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<p class="MsoNormal">Dear all,</p>
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<p class="MsoNormal">We are pleased to release Topaz v0.1.0. <span style=""> </span>Topaz is a novel cryoEM particle picker using deep learning convolutional neural networks within a positive-unlabeled framework:</p>
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<p class="MsoNormal" style="margin-left:.5in"><span class="MsoHyperlink"><a href="https://github.com/tbepler/topaz" id="LPlnk422155" class="OWAAutoLink" previewremoved="true">https://github.com/tbepler/topaz</a></span></p>
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<p class="MsoNormal">In our experience, Topaz is able to pick all orientations of any size and shape particle, to avoid aggregation, to avoid junk and grid substrate, to identify more particles than other methods, and to properly order particles by likelihood.
These advances: 1) enable conventionally difficult single particle projects to move forward; 2) significantly decrease ad-hoc user post-processing (e.g. particle filtering/2D classification); 3) make classification more robust and representative given the
significantly larger number of real particles picked; and 4) increase collection and processing efficiency. These achievements are accomplished by requiring training on only a minimal set of sparse positive particles.</p>
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<p class="MsoNormal">Topaz may be installed on all operating systems using a variety of streamlined methods:</p>
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<p class="MsoNormal" style="margin-left:.5in">Anaconda (Linux, Mac, Windows):<span style="">
</span>conda install topaz -c tbepler -c soumith</p>
<p class="MsoNormal" style="margin-left:.5in">Docker (Linux, Mac, Windows): <span style="">
</span>docker pull semc/topaz</p>
<p class="MsoNormal" style="margin-left:.5in">Singularity (Linux, Mac, Windows):<span style="">
</span>singularity pull shub://dallakyan/topaz_singularity</p>
<p class="MsoNormal" style="margin-left:.5in">SBGrid (Linux): <span style=""> </span><span class="MsoHyperlink"><a href="https://sbgrid.org/software/titles/topaz" id="LPlnk918480" class="OWAAutoLink" previewremoved="true">https://sbgrid.org/software/titles/topaz</a></span></p>
<p class="MsoNormal" style="margin-left:.5in">From source (Linux): <span style="">
</span><span class="MsoHyperlink"><a href="https://github.com/tbepler/topaz/tree/gui#installation" id="LPlnk886232" class="OWAAutoLink" previewremoved="true">Follow Github instructions</a></span></p>
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<p class="MsoNormal">Topaz is open source under GPLv3, is modular, and thus may be integrated into any cryoEM software. In addition, we provide a
<span class="MsoHyperlink"><a href="https://github.com/tbepler/topaz/tree/master/topaz/gui" id="LPlnk349929" class="OWAAutoLink" previewremoved="true">standalone GUI with Topaz</a></span> based entirely on HTML/JavaScript/CSS and thus functional on all modern
web browsers. The GUI may be tested here:</p>
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<p class="MsoNormal" style="margin-left:.5in"><span class="MsoHyperlink"><a href="http://emgweb.nysbc.org/topaz.html" id="LPlnk483995" class="OWAAutoLink" previewremoved="true">http://emgweb.nysbc.org/topaz.html</a></span></p>
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<p class="MsoNormal">A presentation of Topaz’s method and some of its capabilities may be seen here:</p>
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<p class="MsoNormal" style="margin-left:.5in"><span class="MsoHyperlink"><a href="https://www.youtube.com/watch?v=I6PUxeVBQt8" id="LPlnk642808" class="OWAAutoLink" previewremoved="true">https://www.youtube.com/watch?v=I6PUxeVBQt8</a></span></p>
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<p class="MsoNormal">Please report any issues, suggestions, or requests as a <span class="MsoHyperlink">
<a href="https://github.com/tbepler/topaz/issues" id="LPlnk970800" class="OWAAutoLink" previewremoved="true">GitHub issue</a></span>.</p>
<p class="MsoNormal">We hope this software is useful to the cryoEM community.</p>
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<p class="MsoNormal">Best regards,</p>
<p class="MsoNormal">Tristan Bepler, Computer Science & Artificial Intelligence Laboratory @ MIT,
<span class="MsoHyperlink"><a href="mailto:tbepler@mit.edu" id="LPlnk968782" class="OWAAutoLink" previewremoved="true">tbepler@mit.edu</a></span></p>
<p class="MsoNormal">Alex Noble, Simons Electron Microscopy Center @ NYSBC, <span class="MsoHyperlink">
<a href="mailto:anoble@nysbc.org" id="LPlnk196412" class="OWAAutoLink" previewremoved="true">anoble@nysbc.org</a></span>,
<span class="MsoHyperlink"><a href="https://twitter.com/alexjamesnoble" id="LPlnk103441" class="OWAAutoLink" previewremoved="true">twitter</a></span></p>
<p class="MsoNormal">Bonnie Berger, Computer Science & Artificial Intelligence Laboratory @ MIT,
<span class="MsoHyperlink"><a href="mailto:bab@mit.edu" id="LPlnk299198" class="OWAAutoLink" previewremoved="true">bab@mit.edu</a></span></p>
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