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Sections

Sections are cilindrical representations of pieces of a cell. They have a length and a diameter. Sections are the main building block of a simulation in NEURON.

You can use the .connect method to connect :class:`Sections <.objects.Section>` together.

Sections can be subdivided into :class:`Segments <.objects.Segment>` by specifying nseg, the simulator calculates the voltage for each segment, thereby affecting the spatial resolution of the simulation. The position of a segment is represented by its normalized position along the axis of the Segment. This means that a Segment at x=0.5 is in the middle of the Section. By default every section consists of 1 segment and the potential will be calculated for 3 points: At the start (0) and end (1) of the section, and in the middle of every segment (0.5). For 2 segments the simulator would calculate at 0, 0.333..., 0.666... and 1.

.. tab-container:: tab1
    :title: Patch

    .. code-block:: python

        from patch import p
        s = p.Section()
        s.L = 40
        s.diam = 0.4
        s.nseg = 11

        s2 = p.Section()
        s.connect(s2)


.. tab-container:: tab2
    :title: NEURON

    .. code-block:: python

        from neuron import h
        s = h.Section()
        s.L = 40
        s.diam = 0.4
        s.nseg = 11

        s2 = h.Section()
        s.connect(s2)

Retrieving segments

Sections can be called with an x to retrieve the segment at that x. The segments of a Section can also be iterated over.
.. tab-container:: tab1
    :title: Patch

    .. code-block:: python

        s.nseg = 5
        seg05 = s(0.5)
        print(seg05)
        for seg in s:
            print(seg)


.. tab-container:: tab2
    :title: NEURON

    .. code-block:: python

        s.nseg = 5
        seg05 = s(0.5)
        print(seg05)
        for seg in s:
            print(seg)

Recording

You can tell Patch to record the membrane potential of your Section at one or multiple locations by calling the .record function and giving it an x. If x is omitted 0.5 is used.

In NEURON you'd have to create a :class:`Vector <.objects.Vector>` and keep track of it somewhere and find a way to link it back to the Section it recorded, in Patch a section automatically stores its recording vectors in section.recordings.

.. tab-container:: tab1
    :title: Patch

    .. code-block:: python

        s.record(x=1.0)


.. tab-container:: tab2
    :title: NEURON

    .. code-block:: python

        v = h.Vector()
        v.record(s(1.0))
        all_recorders.append(v)

Position in space

With Patch it's very straightforward to define the 3D path of your Section through space. Call the .add_3d function with a 2D array containing the xyz data of your points. Optionally, you can pass another array of diameters.
.. tab-container:: tab1
    :title: Patch

    .. code-block:: python

        s.add_3d([[0, 0, 0], [2, 2, 2]], diameters)


.. tab-container:: tab2
    :title: NEURON

    .. code-block:: python

        s.push()
        points = [[0, 0, 0], [2, 2, 2]]
        for point, diameter in zip(points, diameters):
            h.pt3dadd(*point, diameter)
        h.pop_section()