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Code for detecting and classifying epileptiform activity (EA)

Heining, Katharina


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    "description": "<p><strong>Code for detecting and classifying epileptiform activity (EA)</strong><br>\nWritten by Katharina Heining, last modified 2020/10/20 &nbsp;<br>\nInstitution: University of Freiburg, Germany<br>\nAccompanying Paschen et al. (2020), eLife</p>\n\n<p>The subdirectory <strong>core</strong> contains the main code: &nbsp;</p>\n\n<ul>\n\t<li>&nbsp;<em>ed_detection.py</em>:&nbsp;&nbsp;&nbsp; wrapper for preprocessing, spike detection and spike sorting &nbsp;</li>\n\t<li>&nbsp;<em>artisfaction.py</em>:&nbsp;&nbsp; &nbsp;semiautomatic identification of artifacts</li>\n\t<li>&nbsp;<em>blipS.py</em>:&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; spike detection* blipsort.py:&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; spike sorting</li>\n\t<li>&nbsp;<em>ea_analysis.py</em>:&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; wrapper for burst detection and classification</li>\n\t<li>&nbsp;<em>somify.py</em>:&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; projecting data on a SOM and SOM plotting</li>\n\t<li>&nbsp;<em>helpers.py</em>:&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; supportive functions for the other scripts</li>\n\t<li>&nbsp;<em>ea_management.py</em>:&nbsp;&nbsp; &nbsp;reading data, handling results, recording-class functions</li>\n</ul>\n\n<p><em>configAnalysis.yml</em> contains parameters used for analyses &nbsp;<br>\n<em>som.h5</em> holds the SOM obtained from reference dataset -- see Heining et al. (2019), referenced below.* &nbsp;</p>\n\n<p>The subdirectory <strong>code_for_figures</strong> contains the code used for illustration (Supplementary Figure 1).<br>\n&nbsp;<br>\nThe code contained in this folder is &copy; K. Heining, 2020, developed at the University of Freiburg. &nbsp;<br>\nThis code is made available under the BSD license enclosed with the software (see licence.txt).<br>\nOver 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.<br>\nFor this, you need to cite the paper that describes the code: &nbsp;<br>\n* Heining, K., Kilias, A., Janz, P., H&auml;ussler, U., Kumar, A., Haas, C. A., and Egert, U.<br>\n(2019). Bursts with high and low load of epileptiform spikes show context-dependent<br>\ncorrelations in epileptic mice. eNeuro, 6(5).</p>", 
    "license": {
      "id": "MIT"
    }, 
    "title": "Code for detecting and classifying epileptiform activity (EA)", 
    "notes": "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).", 
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    "keywords": [
      "epileptiform activity", 
      "local field potential", 
      "detection of epileptiform spikes"
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    "publication_date": "2020-10-20", 
    "creators": [
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        "orcid": "0000-0003-1976-3764", 
        "affiliation": "Biomicrotechnology, Department of Microsystems Engineering \u2013 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", 
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