/Dir-001/1788_pyramid
2011-07-07 11:14:17,802 INFO  [       loci.formats.in.MinimalTiffReader] (l.Server-1) Reading IFDs
2011-07-07 11:14:18,899 INFO  [       loci.formats.in.MinimalTiffReader] (l.Server-1) Populating metadata
2011-07-07 11:15:00,019 INFO  [ ome.services.blitz.fire.SessionManagerI] (3-thread-4) Performing requestHeartbeats
2011-07-07 11:18:00,016 INFO  [ ome.services.blitz.fire.SessionManagerI] (3-thread-1) Performing requestHeartbeats

(see attached log for more)

The dataset contains 12 images, 6 of those are big images. The logs show this happens for each large image and it is a very long process. After this process if insight is closed and reopened, the thumbnails display fine. Is this the expected behavior?  If insight would give some feedback, about what was going on in the background that would be good.  Does this processing need to performed for each user that looks at the images?

Insight does not display these images in the "Google Maps" way; it is not tiled and the overview is not shown in the corner. I have importer larger (xy) files that do use the "Google Maps" way.

I saved the original tif file as an ome-tiff using ImageJ/Bio-Formats and imported it. The regular import strategy was used for the ome-tiff. Why the difference with the same size of file?

I can upload the images (> 1GB) if that would be helpful.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20110707/99f5d25d/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: B.log
Type: application/octet-stream
Size: 17120 bytes
Desc: B.log
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20110707/99f5d25d/attachment.obj>

More information about the ome-users mailing list