NDPI support

Mailly Philippe philippe.mailly at snv.jussieu.fr
Tue Jul 17 09:06:42 EDT 2012


The LOCI plugin reading NDPI file is limited to 65000x65000 pixels image 
size, even if you have enough memory. For the moment, nobody can convert 
ndpi file over 65000x65000 pixel which is bored because most of the 
Hamamatsu acquisitions generated files are over this resolution. For 
example a classical histological slide is about 110000x50000.
It will be nice to have some tools that can convert scanner file as NDPI 
to tiff using bigtif library for example.


Le 17/07/2012 14:48, Mathieu Malaterre a écrit :
> It seems to go a little further. Here is what I have:
> Reading IFDs
> Populating metadata
> Populating OME metadata
> java.lang.OutOfMemoryError: Java heap space
> Dumping heap to java_pid16739.hprof ...
> Heap dump file created [673548853 bytes in 0.278 secs]
> Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
> 	at loci.formats.gui.AWTImageTools.makeRGBImage(AWTImageTools.java:576)
> 	at loci.formats.gui.AWTImageTools.makeImage(AWTImageTools.java:207)
> 	at loci.formats.gui.AWTImageTools.makeImage(AWTImageTools.java:494)
> 	at loci.formats.gui.AWTImageTools.openImage(AWTImageTools.java:782)
> 	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)
> Using:
> $ cat bfview
> [...]
>    java -XX:+HeapDumpOnOutOfMemoryError -Xmx1024m -cp
> "$DIR":"$DIR/bio-formats.jar":"$DIR/loci_tools.jar" $PROG "$@"

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