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SPIDER-em (Electron microscopy software) SPIDER and Web Distributions

Joachim Frank and many others over 40 years


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  <identifier identifierType="DOI">10.5281/zenodo.1447157</identifier>
  <creators>
    <creator>
      <creatorName>Joachim Frank and many others over 40 years</creatorName>
      <affiliation>Wadsworth Labs</affiliation>
    </creator>
  </creators>
  <titles>
    <title>SPIDER-em (Electron microscopy software) SPIDER and Web Distributions</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2018</publicationYear>
  <subjects>
    <subject>Cryo-electron microscopy</subject>
    <subject>Single particle reconstruction</subject>
    <subject>Volume segmentation</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2018-07-31</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/1447157</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.1326590</relatedIdentifier>
  </relatedIdentifiers>
  <version>24.08 (2018),   15.11 ( 2008),  &amp;   5.0 (1998) .   Older   releases included for historical interest.</version>
  <rightsList>
    <rights rightsURI="https://opensource.org/licenses/GPL-2.0">GNU General Public License v2.0 only</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;&lt;strong&gt;SPIDER&lt;/strong&gt; (&lt;strong&gt;S&lt;/strong&gt;ystem for &lt;strong&gt;P&lt;/strong&gt;rocessing &lt;strong&gt;I&lt;/strong&gt;mage &lt;strong&gt;D&lt;/strong&gt;ata from &lt;strong&gt;E&lt;/strong&gt;lectron microscopy and &lt;strong&gt;R&lt;/strong&gt;elated fields) is an image processing system for electron microscopy.&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;Emphasis on:
	&lt;ul&gt;
		&lt;li&gt;&lt;a href="https://spider.wadsworth.org/spider_doc/spider/docs/operations_doc.html"&gt;Toolkit for algorithm development&lt;/a&gt;&lt;/li&gt;
		&lt;li&gt;&lt;a href="https://spider.wadsworth.org/spider_doc/spider/docs/philosophy.html"&gt;Averaging of single particle&lt;/a&gt; macromolecules&lt;/li&gt;
		&lt;li&gt;&lt;a href="https://spider.wadsworth.org/spider_doc/spider/docs/strategies.html"&gt;3D reconstruction &lt;/a&gt;&lt;/li&gt;
		&lt;li&gt;&lt;a href="https://spider.wadsworth.org/spider_doc/spider/docs/techs/MSA/index.html"&gt;Multivariate data analysis&lt;/a&gt;&lt;/li&gt;
		&lt;li&gt;&lt;a href="https://spider.wadsworth.org/spider_doc/spider/docs/techs/segment/segment.html"&gt;Object segmentation from volumes&lt;/a&gt;&lt;/li&gt;
		&lt;li&gt;&lt;a href="https://spider.wadsworth.org/spider_doc/spider/docs/techs/lgstr/tomo/tomo.html"&gt;Electron tomography&lt;/a&gt;.&lt;/li&gt;
	&lt;/ul&gt;
	&lt;/li&gt;
	&lt;li&gt;Features:
	&lt;ul&gt;
		&lt;li&gt;Interactive command line interface.&lt;/li&gt;
		&lt;li&gt;Hierarchical modular design for scripting.&lt;/li&gt;
		&lt;li&gt;Graphical User Interface, &lt;a href="https://spider.wadsworth.org/spider_doc/web/docs/web.html"&gt;Web&lt;/a&gt;, for visualizing and interacting with images.&lt;/li&gt;
		&lt;li&gt;&lt;a href="https://spider.wadsworth.org/spider_doc/spider/docs/image_doc.html"&gt;File format&lt;/a&gt; interchangeable with other scientific imaging softwares.&lt;/li&gt;
		&lt;li&gt;Extensive &lt;a href="https://spider.wadsworth.org/spider_doc/spider/docs/documents.html"&gt;documentation&lt;/a&gt; of &lt;a href="https://spider.wadsworth.org/spider_doc/spider/docs/operations_doc.html"&gt;operations&lt;/a&gt; and &lt;a href="https://spider.wadsworth.org/spider_doc/spider/docs/techniques.html"&gt;techniques&lt;/a&gt;.&lt;/li&gt;
		&lt;li&gt;Includes &lt;a href="https://spider.wadsworth.org/spider_doc/spider/src"&gt;executables and source code&lt;/a&gt; for use on Linux.&lt;/li&gt;
		&lt;li&gt;&amp;nbsp;&lt;/li&gt;
	&lt;/ul&gt;
	&lt;/li&gt;
	&lt;li&gt;History:
	&lt;ul&gt;
		&lt;li&gt;Originated in &lt;a href="https://spider.wadsworth.org/spider_doc/spider/docs/spider78.html"&gt;1978&lt;/a&gt; at the &lt;a href="http://www.wadsworth.org/"&gt;Wadsworth Center&lt;/a&gt; in Albany, NY by &lt;a href="http://franklab.cpmc.columbia.edu/franklab"&gt;Joachim Frank&lt;/a&gt; who shared the 2017 Nobel Prize in Chemistry for his pioneering cryo-em research done at the Wadsworth Center in Albany.&lt;/li&gt;
		&lt;li&gt;&amp;nbsp;&lt;/li&gt;
		&lt;li&gt;Contributors (in chronological order): J. Frank, B. Shimkin, H. Dowse, L. Miranda, C. Mannella, J. P. Bretaudiere, M. V. Heel, A. Verschoor, M. Radermacher, A. Leith, J. M. Carazo, P. Penczek, L. Odesanya, S. Sibal, Y. H. Li, M. Ladjadj, Y. Chen, K. R. Lata, J. Zhu, W. P. Liu, B. Rath, C. Yang, B. Baxter, R. Hegerl, A. Frangakis, L. Joyeux, Z. Huang, R. J. Renka, T. Shaikh, J. Sengupta, J. LeBarron, N. Boisset, H. Gao, G. Kishchenko, J. M. Kennedy.&lt;/li&gt;
		&lt;li&gt;&amp;nbsp;&lt;/li&gt;
		&lt;li&gt;Maintained since 2007 by: ArDean Leith &amp;amp; Tanvir Shaikh. During these 11 years they added numerous operations, procedures, parallelizations, and over 500 pages of documentation.&amp;nbsp; There have been no significant contributors other than Leith, Shaikh, Kischenko, and Kennedy since 2007.&lt;/li&gt;
	&lt;/ul&gt;
	&lt;/li&gt;
&lt;/ul&gt;</description>
  </descriptions>
</resource>
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