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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Yes very good idea,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">don't forget the z-layers, as Derek already mentioned.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">E.g.:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">MRXS's z-layers (3D Histech) should maybe not be too difficult, as it is an extension of the already existing MRXS format.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> Peter
<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext"> openslide-users [mailto:openslide-users-bounces+schueffp=mskcc.org@lists.andrew.cmu.edu]
<b>On Behalf Of </b>Derek Magee<br>
<b>Sent:</b> Wednesday, February 07, 2018 8:52 AM<br>
<b>To:</b> PD Dr. M. Weihrauch <m.weihrauch@smartinmedia.com>; openslide-users@lists.andrew.cmu.edu<br>
<b>Subject:</b> [EXTERNAL] RE: Help with viewing slides on the web<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">My 2p, with tentative, but slightly reluctant interest…<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Formats openslide should probably support and doesn’t (probably non exclusive list):<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Zeiss – There’s already a zeiss driver, it’s just not in the main openslide build for reasons to do with NDAs. It works well actually!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Olympus – We wrote our own (non-openslide) driver already. It’s a pretty simple format to reverse engineer (tiff based with some external binary
files for the big images).<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Precipoint – Again some sort of openslide driver already exists (all be it only supporting jpeg .. does anyone know if these scanners actually output anything else? Png/bmp/jp2???). The jury is out on whether this is
production ready until I see some image files.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">DICOM – Some work was done on this but the code is very flaky (lots of asserts rather than proper error checking that cause your code to exit, assumptions about filename conventions, reliance on existence of dicomdir
file, etc.). This one I wouldn’t use in production! I’d say this needs re-writing properly.</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><a name="_MailEndCompose"></a><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Roche BIF – This is supported but broken (due to non uniform grid of tiles assumed to be uniform). It is on my TODO list to look at, but it took
me about a day to get my head round building openslide and how the code is structured and I haven’t had time to look at it since (it’s not that high up the TODO list).
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Also:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">One big disadvantage with openslide currently is that it doesn’t support multi z-plane images (there is no API let alone any code). There are no
plns to fix this. Many vendors (Aperio, Hammamatsu, 3D Histech, Olympus to name a few) can produce these. In fact the lack of supports is variable as some drivers just take the first plane, and others cannot read such files at all. I see no point (from our
point of view) in putting resources into openslide supporting new formats unless this issue is sorted. We have a project that requires this for Aperio and/or Hamamatsu (at least) coming up, so this is on my mind to look at.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Derek<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:windowtext">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:windowtext"> openslide-users [<a href="mailto:openslide-users-bounces+d.r.magee=leeds.ac.uk@lists.andrew.cmu.edu">mailto:openslide-users-bounces+d.r.magee=leeds.ac.uk@lists.andrew.cmu.edu</a>]
<b>On Behalf Of </b>PD Dr. M. Weihrauch<br>
<b>Sent:</b> 07 February 2018 09:32<br>
<b>To:</b> <a href="mailto:openslide-users@lists.andrew.cmu.edu">openslide-users@lists.andrew.cmu.edu</a><br>
<b>Subject:</b> Re: Help with viewing slides on the web<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span lang="EN-GB">Guys:<br>
<br>
Why don't the companies, which read this list (among which is mine) throw together money, hire a full time developer for a year, who integrates all of these currently foreign slide formats that are still missing into OpenSlide (e. g. Olympus, Zeiss, Precipoint,
etc pp)?<br>
<br>
We can get someone e. g. in Germany for €60k /year incl. all costs. If there are 6 or more companies here, each pays €10k. I'd be totally up for it.<br>
<br>
Martin<br>
<br>
<br>
Am 07.02.2018 um 10:06 schrieb Yves Sucaet:<o:p></o:p></span></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<pre><span lang="EN-GB">Hi Jen,<o:p></o:p></span></pre>
<pre><span lang="EN-GB"><o:p> </o:p></span></pre>
<pre><span lang="EN-GB">It seems some work on this was done already in the past:<o:p></o:p></span></pre>
<pre><span lang="EN-GB"><a href="https://github.com/openslide/openslide/issues/168">https://github.com/openslide/openslide/issues/168</a><o:p></o:p></span></pre>
<pre><span lang="EN-GB"><o:p> </o:p></span></pre>
<pre><span lang="EN-GB">Unfortunately, the sample files mentioned in the thread don't seem to exist<o:p></o:p></span></pre>
<pre><span lang="EN-GB">anymore and were never added to the repo at<o:p></o:p></span></pre>
<pre><span lang="EN-GB"><a href="http://openslide.cs.cmu.edu/download/openslide-testdata/">http://openslide.cs.cmu.edu/download/openslide-testdata/</a> (possibly the<o:p></o:p></span></pre>
<pre><span lang="EN-GB">licensing was never resolved?).<o:p></o:p></span></pre>
<pre><span lang="EN-GB"><o:p> </o:p></span></pre>
<pre><span lang="EN-GB">Could you help us help you by providing some new sample files?<o:p></o:p></span></pre>
<pre><span lang="EN-GB"><o:p> </o:p></span></pre>
<pre><span lang="EN-GB">Thanks in advance,<o:p></o:p></span></pre>
<pre><span lang="EN-GB"><o:p> </o:p></span></pre>
<pre><span lang="EN-GB">Yves Sucaet<o:p></o:p></span></pre>
<pre><span lang="EN-GB"><o:p> </o:p></span></pre>
<pre><span lang="EN-GB">------ Original Message ------<o:p></o:p></span></pre>
<pre><span lang="EN-GB">Received: 09:23 AM CET, 02/07/2018<o:p></o:p></span></pre>
<pre><span lang="EN-GB">From: Jen Wei Ying <a href="mailto:jenweiying@gmail.com"><jenweiying@gmail.com></a><o:p></o:p></span></pre>
<pre><span lang="EN-GB">To: <a href="mailto:openslide-users@lists.andrew.cmu.edu">openslide-users@lists.andrew.cmu.edu</a><o:p></o:p></span></pre>
<pre><span lang="EN-GB">Subject: Help with viewing slides on the web<o:p></o:p></span></pre>
<pre><span lang="EN-GB"><o:p> </o:p></span></pre>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<pre><span lang="EN-GB">Hello,<o:p></o:p></span></pre>
<pre><span lang="EN-GB"><o:p> </o:p></span></pre>
<pre><span lang="EN-GB">I’m so sorry to trouble but I’m very new at this and was wondering if<o:p></o:p></span></pre>
<pre><span lang="EN-GB">anyone could help me. I have a small bank of slides scanned using<o:p></o:p></span></pre>
<pre><span lang="EN-GB">Precipoint software. The scans are saved in .vmic format. I want to share<o:p></o:p></span></pre>
<pre><span lang="EN-GB">the slides with other members of my department using a web-based slide<o:p></o:p></span></pre>
<pre><span lang="EN-GB">viewer. We are currently sharing our case log using a WordPress platform.<o:p></o:p></span></pre>
<pre><span lang="EN-GB"><o:p> </o:p></span></pre>
<pre><span lang="EN-GB">Does anyone know of any way in which I can make a web-based viewer directly<o:p></o:p></span></pre>
<pre><span lang="EN-GB">from a .vmic file? I tried converting it to TIFF format using ConvertPoint,<o:p></o:p></span></pre>
<pre><span lang="EN-GB">but the resulting image file is so large that most software can’t open<o:p></o:p></span></pre>
</blockquote>
<pre><span lang="EN-GB">it.<o:p></o:p></span></pre>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<pre><span lang="EN-GB"><o:p> </o:p></span></pre>
<pre><span lang="EN-GB">I would be really grateful for any help!<o:p></o:p></span></pre>
<pre><span lang="EN-GB"><o:p> </o:p></span></pre>
<pre><span lang="EN-GB">Thank you,<o:p></o:p></span></pre>
<pre><span lang="EN-GB">Jen<o:p></o:p></span></pre>
<pre><span lang="EN-GB"><o:p> </o:p></span></pre>
</blockquote>
<pre><span lang="EN-GB"><o:p> </o:p></span></pre>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<pre><span lang="EN-GB">_______________________________________________<o:p></o:p></span></pre>
<pre><span lang="EN-GB">openslide-users mailing list<o:p></o:p></span></pre>
<pre><span lang="EN-GB"><a href="mailto:openslide-users@lists.andrew.cmu.edu">openslide-users@lists.andrew.cmu.edu</a><o:p></o:p></span></pre>
<pre><span lang="EN-GB"><a href="https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users">https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users</a><o:p></o:p></span></pre>
<pre><span lang="EN-GB"><o:p> </o:p></span></pre>
</blockquote>
<pre><span lang="EN-GB"><o:p> </o:p></span></pre>
<pre><span lang="EN-GB"><o:p> </o:p></span></pre>
<pre><span lang="EN-GB">_______________________________________________<o:p></o:p></span></pre>
<pre><span lang="EN-GB">openslide-users mailing list<o:p></o:p></span></pre>
<pre><span lang="EN-GB"><a href="mailto:openslide-users@lists.andrew.cmu.edu">openslide-users@lists.andrew.cmu.edu</a><o:p></o:p></span></pre>
<pre><span lang="EN-GB"><a href="https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users">https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users</a><o:p></o:p></span></pre>
</blockquote>
<p><span lang="EN-GB"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span lang="EN-GB">-- <o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif">--<o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Best regards / Mit freundlichen Grüßen<o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif">PD Dr. med. Martin Weihrauch<o:p></o:p></span></p>
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