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

Mon Dec 12 17:01:19 GMT 2016

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/
   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/.  A summary of a similar collaboration with
   3i 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/>
   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
>
> ------------------------------------------------------------------
> *Hamamatsu Photonics France S.A.R.L *
> 19, rue du Saule Trapu, Parc du Moulin de Massy
> 91300 Massy - France !#PHOTON IS OUR BUSINESS#!
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