[ome-devel] ndpi - NanoZoomer files compatibility with OME

Manuel Stritt manuel.stritt at actelion.com
Tue Dec 13 07:53:37 GMT 2016 

Hello together,

thanks Julien for that initiative, I'd highly appreciate a better support
of NDPI in Bioformats. Just one remark from my side
regarding the NDPI format:
The main problem I see (as far as I understood the format...) is that it's
basically a tiff with a big jpeg "tile" which has the width and height
of the image and not several smaller tiles as usual.
This has the consequence that if width / height are larger than 65536 the
jpeg header cannot cope with this dimensions (16bit fields), so
it's written in the tiff container.
This makes it
a) hard to read with any standard jpeg library
b) hard to read it a random access way

I guess support from Hamamatsu side as Melissa proposed would be a very
good option. But for long-term, one could even think about a
more standardized output of the Hamamatsu scanners (e.g. jpeg compressed
tiled tiff) to avoid many problems from beginning.

I am aware that working on Bioformats is the more realistic approach  ;-)

And: the current NDPI support actually is not that bad, just not as speedy
as some other WSI file formats.

Regards,
Manuel


Dear Julien,

>
> Thank you very much for getting in touch.
>
> > On OME website, we've seen that NanoZoomer file formats (ndpi, ndpis,and
> vmu mainly) are somehow > supported but that the compatibility is not 100%
> assured.
>
> >
>
> > Ranking table: https://www.openmicroscopy.org
> /site/support/bio-formats5.2/supported-formats.html
>
> >
>
> >This might be because OME developers hadn't had access to all the
> relevant information while developing > the software.
>
> Yes, the ratings on our website reflect the fact that we do not have
> official specification documents for the ndpi, ndpis, or vmu/vms formats.
>
> > As hardware makers, we are completely opened to all external software
> development and we especially > think that open source software is a real
> key point for our customers.
>
> > In order to help have as easy and good experience using your tools with
> our images as possible, we
>
> > would like to help improve OME - NanoZoomer compatibility.
>
> > In this context, I would like to ask you which kind of information or
> actions would be needed from our
>
> > side?
>
> As a first step, official specification documents and a set of NanoZoomer
> datasets that represents the full range of acquisitions options would be
> very helpful.  Representative datasets, at a minimum, are necessary if we
> are to proceed with any real changes to Bio-Formats’ NanoZoomer support.
>
> In terms of actually doing the work to update Bio-Formats, there are three
> options:
>
>
>    1.
>
>    The open source OME team can use the provided specifications and
>    datasets to assess and fix any missing features, as time permits and
>    without a definite completion or release date.  For further information,
>    please see: http://blog.openmicroscopy.org
>    /file-formats/community/2016/01/06/format-support/
>    <http://blog.openmicroscopy.org/file-formats/community/2016/01/06/format-support/>
>    2.
>
>    Hamamatsu can commit resources to making any necessary updates to
>    Bio-Formats’ existing NanoZoomer support via our code repositories on
>    GitHub.  For technical details, please see
>    http://www.openmicroscopy.org/site/support/contributing/
>    <http://www.openmicroscopy.org/site/support/contributing/>.  A summary
>    of a similar collaboration with 3i is available here:
>    http://blog.openmicroscopy.org/file-formats/community/2016/0
>    8/31/bf-partnerships/
>    <http://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/>
>    3.
>
>    Hamamatsu can commission Glencoe Software to make any desired updates
>    on a fixed schedule; any changes would then be made available in the next
>    scheduled release of Bio-Formats.  A summary of a similar collaboration
>    with Zeiss is available here: http://blog.openmicroscopy.org
>    /file-formats/community/2016/08/31/bf-partnerships/
>    <http://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/>
>
>
> We would be happy to answer any questions you might have regarding the
> above.
>
> Regards,
>
> -Melissa
>
>
> On Fri, Dec 9, 2016 at 8:51 AM, <jaupetit at hamamatsu.fr> wrote:
>
>> Hello,
>>
>> I'm working as a Support Engineer at Hamamatsu, taking care of the
>> NanoZoomer slide scanners portfolio.
>>
>> Many of our users are using (or wish to use) OME tools in order to handle
>> their whole slide images with open source software.
>>
>> On OME website, we've seen that NanoZoomer file formats (ndpi, ndpis,and
>> vmu mainly) are somehow supported but that the compatibility is not 100%
>> assured.
>>
>> Ranking table: https://www.openmicroscopy.org
>> /site/support/bio-formats5.2/supported-formats.html
>>
>>
>>
>>
>>
>>
>> This might be because OME developers hadn't had access to all the
>> relevant information while developing the software.
>>
>> As hardware makers, we are completely opened to all external software
>> development and we especially think that open source software is a real key
>> point for our customers.
>> In order to help have as easy and good experience using your tools with
>> our images as possible, we would like to help improve OME - NanoZoomer
>> compatibility.
>> In this context, I would like to ask you which kind of information or
>> actions would be needed from our side?
>>
>> As an example, I think we can provide our file format details and a SDK
>> (compatible both with Windows and Linux environments). These are completely
>> free of charge and would only require the approval of a so called Software
>> Licence Agreement.
>>
>>
>> This email is really intended to be a starting point for an open
>> discussion between Hamamatsu and OME developers community so don't hesitate
>> to come back to me with all the question you would have.
>>
>> Looking forward to have a good collaboration,
>> Best regards,
>>
>> *Julien Aupetit*
>> Technical Support Engineer
>> Phone: +33 (0)1 69 53 71 00
>> Fax: +33 (0)1 69 53 71 10
>> Mobile: +33 (0)6 27 81 57 04
>> Email: jaupetit at hamamatsu.fr
>> Web: www.hamamatsu.fr
>>
>> ------------------------------------------------------------------
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