NDPI support

[Yves Sucaet]

Have you tried to increase the memory assigned to your jvm?

Plenty of posts about this, e.g.: 
http://blogs.opcodesolutions.com/roller/java/entry/solve_java_lang_outofmemoryerror_java

hth,

Yves



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
Sent by:        
openslide-users-bounces+sucaet=histogenex.com at lists.andrew.cmu.edu



Hi David,

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 
the
> DLL file that allows us to read the files--- we mostly use it to take 
the
> original NDPI file and chop it into tiles so we can do analysis on 
them...
> Not really a perfect solution, and we are relying on a non-open-source 
DLL
> (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 
NDPI
> files, although last time I tried it (which was probably 6 months to a 
year
> ago), it was a bit flaky.

As mentioned in my post, the NDPI only supports 65000 pixel. Using
current trunk I get:
...
Reading IFDs
Populating metadata
Populating OME metadata
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
                 at loci.common.DataTools.allocate(DataTools.java:863)
                 at 
loci.formats.ChannelMerger.openBytes(ChannelMerger.java:157)
                 at 
loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:305)
                 at 
loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:94)
                 at 
loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:77)
                 at 
loci.formats.gui.ImageViewer.open(ImageViewer.java:347)
                 at 
loci.formats.gui.ImageViewer.main(ImageViewer.java:829)
...

Thanks much !
--
Mathieu
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