I'm using a 64 bit distro so just made my java heap size like 6 GB's---<br><br>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...<br>
<br><br>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<br>
<br><br>dg<br><br><div class="gmail_quote">On Wed, Sep 23, 2009 at 11:25 AM, Curtis Rueden <span dir="ltr"><<a href="mailto:ctrueden@wisc.edu">ctrueden@wisc.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Björn & David,<br><br>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.<br>
<br>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.<br>
<br>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.<br>
<font color="#888888">
<br>-Curtis</font><div><div></div><div class="h5"><br><br><div class="gmail_quote">On Wed, Sep 23, 2009 at 3:28 AM, Björn Quast <span dir="ltr"><<a href="mailto:bquast@evolution.uni-bonn.de" target="_blank">bquast@evolution.uni-bonn.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi David,<br>
<br>
I have had the same importing problems with one layer tif images, when they<br>
exceed a specific image size . There is no problem to import very large multi-<br>
layer tifs (about 500 Mb), but if one layer is to large the import stopped and<br>
I got a message on the console, that the java heap memory was exceeded.<br>
I can only guess, that the importer fails to read in large strips of image<br>
data. tif files may store all image data in one chunk or line by line or in<br>
smaller pieces. But even with line by line stored images I got the problems,<br>
if one layer is to large.<br>
<br>
It also happens, that a few images were imported but than the importer stops.<br>
Again, I can only guess that there is a memory issue.<br>
<br>
In the moment I can not reproduce it, because I have no omero running, but<br>
perhaps I can give more details when my server is up again.<br>
<br>
Björn<br>
<div><div></div><div><br>
David Gutman wrote:<br>
> I am having a lot of problems trying to import images into OMERO. I<br>
> am using the 4.0.3beta code and having issues trying to import any of<br>
> my images.....<br>
><br>
> The images are initially acquired as Aperio SVS files ....they are<br>
> basically a TIFF container with JPEG2000 tiles embedded in them.<br>
> I've tried the following scenarios and still can't get all of my<br>
> images to consistently import, and get all sorts of errors, so wanted<br>
> to see if the community had any thoughts...<br>
><br>
> 1) Split 6 channel SVS file into individual channels using<br>
> tiffsplit--- these images are just standard tiff's, and I can even<br>
> view them with imagemagick, and other graphics viewers (At least the<br>
> small ones)<br>
> This produces 6 images, the really small images seem to import okay<br>
> sometimes, but not always (like 1024x512 or whatever-- these generally<br>
> are just an image of the label on the slide)...<br>
><br>
> So some of the frames, but of course not the large frames (22090x27696<br>
> pixels) will not load either through the GUI or through the command<br>
> line interpreter--- I've restricted this now where I don't even try to<br>
> upload images greater than 250 MegaPixels (so well under 1Gigapixel<br>
> even considering all three channels) ......but I've had issues with<br>
> even much smaller images....<br>
><br>
> Has anyone had any similar issues trying to load in large files with<br>
> the current beta of OMERO I've even tried to transcode some of these<br>
> using the bioformats tools to OME-XML.TIFF files with similar<br>
> disappointing results<br>
><br>
> Oddly-- some of my images upload OK, and some do not...<br>
><br>
> 2966455 2009-09-16 13:57 TCGA-06-0214-01B-03-BS3aad.tif<br>
> 158051 2009-09-16 13:57 TCGA-06-0214-01B-03-BS3aab.tif<br>
><br>
> The "b" image loaded fine, the "d" image did not-- it's not a terribly<br>
> big image, but I keep getting weird errors when I try and import it--<br>
> has anyone had any issues lately with the OMEROIMPORTER function/gui?<br>
<br>
--<br>
</div></div>Dr. Björn Quast<br>
Universität Bonn<br>
Institut für Evolutionsbiologie und Ökologie<br>
53121 Bonn<br>
Tel.: 0228/735758 email: <a href="mailto:bquast@evolution.uni-bonn.de" target="_blank">bquast@evolution.uni-bonn.de</a><br>
<div><div></div><div>_______________________________________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
</div></div></blockquote></div><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>David A Gutman, M.D. Ph.D.<br>Center for Comprehensive Informatics<br>Emory University School of Medicine<br>