{
  "id": 7526,
  "title": "Another Question About Neurons",
  "url": "/competitions/connectomics/discussion/7526",
  "author_name": "",
  "post_date": "2014-03-26T21:01:23.637Z",
  "votes": null,
  "comment_count": 2,
  "views": 765,
  "content": "<p>From another topic:</p>\n<p>[quote=Sagredo;38634]</p>\n<p>I would like to add a further clarification. Salviati told: &quot;The firing of a presynaptic neuron is expected to affect the probability of firing of its postsynaptic neurons. If the presynaptic neuron is excitatory, the postsynaptic probability of firing will rise.&quot;</p>\n<p>This is certainly true! But our simulations are not probabilistic, are real dynamical systems simulations. At every time-step we integrate a system of hundredths of non-linear differential equations, it is not just tossing a dice per neuron to decide whether it will fire or not. We have a full-fledged biophysically realistic simulation behind our simulated data.</p>\n<p>That said, at the phenomenological level, Salviati's comment is true: the post-synaptic probability of firing indeed will rise, if a pre-synaptic neuron fires&#8230; But, the amount of which it will rise is changing, depending as well on what all the other pre-synaptic neurons are doing.</p>\n<p>[/quote]</p>\n<p>I am insufficiently cognizant of the neurophysiology of the zebrafish to gauge what sort of neuron model would be appropriate. This is a design decision you must have faced as well, so I might as well ask.</p>\n<p>What sort of neuron model do you use? Hodgkin-Huxley? Izhikevich? Integrate-and-fire? Something else?&nbsp;With which parameters?&nbsp;Inquiring minds want to know :).</p>\n<p>If you are unwilling to share that information, can you at least tell us which types of neuronal behaviour we can expect?</p>\n<p>Nicked from Izhikevich' site:</p>\n<p><img src=\"http://www.izhikevich.org/publications/figure1.gif\" alt width=\"470\" height=\"622\"></p>\n<p>Which of these behaviours can we expect?</p>\n<p>Kind regards,</p>",
  "messages": [
    {
      "id": "41062",
      "postDate": "03/26/2014 21:01:23",
      "content": "<p>From another topic:</p>\n<p>[quote=Sagredo;38634]</p>\n<p>I would like to add a further clarification. Salviati told: &quot;The firing of a presynaptic neuron is expected to affect the probability of firing of its postsynaptic neurons. If the presynaptic neuron is excitatory, the postsynaptic probability of firing will rise.&quot;</p>\n<p>This is certainly true! But our simulations are not probabilistic, are real dynamical systems simulations. At every time-step we integrate a system of hundredths of non-linear differential equations, it is not just tossing a dice per neuron to decide whether it will fire or not. We have a full-fledged biophysically realistic simulation behind our simulated data.</p>\n<p>That said, at the phenomenological level, Salviati's comment is true: the post-synaptic probability of firing indeed will rise, if a pre-synaptic neuron fires&#8230; But, the amount of which it will rise is changing, depending as well on what all the other pre-synaptic neurons are doing.</p>\n<p>[/quote]</p>\n<p>I am insufficiently cognizant of the neurophysiology of the zebrafish to gauge what sort of neuron model would be appropriate. This is a design decision you must have faced as well, so I might as well ask.</p>\n<p>What sort of neuron model do you use? Hodgkin-Huxley? Izhikevich? Integrate-and-fire? Something else?&nbsp;With which parameters?&nbsp;Inquiring minds want to know :).</p>\n<p>If you are unwilling to share that information, can you at least tell us which types of neuronal behaviour we can expect?</p>\n<p>Nicked from Izhikevich' site:</p>\n<p><img src=\"http://www.izhikevich.org/publications/figure1.gif\" alt width=\"470\" height=\"622\"></p>\n<p>Which of these behaviours can we expect?</p>\n<p>Kind regards,</p>",
      "rawMarkdown": "",
      "votes": null
    },
    {
      "id": "41064",
      "postDate": "03/26/2014 21:15:33",
      "content": "<p>Whoops, already found it (https://sites.google.com/a/chalearn.org/connectomics/help/data). For anyone reading this topic but not the extended data: it's leaky integrate-and-fire.</p>",
      "rawMarkdown": "",
      "votes": null
    },
    {
      "id": "41082",
      "postDate": "03/27/2014 07:50:32",
      "content": "<p>Indeed, just regular IAF. I myself have been working extensively with Izhikevich's&nbsp;models for the same system with mixed populations (regular, fast, bursting...) and the global dynamics are qualitatively&nbsp;the same.</p>\n<p>And just to clarify, the modelled systems are neuronal cultures from cortical areas of rat embryos (DIV 13 if I recall correctly).</p>",
      "rawMarkdown": "",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 41064,
      "author_name": "otdewiljes",
      "author_url": "",
      "post_date": "03/26/2014 21:15:33",
      "content": "<p>Whoops, already found it (https://sites.google.com/a/chalearn.org/connectomics/help/data). For anyone reading this topic but not the extended data: it's leaky integrate-and-fire.</p>",
      "votes": null,
      "replies": []
    },
    {
      "id": 41082,
      "author_name": "orlandi",
      "author_url": "",
      "post_date": "03/27/2014 07:50:32",
      "content": "<p>Indeed, just regular IAF. I myself have been working extensively with Izhikevich's&nbsp;models for the same system with mixed populations (regular, fast, bursting...) and the global dynamics are qualitatively&nbsp;the same.</p>\n<p>And just to clarify, the modelled systems are neuronal cultures from cortical areas of rat embryos (DIV 13 if I recall correctly).</p>",
      "votes": null,
      "replies": []
    }
  ],
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    "41064": "",
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}