<font size=2 face="sans-serif">Have you tried to increase the memory assigned
to your jvm?</font>
<br>
<br><font size=2 face="sans-serif">Plenty of posts about this, e.g.: </font><a href=http://blogs.opcodesolutions.com/roller/java/entry/solve_java_lang_outofmemoryerror_java><font size=2 face="sans-serif">http://blogs.opcodesolutions.com/roller/java/entry/solve_java_lang_outofmemoryerror_java</font></a>
<br>
<br><font size=2 face="sans-serif">hth,</font>
<br>
<br><font size=2 face="sans-serif">Yves</font>
<br>
<br>
<br>
<br><font size=1 color=#5f5f5f face="sans-serif">From:
</font><font size=1 face="sans-serif">Mathieu Malaterre <mathieu.malaterre@gmail.com></font>
<br><font size=1 color=#5f5f5f face="sans-serif">To:
</font><font size=1 face="sans-serif">David Gutman <dagutman@gmail.com></font>
<br><font size=1 color=#5f5f5f face="sans-serif">Cc:
</font><font size=1 face="sans-serif">"openslide-users@lists.andrew.cmu.edu"
<openslide-users@lists.andrew.cmu.edu></font>
<br><font size=1 color=#5f5f5f face="sans-serif">Date:
</font><font size=1 face="sans-serif">17-07-12 14:26</font>
<br><font size=1 color=#5f5f5f face="sans-serif">Subject:
</font><font size=1 face="sans-serif">Re: NDPI support</font>
<br><font size=1 color=#5f5f5f face="sans-serif">Sent by:
</font><font size=1 face="sans-serif">openslide-users-bounces+sucaet=histogenex.com@lists.andrew.cmu.edu</font>
<br>
<hr noshade>
<br>
<br>
<br><tt><font size=2>Hi David,<br>
<br>
On Tue, Jul 17, 2012 at 1:39 PM, David Gutman <dagutman@gmail.com>
wrote:<br>
><br>
> One of the members of my group has written a converter for NDPI files<br>
> using the Hamamatsu API--- basically we wrapped some see code
around the<br>
> DLL file that allows us to read the files--- we mostly use it to take
the<br>
> original NDPI file and chop it into tiles so we can do analysis on
them...<br>
> Not really a perfect solution, and we are relying on a non-open-source
DLL<br>
> (the one from Hamamatsu).... but at least allows us to do some analysis.<br>
<br>
So the question is: can you share this piece of code ? At least for me<br>
this would help me a lot.<br>
<br>
> The format itself is quite weird-- it seems to have broken a lot of<br>
> normal" conventions--- kind of a JPEG stuffed into a TIFF wrapper....<br>
><br>
> The Bioformats program package should also have some support for the
NDPI<br>
> files, although last time I tried it (which was probably 6 months
to a year<br>
> ago), it was a bit flaky.<br>
<br>
As mentioned in my post, the NDPI only supports 65000 pixel. Using<br>
current trunk I get:<br>
...<br>
Reading IFDs<br>
Populating metadata<br>
Populating OME metadata<br>
Exception in thread "main" java.lang.OutOfMemoryError: Java heap
space<br>
at loci.common.DataTools.allocate(DataTools.java:863)<br>
at loci.formats.ChannelMerger.openBytes(ChannelMerger.java:157)<br>
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:305)<br>
at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:94)<br>
at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:77)<br>
at loci.formats.gui.ImageViewer.open(ImageViewer.java:347)<br>
at loci.formats.gui.ImageViewer.main(ImageViewer.java:829)<br>
...<br>
<br>
Thanks much !<br>
--<br>
Mathieu<br>
_______________________________________________<br>
openslide-users mailing list<br>
openslide-users@lists.andrew.cmu.edu<br>
</font></tt><a href="https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users"><tt><font size=2>https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users</font></tt></a><tt><font size=2><br>
</font></tt>
<br>
<br>
<HR><BR>WARNING: This e-mail, including any attachments, may contain CONFIDENTIAL INFORMATION, including privileged and/or health information. It is for the sole use of the intended recipients. Any unauthorized copying, disclosure, distribution, reproduction, use or retention of this email or the information in it, is strictly FORBIDDEN. If you are not an intended recipient, please notify the sender immediately (REPLY this e-mail) and permanently DELETE the related e-mail. Please be aware that this email and replies to it may be monitored by the sender's company for quality assurance, policy compliance and/or security purposes.
<br>