[ome-users] OMERO Import issues...

[Björn Quast]

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