.. _neuromorpho_tut:

Neuromorpho
***********

`Neuromorpho <http://neuromorpho.org/>`_ is a searchable online repository for neuron morphologies. At the time of writing it contains over 168k neurons from 91 different species. While the website features a comprehensive search and some neat stats, it can be useful to download these data to run your own analyses or compare to other data sets.

For that purpose, `navis` provides an interface to neuromorpho that wraps some of their API.

.. code:: ipython3

    # Import navis
    import navis
    
    # Import the actual neuromorpho interface
    import navis.interfaces.neuromorpho as nm

First we can use :func:`navis.interfaces.neuromorpho.get_neuron_fields` to figure out what we can search for:

.. code:: ipython3

    fields = nm.get_neuron_fields()
    fields[:10]




.. parsed-literal::

    ['neuron_id',
     'neuron_name',
     'archive',
     'age_scale',
     'gender',
     'reference_pmid',
     'reference_doi',
     'note',
     'age_classification',
     'brain_region']



Next, we will use :func:`navis.interfaces.neuromorpho.get_available_field_values` to get an idea of the possible values for a given field:

.. code:: ipython3

    species = nm.get_available_field_values('species')
    species[:10]




.. parsed-literal::

    ['mouse',
     'rat',
     'drosophila melanogaster',
     'human',
     'zebrafish',
     'monkey',
     'chimpanzee',
     'Xenopus laevis',
     'Semipalmated sandpiper',
     'C. elegans']



Let's find a couple human neurons, shall we?

.. code:: ipython3

    # Note that we're only fetching the first couple results
    info = nm.find_neurons(species='human', page_limit=10)
    info.head()




.. raw:: html

    <div>
    <style scoped>
        .dataframe tbody tr th:only-of-type {
            vertical-align: middle;
        }
    
        .dataframe tbody tr th {
            vertical-align: top;
        }
    
        .dataframe thead th {
            text-align: right;
        }
    </style>
    <table border="1" class="dataframe">
      <thead>
        <tr style="text-align: right;">
          <th></th>
          <th>neuron_id</th>
          <th>neuron_name</th>
          <th>archive</th>
          <th>note</th>
          <th>age_scale</th>
          <th>gender</th>
          <th>age_classification</th>
          <th>brain_region</th>
          <th>cell_type</th>
          <th>species</th>
          <th>...</th>
          <th>slicing_thickness</th>
          <th>min_age</th>
          <th>max_age</th>
          <th>min_weight</th>
          <th>max_weight</th>
          <th>png_url</th>
          <th>reference_pmid</th>
          <th>reference_doi</th>
          <th>physical_Integrity</th>
          <th>_links</th>
        </tr>
      </thead>
      <tbody>
        <tr>
          <th>0</th>
          <td>102399</td>
          <td>H17-03-010-11-13-01_656411100_m</td>
          <td>Allen Cell Types</td>
          <td></td>
          <td>Year</td>
          <td>Female</td>
          <td>adult</td>
          <td>[neocortex, occipital, middle temporal gyrus]</td>
          <td>[interneuron, Aspiny]</td>
          <td>human</td>
          <td>...</td>
          <td>350</td>
          <td>38.0</td>
          <td>38.0</td>
          <td>Not Reported</td>
          <td>Not Reported</td>
          <td>http://neuromorpho.org/images/imageFiles/Allen...</td>
          <td>[27810003]</td>
          <td>[10.1016/j.neuron.2016.10.019]</td>
          <td>Dendrites Complete, Axon Incomplete</td>
          <td>{'self': {'href': 'http://neuromorpho.org/api/...</td>
        </tr>
        <tr>
          <th>1</th>
          <td>102400</td>
          <td>H17-03-010-11-13-06_651089035_m</td>
          <td>Allen Cell Types</td>
          <td></td>
          <td>Year</td>
          <td>Female</td>
          <td>adult</td>
          <td>[neocortex, occipital, middle temporal gyrus]</td>
          <td>[principal cell, Spiny]</td>
          <td>human</td>
          <td>...</td>
          <td>350</td>
          <td>38.0</td>
          <td>38.0</td>
          <td>Not Reported</td>
          <td>Not Reported</td>
          <td>http://neuromorpho.org/images/imageFiles/Allen...</td>
          <td>[27810003]</td>
          <td>[10.1016/j.neuron.2016.10.019]</td>
          <td>Dendrites Complete, Axon Incomplete</td>
          <td>{'self': {'href': 'http://neuromorpho.org/api/...</td>
        </tr>
        <tr>
          <th>2</th>
          <td>102401</td>
          <td>H17-03-011-11-04-05_650978964_m</td>
          <td>Allen Cell Types</td>
          <td></td>
          <td>Year</td>
          <td>Male</td>
          <td>adult</td>
          <td>[neocortex, occipital, middle temporal gyrus]</td>
          <td>[principal cell, Spiny]</td>
          <td>human</td>
          <td>...</td>
          <td>350</td>
          <td>30.0</td>
          <td>30.0</td>
          <td>Not Reported</td>
          <td>Not Reported</td>
          <td>http://neuromorpho.org/images/imageFiles/Allen...</td>
          <td>[27810003]</td>
          <td>[10.1016/j.neuron.2016.10.019]</td>
          <td>Dendrites &amp; Axon Moderate</td>
          <td>{'self': {'href': 'http://neuromorpho.org/api/...</td>
        </tr>
        <tr>
          <th>3</th>
          <td>102402</td>
          <td>H17-03-011-11-09-04_648981937_m</td>
          <td>Allen Cell Types</td>
          <td></td>
          <td>Year</td>
          <td>Male</td>
          <td>adult</td>
          <td>[neocortex, occipital, middle temporal gyrus]</td>
          <td>[principal cell, Spiny]</td>
          <td>human</td>
          <td>...</td>
          <td>350</td>
          <td>30.0</td>
          <td>30.0</td>
          <td>Not Reported</td>
          <td>Not Reported</td>
          <td>http://neuromorpho.org/images/imageFiles/Allen...</td>
          <td>[27810003]</td>
          <td>[10.1016/j.neuron.2016.10.019]</td>
          <td>Dendrites &amp; Axon Moderate</td>
          <td>{'self': {'href': 'http://neuromorpho.org/api/...</td>
        </tr>
        <tr>
          <th>4</th>
          <td>102403</td>
          <td>H17-06-005-12-15-01_605485782_m</td>
          <td>Allen Cell Types</td>
          <td></td>
          <td>Year</td>
          <td>Male</td>
          <td>adult</td>
          <td>[neocortex, occipital, middle temporal gyrus]</td>
          <td>[interneuron, Aspiny]</td>
          <td>human</td>
          <td>...</td>
          <td>350</td>
          <td>38.0</td>
          <td>38.0</td>
          <td>Not Reported</td>
          <td>Not Reported</td>
          <td>http://neuromorpho.org/images/imageFiles/Allen...</td>
          <td>[27810003]</td>
          <td>[10.1016/j.neuron.2016.10.019]</td>
          <td>Dendrites &amp; Axon Complete</td>
          <td>{'self': {'href': 'http://neuromorpho.org/api/...</td>
        </tr>
      </tbody>
    </table>
    <p>5 rows × 45 columns</p>
    </div>



Now on to fetching some actual neurons! The way you typically want to do this is by passing the `info` for your neurons of interest to :func:`navis.interfaces.neuromorpho.get_neuron`:

.. code:: ipython3

    neurons = nm.get_neuron(info)
    neurons


.. parsed-literal::

    102701 generated an exception: 404 Client Error: Not Found for url: http://neuromorpho.org/dableFiles/ortega/CNG%20version/WT6_02.CNG.swc
    102706 generated an exception: 404 Client Error: Not Found for url: http://neuromorpho.org/dableFiles/ortega/CNG%20version/WT4_02.CNG.swc
    102709 generated an exception: 404 Client Error: Not Found for url: http://neuromorpho.org/dableFiles/ortega/CNG%20version/WT9_02.CNG.swc
    102719 generated an exception: 404 Client Error: Not Found for url: http://neuromorpho.org/dableFiles/ortega/CNG%20version/WT7_02.CNG.swc
    102726 generated an exception: 404 Client Error: Not Found for url: http://neuromorpho.org/dableFiles/ortega/CNG%20version/WT5_02.CNG.swc
    102728 generated an exception: 404 Client Error: Not Found for url: http://neuromorpho.org/dableFiles/ortega/CNG%20version/WT8_02.CNG.swc




.. raw:: html

    &lt;class 'navis.core.neuronlist.NeuronList'&gt; containing 494 neurons (26.0MiB)<div>
    <style scoped>
        .dataframe tbody tr th:only-of-type {
            vertical-align: middle;
        }
    
        .dataframe tbody tr th {
            vertical-align: top;
        }
    
        .dataframe thead th {
            text-align: right;
        }
    </style>
    <table border="1" class="dataframe">
      <thead>
        <tr style="text-align: right;">
          <th></th>
          <th>type</th>
          <th>name</th>
          <th>id</th>
          <th>n_nodes</th>
          <th>n_connectors</th>
          <th>n_branches</th>
          <th>n_leafs</th>
          <th>cable_length</th>
          <th>soma</th>
          <th>units</th>
        </tr>
      </thead>
      <tbody>
        <tr>
          <th>0</th>
          <td>navis.TreeNeuron</td>
          <td>H17-03-010-11-13-01_656411100_m</td>
          <td>102399</td>
          <td>1498</td>
          <td>None</td>
          <td>15</td>
          <td>20</td>
          <td>1684.614746</td>
          <td>[1, 2, 3]</td>
          <td>1 dimensionless</td>
        </tr>
        <tr>
          <th>1</th>
          <td>navis.TreeNeuron</td>
          <td>H17-03-010-11-13-06_651089035_m</td>
          <td>102400</td>
          <td>10451</td>
          <td>None</td>
          <td>69</td>
          <td>81</td>
          <td>13138.289062</td>
          <td>[1, 2, 3]</td>
          <td>1 dimensionless</td>
        </tr>
        <tr>
          <th>...</th>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
        </tr>
        <tr>
          <th>492</th>
          <td>navis.TreeNeuron</td>
          <td>H9-MECP2-T158M-T158M-CREB-17</td>
          <td>103393</td>
          <td>137</td>
          <td>None</td>
          <td>14</td>
          <td>20</td>
          <td>326.003082</td>
          <td>[1, 2, 3]</td>
          <td>1 dimensionless</td>
        </tr>
        <tr>
          <th>493</th>
          <td>navis.TreeNeuron</td>
          <td>H9-MECP2-T158M-T158M-CREB-38</td>
          <td>103394</td>
          <td>172</td>
          <td>None</td>
          <td>43</td>
          <td>52</td>
          <td>324.924866</td>
          <td>[1, 2, 3]</td>
          <td>1 dimensionless</td>
        </tr>
      </tbody>
    </table>
    </div>



As you can see some of these neurons are missing an SWC. That happens occasionally.

Let's plot some of these!

.. code:: ipython3

    import matplotlib.pyplot as plt 
    import seaborn as sns
    
    fig, axes = plt.subplots(1, 10, figsize=(15, 5))
    
    for n, c, ax in zip(neurons, sns.color_palette('muted', len(axes)), axes):
        _ = navis.plot2d(n, method='2d', ax=ax, c=c)
        ax.set_aspect('equal')
        ax.set_axis_off()



.. image:: neuromorpho_tut_files/neuromorpho_tut_11_0.png


That's all for now!