[neuron][파이썬] 22. BallAndStick 여러가지 실험

 

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🙆‍♂️기본적인 코드 구조

---

from neuron import h, gui
from neuron.units import ms, mV
h.load_file('stdrun.hoc')
class Cell:
    def __init__(self, gid, x, y, z, theta):
        self._gid = gid
        self._setup_morphology()
        self.all = self.soma.wholetree()
        self._setup_biophysics()
        self.x = self.y = self.z = 0                     # <-- NEW
        h.define_shape()
        self._rotate_z(theta)                            # <-- NEW        
        self._set_position(x, y, z)                      # <-- NEW
        
    def __repr__(self):
        return '{}[{}]'.format(self.name, self._gid)
    
    # everything below here is NEW
    
    def _set_position(self, x, y, z):
        for sec in self.all:
            for i in range(sec.n3d()):
                sec.pt3dchange(i,
                               x - self.x + sec.x3d(i),
                               y - self.y + sec.y3d(i),
                               z - self.z + sec.z3d(i),
                              sec.diam3d(i))
        self.x, self.y, self.z = x, y, z
    def _rotate_z(self, theta):
        """Rotate the cell about the Z axis."""
        for sec in self.all:
            for i in range(sec.n3d()):
                x = sec.x3d(i)
                y = sec.y3d(i)
                c = h.cos(theta)
                s = h.sin(theta)
                xprime = x * c - y * s
                yprime = x * s + y * c
                sec.pt3dchange(i, xprime, yprime, sec.z3d(i), sec.diam3d(i))
class BallAndStick(Cell):
    name = 'BallAndStick'
    def _setup_morphology(self):
        self.soma = h.Section(name='soma', cell=self)
        self.dend = h.Section(name='dend', cell=self)
        self.dend.connect(self.soma)
        self.soma.L = self.soma.diam = 12.6157
        self.dend.L = 200
        self.dend.diam = 1
    def _setup_biophysics(self):
        for sec in self.all:
            sec.Ra = 100    # Axial resistance in Ohm * cm
            sec.cm = 1      # Membrane capacitance in micro Farads / cm^2
        self.soma.insert('hh')                                          
        for seg in self.soma:
            seg.hh.gnabar = 0.12  # Sodium conductance in S/cm2
            seg.hh.gkbar = 0.036  # Potassium conductance in S/cm2
            seg.hh.gl = 0.0003    # Leak conductance in S/cm2
            seg.hh.el = -54.3     # Reversal potential in mV
        # Insert passive current in the dendrite
        self.dend.insert('pas')                 
        for seg in self.dend:
            seg.pas.g = 0.001  # Passive conductance in S/cm2
            seg.pas.e = -65    # Leak reversal potential mV

일단 기본적으로 Cell 클래스와 BallAndStick 클래스 모습이 이렇습니다.

만드는 방법은 다른 함수를 통해서 만들어진 값들을 배열에 저장합니다.

 

def create_n_BallAndStick(n, r):
    """n = number of cells; r = radius of circle"""
    cells = []
    for i in range(n):
        theta = i * 2 * h.PI / n
        cells.append(BallAndStick(i, h.cos(theta) * r, h.sin(theta) * r, 0, theta))
    return cells

my_cells = create_n_BallAndStick(5, 50)

위 함수를 사용해서 5개의 셀이 들어있는 배열을 만들 수 있고

 

stim = h.NetStim() # Make a new stimulator

# Attach it to a synapse in the middle of the dendrite
# of the first cell in the network. (Named 'syn_' to avoid
# being overwritten with the 'syn' var assigned later.)
syn_ = h.ExpSyn(my_cells[0].dend(0.5))

stim.number = 1
stim.start = 9
ncstim = h.NetCon(stim, syn_)
ncstim.delay = 1
ncstim.weight[0] = 0.04 # NetCon weight is a vector.
syn_.tau = 2

NetStim을 활용하여 전기적 신호를 주입할 수 있습니다.

0번 셀의 dend 0.5부분을 ExpSyn 객체로 연결시켜서 syn_변수로 반환하였고

tau값을 설정했습니다. tau 값은 전류 감쇠에 영향을 줍니다.

recording_cell = my_cells[0]
soma_v = h.Vector().record(recording_cell.soma(0.5)._ref_v)
dend_v = h.Vector().record(recording_cell.dend(0.5)._ref_v)
t = h.Vector().record(h._ref_t)
h.finitialize(-65)
h.continuerun(25)

%matplotlib inline
import matplotlib.pyplot as plt
plt.plot(t, soma_v, label='soma(0.5)')
plt.plot(t, dend_v, label='dend(0.5)')
plt.legend()
plt.show()

기록하고 plot하는 코드입니다. 이제 다양한 부분들을 확인해보겠습니다.

 

🙋‍♂️ 여러 dendrite 붙이기

---

기존 코드의 모습은 이렇습니다.

 

class Cell:
    def __init__(self, gid, x, y, z, theta):
        self._gid = gid
        self._setup_morphology()
        self.all = self.soma.wholetree()
        self._setup_biophysics()
        self.x = self.y = self.z = 0                     # <-- NEW
        h.define_shape()
        self._rotate_z(theta)                            # <-- NEW        
        self._set_position(x, y, z)                      # <-- NEW
        
    def __repr__(self):
        return '{}[{}]'.format(self.name, self._gid)
    
    # everything below here is NEW
    
    def _set_position(self, x, y, z):
        for sec in self.all:
            for i in range(sec.n3d()):
                sec.pt3dchange(i,
                               x - self.x + sec.x3d(i),
                               y - self.y + sec.y3d(i),
                               z - self.z + sec.z3d(i),
                              sec.diam3d(i))
        self.x, self.y, self.z = x, y, z
    def _rotate_z(self, theta):
        """Rotate the cell about the Z axis."""
        for sec in self.all:
            for i in range(sec.n3d()):
                x = sec.x3d(i)
                y = sec.y3d(i)
                c = h.cos(theta)
                s = h.sin(theta)
                xprime = x * c - y * s
                yprime = x * s + y * c
                sec.pt3dchange(i, xprime, yprime, sec.z3d(i), sec.diam3d(i))
class BallAndStick(Cell):
    name = 'BallAndStick'
    def _setup_morphology(self):
        self.soma = h.Section(name='soma', cell=self)
        self.dend1 = h.Section(name='dend1', cell=self)
        self.dend2 = h.Section(name='dend2', cell=self)
        self.dend1.connect(self.soma)
        self.dend2.connect(self.soma)
        self.soma.L = self.soma.diam =12.6157
        self.dend1.L = self.dend2.L= 200
        self.dend1.diam = self.dend2.diam = 1
    def _setup_biophysics(self):
        for sec in self.all:
            sec.Ra = 100    # Axial resistance in Ohm * cm
            sec.cm = 1      # Membrane capacitance in micro Farads / cm^2
        self.soma.insert('hh')                                          
        for seg in self.soma:
            seg.hh.gnabar = 0.12  # Sodium conductance in S/cm2
            seg.hh.gkbar = 0.036  # Potassium conductance in S/cm2
            seg.hh.gl = 0.0003    # Leak conductance in S/cm2
            seg.hh.el = -54.3     # Reversal potential in mV
        # Insert passive current in the dendrite
        self.dend1.insert('pas')                 
        for seg in self.dend1:
            seg.pas.g = 0.001  # Passive conductance in S/cm2
            seg.pas.e = -65    # Leak reversal potential mV
        self.dend2.insert('pas')                 
        for seg in self.dend2:
            seg.pas.g = 0.001  # Passive conductance in S/cm2
            seg.pas.e = -65    # Leak reversal potential mV

dendrite 2개를 붙여서 수정한 모습은 이렇습니다! 잘 연결된 모습입니다.

 

시뮬레이션 돌리고 plot 해보기

recording_cell = my_cells[0]
soma_v = h.Vector().record(recording_cell.soma(0.5)._ref_v)
dend_v1 = h.Vector().record(recording_cell.dend1(0.5)._ref_v)
dend_v2 = h.Vector().record(recording_cell.dend2(0.5)._ref_v)
t = h.Vector().record(h._ref_t)
h.finitialize(-65)
h.continuerun(25)

%matplotlib inline
import matplotlib.pyplot as plt
plt.plot(t, soma_v, label='soma(0.5)')
plt.plot(t, dend_v1, label='dend(0.5)')
plt.plot(t, dend_v2, label='dend(0.5)')
plt.legend()
plt.show()

흥미로운 결과값이 나왔습니다.