NDPI support

David Gutman dagutman at gmail.com
Tue Jul 17 09:17:00 EDT 2012

So we've actually come out with a workaround-- I've tiled and
generated NDPI files much larger than that.. but of course it's a bit
of a hack.

We basically take the input NDPI file, tile it at 40X resolution into
4K x 4K tiles (which we use for image analysis purposes anyway), and
then we've written some code to reassemble the TILED directory into a
single BIGTIFF image.

The end result is something that is BIGTIFF friendly...


The images on here are 20X and 40X SVS files... but I have a number of
similar portals where I have a couple of thousand of similarly
converted NDPI files (although they aren't publicly available...
behind a firewall at my University)...

On Tue, Jul 17, 2012 at 9:06 AM, Mailly Philippe
<philippe.mailly at snv.jussieu.fr> wrote:
> Hi,
> 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.
> Philippe
> 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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David A Gutman, M.D. Ph.D.
Assistant Professor of Biomedical Informatics
Senior Research Scientist, Center for Comprehensive Informatics
Emory University School of Medicine

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