GitHub - ModelDBRepository/236429: 2 Distinct Classes of L2 and L3 Pyramidal Neurons in Human Temporal Cortex (Deitcher et al 2017)

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2 Distinct Classes of L2 and L3 Pyramidal Neurons in Human Temporal Cortex (Deitcher et al 2017)

modeldb.science/236429

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Name		Name	Last commit message	Last commit date
Latest commit History 3 Commits
Morphs_and_trees		Morphs_and_trees
images		images
Figure_6_A1_B1.m		Figure_6_A1_B1.m
Figure_6_A2_B2.m		Figure_6_A2_B2.m
dendrogram_tree_basal_apical.m		dendrogram_tree_basal_apical.m
readme.html		readme.html

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<html>
  This is the readme for the code associated with the paper:<p/>
  Deitcher Y, Eyal G, Kanari L, Verhoog MB, Atenekeng Kahou GA, Mansvelder HD, de Kock CPJ, Segev I (2017) Comprehensive Morpho-Electrotonic Analysis Shows 2 Distinct Classes of L2 and L3 Pyramidal Neurons in Human Temporal Cortex. Cereb Cortex 27:5398-5414<br/>
  <a href="http://dx.doi.org/10.1093/cercor/bhx226">http://dx.doi.org/10.1093/cercor/bhx226</a><p/>

This archive containing matlab and NEURON code was contributed by Y Deitcher and G Eyal.  The matlab programs requires the TREES toolbox freely available from:<br/>
  <a href="http://www.treestoolbox.org/">http://www.treestoolbox.org/</a><p/>
<p/>
To recreate figures 6 A1, B1 dendrograms type Figure_6_A1_B1 on the matlab command prompt.  After a minute you should see:
  <p/>
  <img src="./images/screenshot1.png" alt="screenshot 1">
<p/>
  <img src="./images/screenshot2.png" alt="screenshot 2">
  <p/>
  To recreate the inset run the NEURON file 0471.hoc in the Morphs_and_trees folder (type "nrngui 0471.hoc" at the linux command prompt or for more help see <br/>
  <a href="https://senselab.med.yale.edu/ModelDB/NEURON_DwnldGuide.cshtml">https://senselab.med.yale.edu/ModelDB/NEURON_DwnldGuide.cshtml</a><br/>
  Then click on the nrnmainmenu: Graph -> Shape Plot to see:<p/>
  <img src="./images/screenshot5.png"><p/>
  <p/>
To recreate figures 6 A2, B2 dendrograms type Figure_6_A2_B2 on the matlab command prompt.  After a minute you should see:
  <p/>
  <img src="./images/screenshot3.png" alt="screenshot 3">
<p/>
  <img src="./images/screenshot4.png" alt="screenshot 4">
  <p/>
  To recreate the inset run the NEURON file 1148.hoc in the Morphs_and_trees folder (type "nrngui 1148.hoc" at the linux command prompt or for more help see <br/>
  <a href="https://senselab.med.yale.edu/ModelDB/NEURON_DwnldGuide.cshtml">https://senselab.med.yale.edu/ModelDB/NEURON_DwnldGuide.cshtml</a><br/>
  Then click on the nrnmainmenu: Graph -> Shape Plot to see:<p/>
  <img src="./images/screenshot6.png"><p/>
</html>