One of the members of my group has written a converter for NDPI files using the Hamamatsu API--- basically we wrapped some see code around the DLL file that allows us to read the files--- we mostly use it to take the original NDPI file and chop it into tiles so we can do analysis on them... Not really a perfect solution, and we are relying on a non-open-source DLL (the one from Hamamatsu).... but at least allows us to do some analysis.<div>
<br></div><div><br></div><div>The format itself is quite weird-- it seems to have broken a lot of normal" conventions--- kind of a JPEG stuffed into a TIFF wrapper....</div><div><br></div><div>The Bioformats program package should also have some support for the NDPI files, although last time I tried it (which was probably 6 months to a year ago), it was a bit flaky.</div>
<div><br></div><div><br></div><div><br><br><br><br><br><div class="gmail_quote">On Tue, Jul 17, 2012 at 6:56 AM, Niels Werner Mortensen <span dir="ltr"><<a href="mailto:nwm@sund.ku.dk" target="_blank">nwm@sund.ku.dk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div lang="DA" link="blue" vlink="purple">
<div>
<p class="MsoNormal"><span style="color:#1f497d">Hi all,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1f497d">NDPI is used by the Hamamatsu NanoZoomer HT 2.0<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1f497d">Best regards,<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span lang="EN-GB" style="font-size:7.5pt;font-family:"Verdana","sans-serif";color:gray">Niels Werner Mortensen</span></b><span lang="EN-GB" style="font-size:7.5pt;font-family:"Verdana","sans-serif";color:gray"><br>
IT Project Manager<br>
<br>
<b>Department of Biomedical Sciences<br>
</b>Faculty Of Health Sciences<br>
University of Copenhagen<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:7.5pt;font-family:"Verdana","sans-serif";color:gray">Blegdamsvej 3B,
<br>
DK-2200 Copenhagen N<b><br>
</b>Denmark<b><br>
</b></span><span lang="EN-GB" style="font-size:7.5pt;font-family:"Verdana","sans-serif";color:gray"> </span><b><span lang="EN-GB" style="font-size:7.5pt;font-family:"Verdana","sans-serif";color:gray"><br>
</span></b><span lang="EN-GB" style="font-size:7.5pt;font-family:"Verdana","sans-serif";color:gray">TEL <a href="tel:%2B45%2035327457" value="+4535327457" target="_blank">+45 35327457</a><br>
DIR <a href="tel:%2B45%2028757520" value="+4528757520" target="_blank">+45 28757520</a><br>
MOB <a href="tel:%2B45%2028757520" value="+4528757520" target="_blank">+45 28757520</a><br>
FAX <a href="tel:%2B45%2035327537" value="+4535327537" target="_blank">+45 35327537</a> <br>
Room 12.3.14<br>
<u><a href="mailto:nwm@sund.ku.dk" target="_blank">nwm@sund.ku.dk</a></u></span><span lang="EN-GB" style="font-size:7.5pt;font-family:"Verdana","sans-serif";color:gray"><br>
</span><u><span lang="EN-GB" style="font-size:7.5pt;font-family:"Verdana","sans-serif";color:gray"><a href="http://bmi.ku.dk" target="_blank">bmi.ku.dk</a></span></u><b><span lang="EN-GB" style="font-size:7.5pt;font-family:"Verdana","sans-serif";color:gray"><br>
<br>
<u></u><u></u></span></b></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><img width="320" height="122" src="cid:image001.gif@01CD641B.7FB6BF70" alt="Description: C:\Users\fcp486\AppData\Roaming\Microsoft\Signatures\logo-en.gif"></span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> openslide-users-bounces+nwm=<a href="mailto:sund.ku.dk@lists.andrew.cmu.edu" target="_blank">sund.ku.dk@lists.andrew.cmu.edu</a>
[mailto:<a href="mailto:openslide-users-bounces%2Bnwm" target="_blank">openslide-users-bounces+nwm</a>=<a href="mailto:sund.ku.dk@lists.andrew.cmu.edu" target="_blank">sund.ku.dk@lists.andrew.cmu.edu</a>] <b>On Behalf Of
</b>Yves Sucaet<br>
<b>Sent:</b> 17. juli 2012 11:25<br>
<b>To:</b> <a href="mailto:openslide-users@lists.andrew.cmu.edu" target="_blank">openslide-users@lists.andrew.cmu.edu</a><br>
<b>Subject:</b> Re: NDPI support<u></u><u></u></span></p><div><div class="h5">
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">Hi Mathieu,</span>
<br>
<br>
<span style="font-size:10.0pt;font-family:"Arial","sans-serif"">What vendors and scanners use NDPI?</span>
<br>
<br>
<br>
<br>
<span style="font-size:7.5pt;font-family:"Arial","sans-serif";color:#5f5f5f">From: </span><span style="font-size:7.5pt;font-family:"Arial","sans-serif"">Mathieu Malaterre <<a href="mailto:mathieu.malaterre@gmail.com" target="_blank">mathieu.malaterre@gmail.com</a>></span>
<br>
<span style="font-size:7.5pt;font-family:"Arial","sans-serif";color:#5f5f5f">To: </span><span style="font-size:7.5pt;font-family:"Arial","sans-serif""><a href="mailto:openslide-users@lists.andrew.cmu.edu" target="_blank">openslide-users@lists.andrew.cmu.edu</a></span>
<br>
<span style="font-size:7.5pt;font-family:"Arial","sans-serif";color:#5f5f5f">Date: </span><span style="font-size:7.5pt;font-family:"Arial","sans-serif"">17-07-12 11:05</span>
<br>
<span style="font-size:7.5pt;font-family:"Arial","sans-serif";color:#5f5f5f">Subject: </span><span style="font-size:7.5pt;font-family:"Arial","sans-serif"">NDPI support</span>
<br>
<span style="font-size:7.5pt;font-family:"Arial","sans-serif";color:#5f5f5f">Sent by: </span><span style="font-size:7.5pt;font-family:"Arial","sans-serif""><a href="mailto:openslide-users-bounces+sucaet=histogenex.com@lists.andrew.cmu.edu" target="_blank">openslide-users-bounces+sucaet=histogenex.com@lists.andrew.cmu.edu</a></span>
<u></u><u></u></p>
<div class="MsoNormal" align="center" style="text-align:center">
<hr size="2" width="100%" noshade style="color:gray" align="center">
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
<br>
<br>
<tt><span style="font-size:10.0pt">Hi all,</span></tt><span style="font-size:10.0pt;font-family:"Courier New""><br>
<br>
<tt> As far as I understand there is currently no support for NDPI in</tt><br>
<tt>OpenSlide, ref:</tt><br>
</span><a href="http://lists.andrew.cmu.edu/pipermail/openslide-users/2011-August/000201.html" target="_blank"><tt><span style="font-size:10.0pt">http://lists.andrew.cmu.edu/pipermail/openslide-users/2011-August/000201.html</span></tt></a><span style="font-size:10.0pt;font-family:"Courier New""><br>
<br>
<tt> I was wondering if anyone worked on a small command line converter</tt><br>
<tt>using the NDPRead.h API</tt><br>
<br>
</span><a href="http://imagetests.googlecode.com/svn/trunk/NDPRead.h" target="_blank"><tt><span style="font-size:10.0pt">http://imagetests.googlecode.com/svn/trunk/NDPRead.h</span></tt></a><span style="font-size:10.0pt;font-family:"Courier New""><br>
<br>
<tt>Thanks for comments,</tt><br>
<tt>-- </tt><br>
<tt>Mathieu</tt><br>
<tt>_______________________________________________</tt><br>
<tt>openslide-users mailing list</tt><br>
<tt><a href="mailto:openslide-users@lists.andrew.cmu.edu" target="_blank">openslide-users@lists.andrew.cmu.edu</a></tt><br>
</span><a href="https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users" target="_blank"><tt><span style="font-size:10.0pt">https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users</span></tt></a><span style="font-size:10.0pt;font-family:"Courier New""><br>
<br>
</span><u></u><u></u></p>
<div class="MsoNormal" align="center" style="text-align:center">
<hr size="2" width="100%" align="center">
</div>
<p class="MsoNormal"><br>
WARNING: This e-mail, including any attachments, may contain CONFIDENTIAL INFORMATION, including privileged and/or health information. It is for the sole use of the intended recipients. Any unauthorized copying, disclosure, distribution, reproduction, use or
retention of this email or the information in it, is strictly FORBIDDEN. If you are not an intended recipient, please notify the sender immediately (REPLY this e-mail) and permanently DELETE the related e-mail. Please be aware that this email and replies to
it may be monitored by the sender's company for quality assurance, policy compliance and/or security purposes.
<u></u><u></u></p>
</div></div></div>
<br clear="all">
</div>
<br>_______________________________________________<br>
openslide-users mailing list<br>
<a href="mailto:openslide-users@lists.andrew.cmu.edu">openslide-users@lists.andrew.cmu.edu</a><br>
<a href="https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users" target="_blank">https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users</a><br>
<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>David A Gutman, M.D. Ph.D.<br>Assistant Professor of Biomedical Informatics<br>Senior Research Scientist, Center for Comprehensive Informatics<br>Emory University School of Medicine<br>
</div>