[ome-users] slow or failing import of large files with large X by Y size

[Melissa Linkert]

Hi Damir,

> Thanks for the quick response. I've just uploaded the 3 files
> described below. I'm mostly concerned at this point about the import
> failure of file3.tif.

Thank you for uploading the problematic files.

It looks like there are two distinct problems: one is that file3.tif
is not viewable (which I can reproduce), and the other is the time
required to import .lsm files (which I cannot reproduce).

For the file3.tif problem, increasing the amount of memory available to
the server should help.  It looks like that file was saved using ImageJ;
for the future, you may wish to use the Bio-Formats exporter plugin to
save TIFFs from ImageJ, as that will save TIFFs in such a way as to
prevent this problem without requiring more memory.

For the .lsm import times, I consistently see that file1.lsm imports in
10-12 minutes (also on Ubuntu 12.04 with Ice 3.4).  Are you able to
consistently reproduce that that file takes 30+ minutes?  If so, could
you please send a copy of the server logs so that we can investigate
further?

Regards,
-Melissa

On Mon, Feb 25, 2013 at 12:24:40PM -0800, Damir Sudar wrote:
> Hi Petr,
> 
> Thanks for the quick response. I've just uploaded the 3 files
> described below. I'm mostly concerned at this point about the import
> failure of file3.tif.
> 
> Thanks,
> - Damir
> On 2/25/2013 1:50 AM, Petr Walczysko wrote:
> >Hello Damir
> >
> >Thank you very much for your feedback.
> >Could you please upload the files in question using out QA ?
> >Please go to
> >http://qa.openmicroscopy.org.uk/qa/upload/
> >and follow the instructions.
> >It would help us to investigate the problem.
> >Thank you
> >All the best
> >Petr
> >
> >
> >
> >On 23 Feb 2013, at 01:16, Damir Sudar <dsudar at lbl.gov
> ><mailto:dsudar at lbl.gov>>
> > wrote:
> >
> >>Hi all,
> >>
> >>On my installation (Omero 4.4.5/Ice 3.4 on Ubuntu 12.04LTS
> >>64-bit) I see the following strange import (using
> >>Insight/Importer 4.4.5) behavior:
> >>File1.lsm: 102MB is 5120 by 5120 pixels in 2 channels takes
> >>30-40 minutes to import
> >>File2.lsm: 207MB  is 1024 by 1024 pixels by 50 Z-slices takes 1
> >>minute to import
> >>File3.tif: 100MB  is 10240 by 10240 pixels simple 8-bit TIFF,
> >>import finishes in a few seconds without errors but the
> >>resulting image in Omero will not open and gives error: "The
> >>image could not be opened. The image is not a valid image." But
> >>the archived version can be downloaded without trouble.
> >>
> >>So there appears to be something wrong with importing image with
> >>large X by Y sizes. Has anyone seen this as well and is there a
> >>solution?
> >>
> >>Thanks,
> >>- Damir
> >>
> >>-- 
> >>Damir Sudar - Staff Scientist and Deputy for Technology
> >>Lawrence Berkeley Laboratory / Life Sciences Division
> >>One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
> >>T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov
> >><mailto:DSudar at lbl.gov>
> >>WWW: http://www.lbl.gov/lsd/People_&_Organization/Scientific_Staff_Directory/Sudar_Lab.html
> >>
> >>_______________________________________________
> >>ome-users mailing list
> >>ome-users at lists.openmicroscopy.org.uk
> >><mailto:ome-users at lists.openmicroscopy.org.uk>
> >>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >>
> >
> >
> >The University of Dundee is a registered Scottish Charity, No:
> >SC015096
> 
> -- 
> Damir Sudar - Staff Scientist and Deputy for Technology
> Lawrence Berkeley Laboratory / Life Sciences Division
> One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
> T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov
> WWW: http://www.lbl.gov/lsd/People_&_Organization/Scientific_Staff_Directory/Sudar_Lab.html
> 

> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users