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Code for detecting and classifying epileptiform activity (EA)

Heining, Katharina


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  <identifier identifierType="DOI">10.5281/zenodo.4110614</identifier>
  <creators>
    <creator>
      <creatorName>Heining, Katharina</creatorName>
      <givenName>Katharina</givenName>
      <familyName>Heining</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-1976-3764</nameIdentifier>
      <affiliation>Biomicrotechnology, Department of Microsystems Engineering – IMTEK, Faculty of Engineering, University of Freiburg, 79110 Freiburg, Germany; Bernstein Center Freiburg, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Code for detecting and classifying epileptiform activity (EA)</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <subjects>
    <subject>epileptiform activity</subject>
    <subject>local field potential</subject>
    <subject>detection of epileptiform spikes</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2020-10-20</date>
  </dates>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/4110614</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.4110613</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://opensource.org/licenses/MIT">MIT License</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;&lt;strong&gt;Code for detecting and classifying epileptiform activity (EA)&lt;/strong&gt;&lt;br&gt;
Written by Katharina Heining, last modified 2020/10/20 &amp;nbsp;&lt;br&gt;
Institution: University of Freiburg, Germany&lt;br&gt;
Accompanying Paschen et al. (2020), eLife&lt;/p&gt;

&lt;p&gt;The subdirectory &lt;strong&gt;core&lt;/strong&gt; contains the main code: &amp;nbsp;&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;&amp;nbsp;&lt;em&gt;ed_detection.py&lt;/em&gt;:&amp;nbsp;&amp;nbsp;&amp;nbsp; wrapper for preprocessing, spike detection and spike sorting &amp;nbsp;&lt;/li&gt;
	&lt;li&gt;&amp;nbsp;&lt;em&gt;artisfaction.py&lt;/em&gt;:&amp;nbsp;&amp;nbsp; &amp;nbsp;semiautomatic identification of artifacts&lt;/li&gt;
	&lt;li&gt;&amp;nbsp;&lt;em&gt;blipS.py&lt;/em&gt;:&amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; spike detection* blipsort.py:&amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; spike sorting&lt;/li&gt;
	&lt;li&gt;&amp;nbsp;&lt;em&gt;ea_analysis.py&lt;/em&gt;:&amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; wrapper for burst detection and classification&lt;/li&gt;
	&lt;li&gt;&amp;nbsp;&lt;em&gt;somify.py&lt;/em&gt;:&amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; projecting data on a SOM and SOM plotting&lt;/li&gt;
	&lt;li&gt;&amp;nbsp;&lt;em&gt;helpers.py&lt;/em&gt;:&amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; supportive functions for the other scripts&lt;/li&gt;
	&lt;li&gt;&amp;nbsp;&lt;em&gt;ea_management.py&lt;/em&gt;:&amp;nbsp;&amp;nbsp; &amp;nbsp;reading data, handling results, recording-class functions&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;em&gt;configAnalysis.yml&lt;/em&gt; contains parameters used for analyses &amp;nbsp;&lt;br&gt;
&lt;em&gt;som.h5&lt;/em&gt; holds the SOM obtained from reference dataset -- see Heining et al. (2019), referenced below.* &amp;nbsp;&lt;/p&gt;

&lt;p&gt;The subdirectory &lt;strong&gt;code_for_figures&lt;/strong&gt; contains the code used for illustration (Supplementary Figure 1).&lt;br&gt;
&amp;nbsp;&lt;br&gt;
The code contained in this folder is &amp;copy; K. Heining, 2020, developed at the University of Freiburg. &amp;nbsp;&lt;br&gt;
This code is made available under the BSD license enclosed with the software (see licence.txt).&lt;br&gt;
Over and above the legal restrictions imposed by this license, if you use this software for an academic publication then you are obliged to provide proper attribution.&lt;br&gt;
For this, you need to cite the paper that describes the code: &amp;nbsp;&lt;br&gt;
* Heining, K., Kilias, A., Janz, P., H&amp;auml;ussler, U., Kumar, A., Haas, C. A., and Egert, U.&lt;br&gt;
(2019). Bursts with high and low load of epileptiform spikes show context-dependent&lt;br&gt;
correlations in epileptic mice. eNeuro, 6(5).&lt;/p&gt;</description>
    <description descriptionType="Other">This work was supported by the German Research Foundation as part of the Cluster of Excellence 'BrainLinks-BrainTools' within the framework of the German Excellence Initiative (grant number EXC 1086) and through grant no INST 39/963-1 FUGG (bwForCluster NEMO), the State of Baden-Wuerttemberg through bwHPC, and by the Federal Ministry of Education and Research (BMBF, grant number FKZ 1GQ0830 and 16PGF0070), co-financed by the European Union/European Regional Development Fund (TIGER, A31).</description>
  </descriptions>
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