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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I’m not sure if this is relevant, but HeteroGenius MIM supports working with 3D stacks and can read individual mrxs slides (via openslide), allowing 3D annotation/visualisation
and export:<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"><a href="http://www.medicalimagemanager.com/static/MIM/features/3d/index.html">http://www.medicalimagemanager.com/static/MIM/features/3d/index.html</a><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">let me know if you want more information. We have a lot of experience working with 3D stacks here in Leeds.<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">Yours<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">Derek Magee<o:p></o:p></span></p>
<p class="MsoNormal"><a name="_MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></a></p>
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<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 [mailto:openslide-users-bounces+d.r.magee=leeds.ac.uk@lists.andrew.cmu.edu]
<b>On Behalf Of </b>Peter via openslide-users<br>
<b>Sent:</b> 20 January 2017 20:41<br>
<b>To:</b> coleman@proscia.com<br>
<b>Cc:</b> openslide-users@lists.andrew.cmu.edu<br>
<b>Subject:</b> RE: 3D Histech on Openslide?<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thank you for the fast response.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" 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.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Peter<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" 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 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""> Coleman Stavish [<a href="mailto:coleman@proscia.com">mailto: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">openslide-users@lists.andrew.cmu.edu</a><br>
<b>Subject:</b> Re: 3D Histech on Openslide?<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span lang="EN-US">Hi Peter,<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal"><span lang="EN-US">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?<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal"><span lang="EN-US">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/">http://openslide.org/formats/mirax/</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US">Illustrated poorly, an example structure that Openslide could read would look like this:<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal"><span lang="EN-US">Slide.mrxs<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US">Slide/<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US"> -> Data0000.dat<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US"> -> Data0001.dat<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US"> -> ...<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US"> -> Index.dat<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US"> -> Slidedat.ini<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal"><span lang="EN-US">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.<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US">Best,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US">Coleman<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US">Coleman Stavish<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US">Chief Technology Officer<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US">Proscia Inc.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US"><a href="mailto:coleman@proscia.com">coleman@proscia.com</a><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US"><a href="https://proscia.com">https://proscia.com</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span lang="EN-US">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.cmu.edu</a>> wrote:<o:p></o:p></span></p>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Is it possible to view 3D Slides (e.g. 3D Histech from Mirax) with openslide?<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">If not, how could that be implemented? What would you need for that? An example slide?<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Best,<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Peter<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Dr. Peter J. Schueffler<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:10.0pt;color:gray">Postdoctoral Researcher<br>
MSKCC, Computational Pathology Lab<br>
485 Lexington Ave<br>
New York, NY 10017</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:10.0pt;color:gray"><a href="tel:(646)%20888-8116" target="_blank">+1-646-888-8116</a></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><u><span lang="EN-US" style="font-size:10.0pt;color:#548DD4"><a href="mailto:schueffp@mskcc.org" target="_blank">schueffp@mskcc.org</a></span></u><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><u><span lang="EN-US" style="font-size:10.0pt;color:#548DD4"><a href="http://www.thomasfuchslab.org" target="_blank">www.thomasfuchslab.org</a></span></u><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> <o:p></o:p></span></p>
</div>
<p><span lang="EN-US">=====================================================================<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>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="EN-US"><br>
_______________________________________________<br>
openslide-users mailing list<br>
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<p class="MsoNormal"><span lang="EN-US"><br>
<br clear="all">
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span lang="EN-US">-- <o:p></o:p></span></p>
<div>
<div>
<p class="MsoNormal"><span lang="EN-US" style="font-size:9.0pt;color:#707077">Coleman</span><span lang="EN-US"><o:p></o:p></span></p>
</div>
</div>
</div>
<p><span lang="EN-US">=====================================================================<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.<o:p></o:p></span></p>
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