<div dir="ltr">To my knowledge, Openslide cannot read data from alternate focal planes or handle z-stack images (see: <a href="https://github.com/openslide/openslide/issues/31">https://github.com/openslide/openslide/issues/31</a>). From that discussion, it seems like a non-negligible work would be required to add that sort of functionality to the API. However, I don't think the public Openslide dataset has any multiplane MIRAX images, so if you are able to contribute one publicly, I'm sure the project would appreciate it.<div><br></div><div>Coleman</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jan 20, 2017 at 3:41 PM, <span dir="ltr"><<a href="mailto:schueffp@mskcc.org" target="_blank">schueffp@mskcc.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Thank you for the fast response.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">I meant the first case, three-dimensional reconstructions from serial sections, generated by a 3D Histech scanner. Such that openslide has another handle in
which one can adjust the z-layer.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Best,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Peter<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Coleman Stavish [mailto:<a href="mailto:coleman@proscia.com" target="_blank">coleman@proscia.com</a>]
<br>
<b>Sent:</b> Friday, January 20, 2017 3:30 PM<br>
<b>To:</b> Schueffler, Peter/Sloan Kettering Institute<br>
<b>Cc:</b> <a href="mailto:openslide-users@lists.andrew.cmu.edu" target="_blank">openslide-users@lists.andrew.<wbr>cmu.edu</a><br>
<b>Subject:</b> Re: 3D Histech on Openslide?<u></u><u></u></span></p>
</div><div><div class="h5">
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<p class="MsoNormal">Hi Peter,<u></u><u></u></p>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">To be clear, do you mean three-dimensional tissue reconstructions from serial sections? Or do you mean the standard 2D WSI captured by a 3DHISTECH scanner?<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">If you're referring to the latter, Openslide officially supports the MIRAX (.mrxs) format that most if not all 3DHISTECH scanners output. From my experience, the 3DHISTECH software exports a single WSI as a directory of many files, one
of which has the extension ".mrxs". In order for Openslide to successfully read the MIRAX image, the .mrxs file must exist in the same parent directory as the directory containing the .dat files. Further, that directory must have the same name (without the
extension) as the .mrxs file. More information can be found here: <a href="http://openslide.org/formats/mirax/" target="_blank">http://openslide.org/<wbr>formats/mirax/</a><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Illustrated poorly, an example structure that Openslide could read would look like this:<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Slide.mrxs<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Slide/<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> -> Data0000.dat<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> -> Data0001.dat<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> -> ...<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> -> Index.dat<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> -> Slidedat.ini<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">While supporting one of our clients with a 3DHISTECH scanner and software, we found that MIRAX images exported using the 3DHISTECH "batch export" feature were in some way malformed, and Openslide failed to read them. The same images exported
one at a time had no problems. The only noticeable difference at first glance was that the .dat files were in a different order dependent on whether the image was batch-exported or solo-exported. This may not affect you, but I thought I would share it with
the mailing list.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Best,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Coleman<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Coleman Stavish<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Chief Technology Officer<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Proscia Inc.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><a href="mailto:coleman@proscia.com" target="_blank">coleman@proscia.com</a><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><a href="https://proscia.com" target="_blank">https://proscia.com</a><u></u><u></u></p>
</div>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<p class="MsoNormal">On Fri, Jan 20, 2017 at 3:00 PM, Peter via openslide-users <<a href="mailto:openslide-users@lists.andrew.cmu.edu" target="_blank">openslide-users@lists.andrew.<wbr>cmu.edu</a>> wrote:<u></u><u></u></p>
<div>
<div>
<p class="MsoNormal">Is it possible to view 3D Slides (e.g. 3D Histech from Mirax) with openslide?<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">If not, how could that be implemented? What would you need for that? An example slide?<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Best,<u></u><u></u></p>
<p class="MsoNormal">Peter<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Dr. Peter J. Schueffler<u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:gray">Postdoctoral Researcher<br>
MSKCC, Computational Pathology Lab<br>
485 Lexington Ave<br>
New York, NY 10017</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:gray"><a href="tel:(646)%20888-8116" target="_blank">+1-646-888-8116</a></span><u></u><u></u></p>
<p class="MsoNormal"><u><span style="font-size:10.0pt;color:#548dd4"><a href="mailto:schueffp@mskcc.org" target="_blank">schueffp@mskcc.org</a></span></u><u></u><u></u></p>
<p class="MsoNormal"><u><span style="font-size:10.0pt;color:#548dd4"><a href="http://www.thomasfuchslab.org" target="_blank">www.thomasfuchslab.org</a></span></u><u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
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______________________________<wbr>_________________<br>
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</div>
<p class="MsoNormal"><br>
<br clear="all">
<u></u><u></u></p>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<p class="MsoNormal">-- <u></u><u></u></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#707077">Coleman</span><u></u><u></u></p>
</div>
</div>
</div>
</div></div></div><div><div class="h5">
<p>==============================<wbr>==============================<wbr>=========<br>
<br>
Please note that this e-mail and any files transmitted from<br>
Memorial Sloan Kettering Cancer Center may be privileged, confidential,<br>
and protected from disclosure under applicable law. If the reader of<br>
this message is not the intended recipient, or an employee or agent<br>
responsible for delivering this message to the intended recipient,<br>
you are hereby notified that any reading, dissemination, distribution,<br>
copying, or other use of this communication or any of its attachments<br>
is strictly prohibited. If you have received this communication in<br>
error, please notify the sender immediately by replying to this message<br>
and deleting this message, any attachments, and all copies and backups<br>
from your computer.<br></p></div></div></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><font color="#707077"><span style="font-size:12px">Coleman</span></font></div></div>
</div>