[ome-users] OMERO Import issues...

[David Gutman]

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?






-- 
David A Gutman, M.D. Ph.D.
Center for Comprehensive Informatics
Emory University School of Medicine