Section and Segment Selection
Dot notation for properties
Since sections share property names eg. a length called
it is always necessary to specify which section is being discussed;
this is done using dot notation, e.g.
dendrite.L = dendrite.L + dendrite.L axon.v = soma.v print(soma.gnabar) axon.nseg *= 3
This notation is necessary when one needs to refer to more than one section within a single statement.
sec= for functions
Many NEURON functions refer to a specific Section. In recent versions of NEURON,
most of these either are available as section methods or take a section or segment
directly. For older code or for the remaining exceptions, the active section may
be specified using a
sec= keyword argument.
my_iclamp = h.IClamp(0.25, sec=soma) # better to use h.IClamp(soma(0.25)) though num_pts_3d = h.n3d(sec=apical) # could get the same value as an int via apical.n3d()
sec= keyword argument is specified, the functions will use NEURON’s
default Section (sometimes called the currently accessed section),
which can be identified via
The default Section is controlled by a stack; it is initially
the first Section created but entries may be pushed onto or popped off of the
stack by the following commands. Use this only as a last resort.
- Take the currently accessed section off the section stack. This can only be used after
a function which pushes a section on the section stack such as
from neuron import h soma = h.Section(name='soma') apical = h.Section(name='apical') stims = [h.IClamp(soma(i / 4.)) for i in range(5)] + [h.IClamp(apical(0.5))] for stim in stims: x = stim.get_loc() print("location of %s is %s(%g)" % (stim, h.secname(), x)) h.pop_section()
(Note: in this example as
nseg=1, the current clamps will either be at position 0, 0.5, or 1.)
(Note: a more Pythonic way to get the location of the point-process
stimis to use
seg = stim.get_segment(), but this is shown as an example of using
This function, along with
h.pop_section()should only be used as a last resort. It will place a specified section on the top of the section stack, becoming the current section to which all operations apply. It is probably always better to use
- Push the section identified by the number returned by
h.this_section(), etc. which you desire to be the currently accessed section. Any section pushed must have a corresponding
h.pop_section()later or else the section stack will be corrupted. The number is not guaranteed to be the same across separate invocations of NEURON.
- Push the section identified by the name obtained from sectionname(strdef). Note: at this time the implementation iterates over all sections to find the proper one; so do not use in loops.
from neuron import h soma = h.Section(name='soma') apical = h.Section(name='apical') # get a number to allow pushing by number soma_id = h.this_section(sec=soma) # push by name h.push_section('apical') # push by number h.push_section(soma_id) # RuntimeError -- no such section h.push_section('basal')