<div dir="ltr"><div class="gmail_extra">Hello together,</div><div class="gmail_extra"><br></div><div class="gmail_extra">thanks Julien for that initiative, I'd highly appreciate a better support of NDPI in Bioformats. Just one remark from my side</div><div class="gmail_extra">regarding the NDPI format:</div><div class="gmail_extra">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</div><div class="gmail_extra">of the image and not several smaller tiles as usual.</div><div class="gmail_extra">This has the consequence that if width / height are larger than 65536 the jpeg header cannot cope with this dimensions (16bit fields), so</div><div class="gmail_extra">it's written in the tiff container.</div><div class="gmail_extra">This makes it</div><div class="gmail_extra">a) hard to read with any standard jpeg library</div><div class="gmail_extra">b) hard to read it a random access way</div><div class="gmail_extra"><br></div><div class="gmail_extra">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</div><div class="gmail_extra">more standardized output of the Hamamatsu scanners (e.g. jpeg compressed tiled tiff) to avoid many problems from beginning.</div><div class="gmail_extra"><br></div><div class="gmail_extra">I am aware that working on Bioformats is the more realistic approach ;-)</div><div class="gmail_extra"><br></div><div class="gmail_extra">And: the current NDPI support actually is not that bad, just not as speedy as some other WSI file formats.</div><div class="gmail_extra"><br></div><div class="gmail_extra">Regards,</div><div class="gmail_extra">Manuel</div><div class="gmail_extra"><br></div><div class="gmail_extra"><span style="font-family:arial;font-size:13.3333px;white-space:pre-wrap"><br></span></div><div class="gmail_extra"><span style="font-family:arial;font-size:13.3333px;white-space:pre-wrap">Dear Julien,</span></div><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><span id="gmail-m_-290202499922787002m_944475167866049506m_4292309245390618761gmail-docs-internal-guid-bf3556b1-f3f3-93a7-c8a7-b8a5d781584d"><div dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><br></div><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:13.3333px;font-family:arial;vertical-align:baseline;white-space:pre-wrap">Thank you very much for getting in touch.</span></p><div dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><br></div><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:13.3333px;font-family:arial;vertical-align:baseline;white-space:pre-wrap">> 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. </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:13.3333px;font-family:arial;vertical-align:baseline;white-space:pre-wrap">></span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:13.3333px;font-family:arial;vertical-align:baseline;white-space:pre-wrap">> Ranking table: </span><a href="https://www.openmicroscopy.org/site/support/bio-formats5.2/supported-formats.html" style="text-decoration:none" target="_blank"><span style="font-size:13.3333px;font-family:arial;color:rgb(0,0,255);text-decoration:underline;vertical-align:baseline;white-space:pre-wrap">https://www.openmicroscopy.org<wbr>/site/support/bio-formats5.2/s<wbr>upported-formats.html</span></a><span style="font-size:12.6667px;font-family:arial;vertical-align:baseline;white-space:pre-wrap"> </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:13.3333px;font-family:arial;vertical-align:baseline;white-space:pre-wrap">> </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:13.3333px;font-family:arial;vertical-align:baseline;white-space:pre-wrap">>This might be because OME developers hadn't had access to all the relevant information while developing > the software.</span><span style="font-size:12.6667px;font-family:arial;vertical-align:baseline;white-space:pre-wrap"> </span></p><div dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><br></div><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:13.3333px;font-family:arial;vertical-align:baseline;white-space:pre-wrap">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.</span></p><div dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><br></div><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:13.3333px;font-family:arial;vertical-align:baseline;white-space:pre-wrap">> 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.</span><span style="font-size:12.6667px;font-family:arial;vertical-align:baseline;white-space:pre-wrap"> </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:13.3333px;font-family:arial;vertical-align:baseline;white-space:pre-wrap">> In order to help have as easy and good experience using your tools with our images as possible, we </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:13.3333px;font-family:arial;vertical-align:baseline;white-space:pre-wrap">> would like to help improve OME - NanoZoomer compatibility.</span><span style="font-size:12.6667px;font-family:arial;vertical-align:baseline;white-space:pre-wrap"> </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:13.3333px;font-family:arial;vertical-align:baseline;white-space:pre-wrap">> In this context, I would like to ask you which kind of information or actions would be needed from our </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:13.3333px;font-family:arial;vertical-align:baseline;white-space:pre-wrap">> side?</span><span style="font-size:12.6667px;font-family:arial;vertical-align:baseline;white-space:pre-wrap"> </span></p><div dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><br></div><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:13.3333px;font-family:arial;vertical-align:baseline;white-space:pre-wrap">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.</span></p><div dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><br></div><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:13.3333px;font-family:arial;vertical-align:baseline;white-space:pre-wrap">In terms of actually doing the work to update Bio-Formats, there are three options:</span></p><div dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><br></div><ol style="margin-top:0pt;margin-bottom:0pt"><li dir="ltr" style="list-style-type:decimal;font-size:13.3333px;font-family:arial;vertical-align:baseline"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:13.3333px;vertical-align:baseline;white-space:pre-wrap">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: </span><a href="http://blog.openmicroscopy.org/file-formats/community/2016/01/06/format-support/" style="text-decoration:none" target="_blank"><span style="font-size:13.3333px;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap">http://blog.openmicroscopy.org<wbr>/file-formats/community/2016/0<wbr>1/06/format-support/</span></a></p></li><li dir="ltr" style="list-style-type:decimal;font-size:13.3333px;font-family:arial;vertical-align:baseline"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:13.3333px;vertical-align:baseline;white-space:pre-wrap">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 </span><a href="http://www.openmicroscopy.org/site/support/contributing/" style="text-decoration:none" target="_blank"><span style="font-size:13.3333px;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap">http://www.openmicroscopy.org/<wbr>site/support/contributing/</span></a><span style="font-size:13.3333px;vertical-align:baseline;white-space:pre-wrap">. A summary of a similar collaboration with 3i is available here: </span><a href="http://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/" style="text-decoration:none" target="_blank"><span style="font-size:13.3333px;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap">http://blog.openmicroscopy.org<wbr>/file-formats/community/2016/0<wbr>8/31/bf-partnerships/</span></a></p></li><li dir="ltr" style="list-style-type:decimal;font-size:13.3333px;font-family:arial;vertical-align:baseline"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:13.3333px;vertical-align:baseline;white-space:pre-wrap">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: </span><a href="http://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/" style="text-decoration:none" target="_blank"><span style="font-size:13.3333px;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap">http://blog.openmicroscopy.org<wbr>/file-formats/community/2016/0<wbr>8/31/bf-partnerships/ </span></a></p></li></ol><div dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><br></div><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:13.3333px;font-family:arial;vertical-align:baseline;white-space:pre-wrap">We would be happy to answer any questions you might have regarding the above.</span></p><div dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><br></div><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:13.3333px;font-family:arial;vertical-align:baseline;white-space:pre-wrap">Regards,</span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:13.3333px;font-family:arial;vertical-align:baseline;white-space:pre-wrap">-Melissa</span></p><div><span style="font-size:13.3333px;font-family:arial;vertical-align:baseline;white-space:pre-wrap"><br></span></div></span><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Dec 9, 2016 at 8:51 AM, <span dir="ltr"><<a href="mailto:jaupetit@hamamatsu.fr" target="_blank">jaupetit@hamamatsu.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><font size="2" face="sans-serif">Hello,</font>
<br>
<br><font size="2" face="sans-serif">I'm working as a Support Engineer at
Hamamatsu, taking care of the NanoZoomer slide scanners portfolio.</font>
<br>
<br><font size="2" face="sans-serif">Many of our users are using (or wish
to use) OME tools in order to handle their whole slide images with open
source software.</font>
<br>
<br><font size="2" face="sans-serif">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. </font>
<br>
<br><font size="2" face="sans-serif">Ranking table: </font><a href="https://www.openmicroscopy.org/site/support/bio-formats5.2/supported-formats.html" target="_blank"><font size="2" color="blue" face="sans-serif">https://www.openmicroscopy.org<wbr>/site/support/bio-formats5.2/s<wbr>upported-formats.html</font></a>
<br><font size="2" face="sans-serif"> </font>
<br><img src="cid:_1_071BD878071BD60C00519D45C1258084" style="border: 0px solid;">
<br>
<br>
<br><img src="cid:_1_071BE1EC071BDF8000519D45C1258084" style="border: 0px solid;">
<br>
<br><font size="2" face="sans-serif">This might be because OME developers
hadn't had access to all the relevant information while developing the
software.</font>
<br>
<br><font size="2" face="sans-serif">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.</font>
<br><font size="2" face="sans-serif">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.</font>
<br><font size="2" face="sans-serif">In this context, I would like to ask
you which kind of information or actions would be needed from our side?</font>
<br>
<br><font size="2" face="sans-serif">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.</font>
<br>
<br>
<br><font size="2" face="sans-serif">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.</font>
<br>
<br><font size="2" face="sans-serif">Looking forward to have a good collaboration,</font>
<br><font size="2" face="sans-serif">Best regards,</font>
<br><font size="2" face="sans-serif"><br>
</font><font size="2" face="Arial"><b>Julien Aupetit</b><br>
Technical Support Engineer</font>
<br>
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<tbody><tr>
<td width="48" style="font-size:10pt;font-family:arial">Phone: </td>
<td width="240" style="font-size:10pt;font-family:arial"><a href="tel:%2B33%20%280%291%2069%2053%2071%2000" value="+33169537100" target="_blank">+33 (0)1 69 53 71 00</a> </td>
</tr>
<tr>
<td align="left">Fax: </td>
<td align="left"><a href="tel:%2B33%20%280%291%2069%2053%2071%2010" value="+33169537110" target="_blank">+33 (0)1 69 53 71 10</a> </td>
</tr>
<tr>
<td align="left">Mobile: </td>
<td align="left"><a href="tel:%2B33%20%280%296%2027%2081%2057%2004" value="+33627815704" target="_blank">+33 (0)6 27 81 57 04</a> </td>
</tr>
<tr>
<td align="left">Email:</td>
<td align="left"><a href="mailto:jaupetit@hamamatsu.fr" target="_blank">jaupetit@hamamatsu.fr</a></td>
</tr>
<tr>
<td height="18">Web:</td>
<td align="left"><a href="http://www.hamamatsu.fr" target="_blank">www.hamamatsu.fr</a></td>
</tr>
</tbody></table>
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