NDPI format support in OpenSlide - are there any forecasts?

[David Gutman]

Yeah---- actively decoding the NDPI files is a huge pain, mostly because
the NDPI format breaks most if not all standards and so requires a lot of
tweaking.  The Bioformats library, in theory, can read these, although it
actually breaks with files bigger than 65Kx65K pixels.

I wound up doing a bit of hacking to transcode NDPI files so I can use them
on my imaging portal (  http://cancer.digitalslidearchive.net/ ) but I
didn't use openslide for decoding.

IF you check the archives, there are a bit of very detailed conversations
about where/how/what is needed to integrate NDPI files...  between what's
posted here, and what one could glean from the support now integrated into
Bioformats... it's more of a matter as Adam said of having a dedicated
coder work on it, vs being an impossible challenge.


dg

On Sun, Oct 7, 2012 at 9:16 AM, Adam Goode <adam at spicenitz.org> wrote:

> I am not sure if anyone is actively working on this. Benjamin would
> probably know better. There have been some recent discussions about
> workarounds on this list.
>
> If you could donate a few weeks time of an experienced developer, it could
> probably be done.
>
> Adam
> On Oct 7, 2012 9:08 AM, "Daniel Alievsky" <daniel at smartimtech.com> wrote:
>
>> Hello,
>>
>> our company is using OpenSlide for reading extra-large images in our
>> Simagis Live system (http://live.simagis.com/) - web-based Java
>> application for storing and processing very large images.
>> OpenSlide is a good system, allowing to read most popular formats, but
>> right now we urgently need an ability to read .ndpi files (Hamamatsu
>> format), and the last OpenSlide version failed to read them:
>> http://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu/
>> (I used the last Windows binaries from http://openslide.org/download/.
>> An attempt to access these 3 .ndpi-files shows a set of error messages
>> boxes and fails.)
>>
>> It seems to be strange, because OpenSlide successfully reads another
>> Hamamatsu VMS-format, not packed into a single file:
>> http://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu-vms/
>> Unfortunately, I didn't find any ready C++ or Java library, allowing to
>> read .ndpi-files, containing images larger than 65530x65530, and it is a
>> problem - right now we need to read .ndpi-files of our customers with
>> very large pictures.
>>
>> Could you tell us, are you planning to add the support of .ndpi-files
>> into new OpenSlide versions in the nearest future? Are there any time
>> forecasts here?
>>
>> Thank you.
>>
>> Best regards,
>> Daniel Alievsky
>> Smart Imaging Technologies company
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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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