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<p class="MsoNormal">Dear 3DEM community,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">On this day in 1999, I announced the first version of <i>Situs</i> on this mailing list. I did not know at that time that cryo-EM and tomography-based modeling would keep me and my computational group busy for my whole career, but here
we are, 25 years later! <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">To celebrate the anniversary, we are rolling out a new version of
<i>Situs</i> with cutting-edge tools for tracing filaments in 3D tomograms:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><b>Spaghetti Tracer</b> (fast tracing of semi-ordered filament bundles in tomograms) [1]<o:p></o:p></p>
<p class="MsoNormal"><b>Struwwel Tracer</b> (fast tracing of random oriented filament networks in tomograms) [2], and
<o:p></o:p></p>
<p class="MsoNormal"><b>elConDe</b> (template-constrained deconvolution of semi-ordered filaments) [3].<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Please check out the software web site with details on the rollout:
<a href="https://urldefense.com/v3/__https://situs.biomachina.org/__;!!Mih3wA!BL01bC5bg1GJBQ1jykwsO9g4plAjMa1kCGtoEDovCaFO6dmMkyd7zCdhaMzdb-eUiehNMvoa8DfAeYAfTwzw$">https://situs.biomachina.org/</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I would also like to dedicate this release to the memory of two students we lost over the years, my student Paul Boyle from Ireland, a
<i>Situs</i> developer who passed away twenty years ago [4], and Manfred Auer’s student Junha Song from South Korea, a coauthor of [3], who passed away last year (see acknowledgement/dedication in [2]). It has been a privilege and inspiration to work with them.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best wishes for the next 25 years.<o:p></o:p></p>
<p class="MsoNormal">Willy<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="color:#0033CC;mso-ligatures:none">Willy Wriggers, Ph.D.</span><span style="mso-ligatures:none"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#0033CC;mso-ligatures:none">Frank Batten Chair</span><span style="mso-ligatures:none">
<span style="color:#0033CC">of Mechanical and Aerospace Engineering</span><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#0033CC;mso-ligatures:none">Old Dominion University</span><span style="mso-ligatures:none"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#0033CC;mso-ligatures:none">238 Kaufman Hall</span><span style="mso-ligatures:none"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#0033CC;mso-ligatures:none">Norfolk, Virginia 23529</span><span style="mso-ligatures:none"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">[1] Salim Sazzed, Peter Scheible, Jing He, Willy Wriggers. Spaghetti Tracer: A Framework for Tracing Semiregular Filamentous Densities in 3D Tomograms. Biomolecules 12 (8), 1022, 2022
<a href="https://urldefense.com/v3/__https://www.mdpi.com/2218-273X/12/8/1022__;!!Mih3wA!BL01bC5bg1GJBQ1jykwsO9g4plAjMa1kCGtoEDovCaFO6dmMkyd7zCdhaMzdb-eUiehNMvoa8DfAeZITSWyQ$">https://www.mdpi.com/2218-273X/12/8/1022</a><o:p></o:p></p>
<p class="MsoNormal">[2] Salim Sazzed, Peter Scheible, Jing He, Willy Wriggers. Untangling Irregular Actin Cytoskeleton Architectures in Tomograms of the Cell with Struwwel Tracer. International Journal of Molecular Sciences 24 (24), 17183, 2023
<a href="https://urldefense.com/v3/__https://www.mdpi.com/1422-0067/24/24/17183__;!!Mih3wA!BL01bC5bg1GJBQ1jykwsO9g4plAjMa1kCGtoEDovCaFO6dmMkyd7zCdhaMzdb-eUiehNMvoa8DfAeZK2nLsh$">https://www.mdpi.com/1422-0067/24/24/17183</a><o:p></o:p></p>
<p class="MsoNormal">[3] Julio Kovacs, Junha Song, Manfred Auer, Jing He, Wade Hunter, Willy Wriggers. Correction of missing-wedge artifacts in filamentous tomograms by template-based constrained deconvolution. Journal of chemical information and modeling 60
(5), 2626-2633, 2020 <a href="https://urldefense.com/v3/__https://pubs.acs.org/doi/10.1021/acs.jcim.9b01111__;!!Mih3wA!BL01bC5bg1GJBQ1jykwsO9g4plAjMa1kCGtoEDovCaFO6dmMkyd7zCdhaMzdb-eUiehNMvoa8DfAeVQMNZDR$">
https://pubs.acs.org/doi/10.1021/acs.jcim.9b01111</a><o:p></o:p></p>
<p class="MsoNormal">[4] <a href="https://urldefense.com/v3/__https://w.biomachina.org/people/pboyle/__;!!Mih3wA!BL01bC5bg1GJBQ1jykwsO9g4plAjMa1kCGtoEDovCaFO6dmMkyd7zCdhaMzdb-eUiehNMvoa8DfAedJ4jz7Y$">https://w.biomachina.org/people/pboyle/</a><o:p></o:p></p>
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