[ome-users] OMERO Import issues...
Brian Loranger
brian.loranger at lifesci.dundee.ac.uk
Wed Sep 23 16:46:50 BST 2009
Hi Guys,
In regards to your other question David (the one with the very large
4K x 4K jpeg images):
Without looking at your server logs and the OMERO database its hard to
say, but I would hazard a guess that you're running into the same
problem server side - a memory issue. I would likewise see about
increasing the memory allocation to the server and see if that helps.
Barring that, poking around in the OMERO db and log files will
probably give you a lead on what the problem is.
Cheers,
Brian Loranger
Software Developer, Open Microscopy Environment
Division of Gene Regulation and Expression
University of Dundee
(The University of Dundee is a registered Scottish charity, No:
SC015096)
On 23 Sep 2009, at 16:28, David Gutman wrote:
> I'm using a 64 bit distro so just made my java heap size like 6
> GB's---
>
> I'll have to double check my images-- they were just 16 megapixels
> (4k*4k) image tiles I had alreaduy converted from tiff--> JPG to
> hopefully resolve some of the issues I had been having...
>
>
> But still seemed to choke-- this time I was able to get them to
> import, but when I actually tried to load them through the
> webclient, it just kept displaying a "no image" tag for the
> thumbail.. kind of odd
>
>
> dg
>
> On Wed, Sep 23, 2009 at 11:25 AM, Curtis Rueden <ctrueden at wisc.edu>
> wrote:
> Hi Björn & David,
>
> Thanks for the feedback, and sorry for your trouble importing large
> image planes. As of Beta 4.0.3, the OMERO.importer defaults to a
> maximum heap size of 1024 MB. So any image planes of 1 GB or more
> are certainly too large to process successfully, and even image
> planes over 512 MB may have problems due to temporary overhead or
> garbage collection issues.
>
> One workaround is to increase the maximum heap size. With a 32-bit
> JVM, this limit can often be 1536 or even ~1800 GB depending on your
> operating system. The process for increasing the heap size is
> platform-dependent, however. For example, on Mac OS X, right click
> the OMERO.importer icon, choose "Show package contents," navigate
> into Contents, and edit the Info.plist file's line "-Xmx1024M" to
> read "-Xmx1700M" or whatever value you wish to try.
>
> That said, we have plans to improve the support for large image
> planes by processing them in tiles, negating the need for such a
> large amount of RAM at once. Unfortunately, this support is not
> planned until at least Beta 4.2. The Bio-Formats readers already
> support processing an image plane in tiles, but the writers do not,
> so the bfconvert command line tool does not yet support this either.
>
> -Curtis
>
>
> On Wed, Sep 23, 2009 at 3:28 AM, Björn Quast <bquast at evolution.uni-bonn.de
> > wrote:
> Hi David,
>
> I have had the same importing problems with one layer tif images,
> when they
> exceed a specific image size . There is no problem to import very
> large multi-
> layer tifs (about 500 Mb), but if one layer is to large the import
> stopped and
> I got a message on the console, that the java heap memory was
> exceeded.
> I can only guess, that the importer fails to read in large strips of
> image
> data. tif files may store all image data in one chunk or line by
> line or in
> smaller pieces. But even with line by line stored images I got the
> problems,
> if one layer is to large.
>
> It also happens, that a few images were imported but than the
> importer stops.
> Again, I can only guess that there is a memory issue.
>
> In the moment I can not reproduce it, because I have no omero
> running, but
> perhaps I can give more details when my server is up again.
>
> Björn
>
> David Gutman wrote:
> > I am having a lot of problems trying to import images into
> OMERO. I
> > am using the 4.0.3beta code and having issues trying to import any
> of
> > my images.....
> >
> > The images are initially acquired as Aperio SVS files ....they are
> > basically a TIFF container with JPEG2000 tiles embedded in them.
> > I've tried the following scenarios and still can't get all of my
> > images to consistently import, and get all sorts of errors, so
> wanted
> > to see if the community had any thoughts...
> >
> > 1) Split 6 channel SVS file into individual channels using
> > tiffsplit--- these images are just standard tiff's, and I can even
> > view them with imagemagick, and other graphics viewers (At least the
> > small ones)
> > This produces 6 images, the really small images seem to import
> okay
> > sometimes, but not always (like 1024x512 or whatever-- these
> generally
> > are just an image of the label on the slide)...
> >
> > So some of the frames, but of course not the large frames
> (22090x27696
> > pixels) will not load either through the GUI or through the command
> > line interpreter--- I've restricted this now where I don't even
> try to
> > upload images greater than 250 MegaPixels (so well under 1Gigapixel
> > even considering all three channels) ......but I've had issues with
> > even much smaller images....
> >
> > Has anyone had any similar issues trying to load in large files with
> > the current beta of OMERO I've even tried to transcode some of
> these
> > using the bioformats tools to OME-XML.TIFF files with similar
> > disappointing results
> >
> > Oddly-- some of my images upload OK, and some do not...
> >
> > 2966455 2009-09-16 13:57 TCGA-06-0214-01B-03-BS3aad.tif
> > 158051 2009-09-16 13:57 TCGA-06-0214-01B-03-BS3aab.tif
> >
> > The "b" image loaded fine, the "d" image did not-- it's not a
> terribly
> > big image, but I keep getting weird errors when I try and import
> it--
> > has anyone had any issues lately with the OMEROIMPORTER function/
> gui?
>
> --
> Dr. Björn Quast
> Universität Bonn
> Institut für Evolutionsbiologie und Ökologie
> 53121 Bonn
> Tel.: 0228/735758 email: bquast at evolution.uni-bonn.de
> _______________________________________________
> ome-users mailing list
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>
>
>
>
> --
> David A Gutman, M.D. Ph.D.
> Center for Comprehensive Informatics
> Emory University School of Medicine
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
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Brian Loranger
Software Developer, Open Microscopy Environment
Division of Gene Regulation and Expression
University of Dundee
(The University of Dundee is a registered Scottish charity, No:
SC015096)
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