sucaet at histogenex.com
Tue Jul 17 08:30:53 EDT 2012
Have you tried to increase the memory assigned to your jvm?
Plenty of posts about this, e.g.:
From: Mathieu Malaterre <mathieu.malaterre at gmail.com>
To: David Gutman <dagutman at gmail.com>
Cc: "openslide-users at lists.andrew.cmu.edu"
<openslide-users at lists.andrew.cmu.edu>
Date: 17-07-12 14:26
Subject: Re: NDPI support
openslide-users-bounces+sucaet=histogenex.com at lists.andrew.cmu.edu
On Tue, Jul 17, 2012 at 1:39 PM, David Gutman <dagutman at gmail.com> wrote:
> One of the members of my group has written a converter for NDPI files
> using the Hamamatsu API--- basically we wrapped some see code around
> DLL file that allows us to read the files--- we mostly use it to take
> original NDPI file and chop it into tiles so we can do analysis on
> Not really a perfect solution, and we are relying on a non-open-source
> (the one from Hamamatsu).... but at least allows us to do some analysis.
So the question is: can you share this piece of code ? At least for me
this would help me a lot.
> The format itself is quite weird-- it seems to have broken a lot of
> normal" conventions--- kind of a JPEG stuffed into a TIFF wrapper....
> The Bioformats program package should also have some support for the
> files, although last time I tried it (which was probably 6 months to a
> ago), it was a bit flaky.
As mentioned in my post, the NDPI only supports 65000 pixel. Using
current trunk I get:
Populating OME metadata
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
Thanks much !
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