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<p>Dear all,</p>
<p>I also take this mail to announce the release of Xmipp 19.04.
It's release notes are in <a
href="https://github.com/I2PC/xmipp/wiki/Release-notes">https://github.com/I2PC/xmipp/wiki/Release-notes</a>
and this new version contains many new algorithms like stream
processing up to 3D reconstruction and estimation of 3D
heterogeneity, MotionCorrB (a very fast movie alignment using
B-splines that generalizes MotionCorr2 and our Optical Flow), deep
consensus (an algorithm to merge the output of multiple particle
pickers and save 2D classification time), swarm consensus (an
algorithm that automatically constructs initial volumes based on
proposals by other algorithms), initial volume validation using
SAXS experiments, highres (3D reconstruction of homogeneous
populations), angular consensus (an algorithm to compare the
angular assignment by two different algorithms), heterogeneity
metaprotocol (3D classification) allowing detailed control of the
intermediate steps, many resolution algorithms measuring the
resolution locally, directionally and in tomograms (MonoRes,
MonoDir and MonoTomo), and localDeblur (an algorithm to sharpen
maps that uses the local resolution information).</p>
<p>A short presentation with some of these results can be seen at</p>
<p><a class="moz-txt-link-freetext" href="https://drive.google.com/file/d/1r3RnOw8pkp-BH5KvCxvAdoe-HUPtCddo/view?usp=sharing">https://drive.google.com/file/d/1r3RnOw8pkp-BH5KvCxvAdoe-HUPtCddo/view?usp=sharing</a></p>
<p>Kind regards, Carlos Oscar<br>
</p>
<div class="moz-cite-prefix">El 16/05/2019 a las 14:22, Pablo Conesa
escribió:<br>
</div>
<blockquote type="cite"
cite="mid:8fc25b42-c012-557b-95dd-2f48dbb265a3@cnb.csic.es">
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<p><b style="font-weight:normal;"
id="docs-internal-guid-6abb2f01-7fff-8cb8-9ccf-1500dc8bc630">
</b></p>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align:
justify;"><b style="font-weight:normal;"
id="docs-internal-guid-6abb2f01-7fff-8cb8-9ccf-1500dc8bc630"><span style="font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">Dear all,</span></b></p>
<b style="font-weight:normal;"
id="docs-internal-guid-6abb2f01-7fff-8cb8-9ccf-1500dc8bc630"> <br>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align:
justify;"><span style="font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">We are pleased to announce the new major release of version <a moz-do-not-send="true" href="http://scipion.i2pc.es">SCIPION 2.0</a>. It is freely available for download on Linux here:</span></p>
<br>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align:
justify;"><a href="http://scipion.i2pc.es/download_form"
style="text-decoration:none;" moz-do-not-send="true"><span style="font-size:11pt;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:underline;-webkit-text-decoration-skip:none;text-decoration-skip-ink:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">http://scipion.i2pc.es/download_form</span></a></p>
<br>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align:
justify;"><span style="font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">Key changes for version 2.0 are:</span></p>
<br>
<ul style="margin-top:0pt;margin-bottom:0pt;">
<li dir="ltr" style="list-style-type:disc;font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align: justify;"><span style="font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">Almost all existing EM packages were updated, such as RELION3, EMAN2.21, Gctf 1.18, SPIDER 25.02, Motioncor2-1.2.1 and others.</span></p></li>
</ul>
<br>
<ul style="margin-top:0pt;margin-bottom:0pt;">
<li dir="ltr" style="list-style-type:disc;font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align: justify;"><span style="font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">Model building tools from CCP4, Chimera, Phenix and powerfit have been added.</span></p></li>
</ul>
<br>
<ul style="margin-top:0pt;margin-bottom:0pt;">
<li dir="ltr" style="list-style-type:disc;font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align: justify;"><span style="font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">Several improvements for streaming: multi-GPU jobs distribution, more protocols supporting batch processing, jobs scheduling, new XMIPP streaming protocols (movie maxshift, ctf selection, GL2D classification on GPU etc.)</span></p></li>
</ul>
<br>
<ul style="margin-top:0pt;margin-bottom:0pt;">
<li dir="ltr" style="list-style-type:disc;font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align: justify;"><span style="font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">Multiple workflow usability and GUI improvements as well as bug fixes for several tasks.</span></p></li>
</ul>
</b><b style="font-weight:normal;"
id="docs-internal-guid-6abb2f01-7fff-8cb8-9ccf-1500dc8bc630"><br>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align:
justify;"><span style="font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;"></span></p>
<ul style="margin-top:0pt;margin-bottom:0pt;">
<li dir="ltr" style="list-style-type:disc;font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align: justify;"><span style="font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">Pluginization: each EM package is now a plugin developed and updated independently from Scipion core. This is a first step towards making Scipion even more modular and easy to use and install for both users and developers. The new repository hosting official plugins is now here:</span></p></li>
</ul>
<br>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;margin-left:
36pt;text-align: justify;"><a
href="https://github.com/scipion-em"
style="text-decoration:none;" moz-do-not-send="true"><span style="font-size:11pt;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:underline;-webkit-text-decoration-skip:none;text-decoration-skip-ink:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">https://github.com/scipion-em</span></a></p>
<br>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;margin-left:
36pt;text-align: justify;"><span style="font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">For your convenience we have developed a Plugin Manager which provides an easy GUI to manage plugins and associated binaries. We already have over 30 plugins including several new ones, such as 3DFSC, CryoEF, Sphire (crYOLO), EMPIAR depositor and others. For more information on each plugin consult its corresponding repo and/ or developers.</span></p>
<br>
<ul style="margin-top:0pt;margin-bottom:0pt;">
<li dir="ltr" style="list-style-type:disc;font-size:11pt;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align: justify;"><span style="font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">For developers and facility managers we now have a slack workspace where you can easily reach other developers and facility staff to get a quick feedback: </span><a href="https://scipion.slack.com/" style="text-decoration:none;" moz-do-not-send="true"><span style="font-size:11pt;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:underline;-webkit-text-decoration-skip:none;text-decoration-skip-ink:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">https://scipion.slack.com/</span></a><span style="font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">. Contact us at </span><a href="mailto:scipion@cnb.csic.es" style="text-decoration:none;" moz-do-not-send="true"><span style="font-size:11pt;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:underline;-webkit-text-decoration-skip:none;text-decoration-skip-ink:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">scipion@cnb.csic.es</span></a><span style="font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;"> for an invitation.</span></p></li>
</ul>
<br>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align:
justify;"><span style="font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">Installation instructions, pre-requisites and a <a moz-do-not-send="true" href="https://scipion-em.github.io/docs/docs/developer/release-notes.html?highlight=release#v2-0-2019-05-16-diocletian">full list of changes</a> are available on our new documentation </span><a
href="https://scipion-em.github.io/docs/"
style="text-decoration:none;" moz-do-not-send="true"><span style="font-size:11pt;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:underline;-webkit-text-decoration-skip:none;text-decoration-skip-ink:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">website</span></a><span style="font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">.</span></p>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align:
justify;"><span style="font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">
</span></p>
<br>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:11pt;font-family:Arial;color:#222222;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">Best wishes,</span></p>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><a
href="http://scipion.i2pc.es/#whoweare"
style="text-decoration:none;" moz-do-not-send="true"><span style="font-size:11pt;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:400;font-style:normal;font-variant:normal;text-decoration:underline;-webkit-text-decoration-skip:none;text-decoration-skip-ink:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">Scipion team</span></a></p>
</b><br class="Apple-interchange-newline">
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
3dem mailing list
<a class="moz-txt-link-abbreviated" href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a>
<a class="moz-txt-link-freetext" href="https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem">https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem</a>
</pre>
</blockquote>
<pre class="moz-signature" cols="72">--
------------------------------------------------------------------------
Carlos Oscar Sánchez Sorzano e-mail: <a class="moz-txt-link-abbreviated" href="mailto:coss@cnb.csic.es">coss@cnb.csic.es</a>
Biocomputing unit <a class="moz-txt-link-freetext" href="http://i2pc.es/coss">http://i2pc.es/coss</a>
National Center of Biotechnology (CSIC)
c/Darwin, 3
Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510
28049 MADRID (SPAIN) Fax: 34-91-585 4506
------------------------------------------------------------------------
</pre>
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