<div dir="ltr">Hi Peter,<div><br></div><div>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?</div><div><br></div><div>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></div><div><br></div><div>Illustrated poorly, an example structure that Openslide could read would look like this:</div><div><br></div><div>Slide.mrxs</div><div>Slide/</div><div> -> Data0000.dat</div><div> -> Data0001.dat</div><div> -> ...</div><div> -> Index.dat</div><div> -> Slidedat.ini</div><div><br></div><div>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.</div><div><br></div><div>Best,</div><div>Coleman</div><div><br></div><div><br></div><div>Coleman Stavish</div><div>Chief Technology Officer</div><div>Proscia Inc.</div><div><a href="mailto:coleman@proscia.com">coleman@proscia.com</a></div><div><a href="https://proscia.com">https://proscia.com</a></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jan 20, 2017 at 3:00 PM, Peter via openslide-users <span dir="ltr"><<a href="mailto:openslide-users@lists.andrew.cmu.edu" target="_blank">openslide-users@lists.andrew.cmu.edu</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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<div class="m_-3891823462930689727WordSection1">
<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<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:gray"><a href="tel:(646)%20888-8116" value="+16468888116" target="_blank">+1-646-888-8116</a><u></u><u></u></span></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><u></u><u></u></span></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><u></u><u></u></span></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
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<br></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>
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