def jjm_resistance(baseline_start, baseline_end, cap_trans_start,
cap_trans_end, amplitude):
#time arguments in msec, amplitude argument in mV
stf.set_channel(0)
stf.set_base_start(baseline_start, True)
stf.set_base_end(baseline_end, True)
stf.set_peak_start(cap_trans_start, True)
stf.set_peak_end(cap_trans_end, True)
stf.measure()
baseline = float(stf.get_base())
peak = float(stf.get_peak())
real_peak = baseline - peak
amplitude = float(amplitude)
amplitude_V = amplitude / (10**(3))
real_peak_A = real_peak / (10**(12))
Rs_Ohm = amplitude_V / abs(real_peak_A)
Rs = Rs_Ohm / (10**(6))
return (real_peak, Rs)
def final():
"""Creates a final template"""
stf.set_peak_start(100)
stf.set_peak_end(599)
stf.set_fit_start(100)
stf.set_fit_end(599)
stf.set_peak_mean(3)
stf.set_base_start(0)
stf.set_base_end(100)
stf.measure()
return stf.leastsq(5)
def preliminary():
"""Creates a preliminary template"""
stf.set_peak_start(209900)
stf.set_peak_end(210500)
stf.set_fit_start(209900)
stf.set_fit_end(210400)
stf.set_peak_mean(3)
stf.set_base_start(209600)
stf.set_base_end(209900)
stf.measure()
return stf.leastsq(5)
def final():
"""Creates a final template"""
stf.set_peak_start(100)
stf.set_peak_end(599)
stf.set_fit_start(100)
stf.set_fit_end(599)
stf.set_peak_mean(3)
stf.set_base_start(0)
stf.set_base_end(100)
stf.measure()
return stf.leastsq(5)
def batch_cursors():
"""Sets appropriate cursor positions for analysing
the extracted events."""
stf.set_peak_start(100)
stf.set_peak_end(598)
stf.set_fit_start(120)
stf.set_fit_end(598)
stf.set_peak_mean(3)
stf.set_base_start(0)
stf.set_base_end(100)
stf.measure()
def preliminary():
"""Creates a preliminary template"""
stf.set_peak_start(209900)
stf.set_peak_end(210500)
stf.set_fit_start(209900)
stf.set_fit_end(210400)
stf.set_peak_mean(3)
stf.set_base_start(209600)
stf.set_base_end(209900)
stf.measure()
return stf.leastsq(5)
def batch_cursors():
"""Sets appropriate cursor positions for analysing
the extracted events."""
stf.set_peak_start(100)
stf.set_peak_end(598)
stf.set_fit_start(120)
stf.set_fit_end(598)
stf.set_peak_mean(3)
stf.set_base_start(0)
stf.set_base_end(100)
stf.measure()
def batch_cursors():
"""
Sets peak, base and fit cursors around a synaptic event
for the batch analysis of the extracted events.
"""
stf.base.cursor_index = (000, 100)
stf.peak.cursor_index = (100, 598)
stf.fit.cursor_index = (120, 598)
stf.set_peak_mean(3)
stf.measure() # update cursors
def yvalue(origin, interval):
stf.set_fit_start(origin, True)
stf.set_fit_end(origin + interval, True)
stf.measure()
x = int(stf.get_fit_end(False))
y = []
for i in range(stf.get_size_channel()):
stf.set_trace(i)
y.append(stf.get_trace(i)[x])
return y
def update(self):
""" update current trace sampling rate,
cursors position and measurements (peak, baseline & AP kinetics)
according to the threshold value set at construction or when
the object is called with a threshold argument.
"""
# set slope
stf.set_slope(self._thr) # on stf v0.93 or above
# update sampling rate
self._dt = stf.get_sampling_interval()
# update cursors and AP kinetics (peak and half-width)
stf.measure()
def update(self):
""" update current trace sampling rate,
cursors position and measurements (peak, baseline & AP kinetics)
according to the threshold value set at construction or when
the object is called with a threshold argument.
"""
# set slope
stf.set_slope(self._thr) # on stf v0.93 or above
# update sampling rate
self._dt = stf.get_sampling_interval()
# update cursors and AP kinetics (peak and half-width)
stf.measure()
def final():
"""
Sets peak, base and fit cursors around a synaptic event
and performs a biexponetial fit to create the final template
for event detection.
"""
stf.base.cursor_index = (000, 100)
stf.peak.cursor_index = (100, 599)
stf.fit.cursor_index = (100, 599)
stf.set_peak_mean(3)
stf.measure() # update cursors
return stf.leastsq(5)
def preliminary():
"""
Sets peak, base and fit cursors around a synaptic event
and performs a biexponential fit to create the preliminary template
for event detection.
"""
stf.base.cursor_index = (209600, 209900)
stf.peak.cursor_index = (209900, 210500)
stf.fit.cursor_index = (209900, 210400)
stf.set_peak_mean(3)
stf.measure() # update cursors
return stf.leastsq(5)
def resistance( base_start, base_end, peak_start, peak_end, amplitude):
"""Calculates the resistance from a series of voltage clamp traces.
Keyword arguments:
base_start -- Starting index (zero-based) of the baseline cursors.
base_end -- End index (zero-based) of the baseline cursors.
peak_start -- Starting index (zero-based) of the peak cursors.
peak_end -- End index (zero-based) of the peak cursors.
amplitude -- Amplitude of the voltage command.
Returns:
The resistance.
"""
if not stf.check_doc():
print('Couldn\'t find an open file; aborting now.')
return 0
#A temporary array to calculate the average:
array = np.empty( (stf.get_size_channel(), stf.get_size_trace()) )
for n in range( 0, stf.get_size_channel() ):
# Add this trace to set:
array[n] = stf.get_trace( n )
# calculate average and create a new section from it:
stf.new_window( np.average(set, 0) )
# set peak cursors:
# -1 means all points within peak window.
if not stf.set_peak_mean(-1):
return 0
if not stf.set_peak_start(peak_start):
return 0
if not stf.set_peak_end(peak_end):
return 0
# set base cursors:
if not stf.set_base_start(base_start):
return 0
if not stf.set_base_end(base_end):
return 0
# measure everything:
stf.measure()
# calculate r_seal and return:
return amplitude / (stf.get_peak()-stf.get_base())
def jjm_peak(baseline_start, baseline_end, p_start, p_end):
#time arguments in msec, amplitude argument in mV
stf.set_channel(0)
stf.set_base_start(baseline_start, True)
stf.set_base_end(baseline_end, True)
stf.set_peak_start(p_start, True)
stf.set_peak_end(p_end, True)
stf.measure()
baseline = float(stf.get_base())
peak = float(stf.get_peak())
real_peak = abs(baseline - peak)
return (real_peak)
def resistance(base_start, base_end, peak_start, peak_end, amplitude):
"""Calculates the resistance from a series of voltage clamp traces.
Keyword arguments:
base_start -- Starting index (zero-based) of the baseline cursors.
base_end -- End index (zero-based) of the baseline cursors.
peak_start -- Starting index (zero-based) of the peak cursors.
peak_end -- End index (zero-based) of the peak cursors.
amplitude -- Amplitude of the voltage command.
Returns:
The resistance.
"""
if not stf.check_doc():
print('Couldn\'t find an open file; aborting now.')
return 0
#A temporary array to calculate the average:
array = np.empty((stf.get_size_channel(), stf.get_size_trace()))
for n in range(0, stf.get_size_channel()):
# Add this trace to set:
array[n] = stf.get_trace(n)
# calculate average and create a new section from it:
stf.new_window(np.average(set, 0))
# set peak cursors:
# -1 means all points within peak window.
if not stf.set_peak_mean(-1):
return 0
if not stf.set_peak_start(peak_start):
return 0
if not stf.set_peak_end(peak_end):
return 0
# set base cursors:
if not stf.set_base_start(base_start):
return 0
if not stf.set_base_end(base_end):
return 0
# measure everything:
stf.measure()
# calculate r_seal and return:
return amplitude / (stf.get_peak() - stf.get_base())
def increment_params(params, is_time, increment):
"""increment cursors by input time points"""
peak_1_s = params[0] + increment
peak_1_e = params[1] + increment
peak_2_s = params[2] + increment
peak_2_e = params[3] + increment
stf.set_base_start(peak_1_s, is_time=True)
stf.set_base_end(peak_1_e, is_time=True)
stf.set_peak_start(peak_2_s, is_time=True)
stf.set_peak_end(peak_2_e, is_time=True)
stf.measure()
print(peak_1_s, peak_1_e, peak_2_s, peak_2_e)
return (params)
def set_params(params):
"""sets baseline and peak curors to input time values
(use timevalues not samples"""
peak_1_s = params[0]
peak_1_e = params[1]
peak_2_s = params[2]
peak_2_e = params[3]
stf.set_base_start(peak_1_s, is_time=True)
stf.set_base_end(peak_1_e, is_time=True)
stf.set_peak_start(peak_2_s, is_time=True)
stf.set_peak_end(peak_2_e, is_time=True)
stf.measure()
print(peak_1_s, peak_1_e, peak_2_s, peak_2_e)
return (params)
def trainpeaks():
"""
Measure a 20 Hz train of peaks starting at 260 ms into the trace
"""
pk = []
for i in range(5):
stf.set_base_start(
int(255 / stf.get_sampling_interval()) +
(50 / stf.get_sampling_interval()) * i)
stf.set_base_end(
int(259 / stf.get_sampling_interval()) +
(50 / stf.get_sampling_interval()) * i)
stf.set_peak_start(
int(260.5 / stf.get_sampling_interval()) +
(50 / stf.get_sampling_interval()) * i)
stf.set_peak_end(
int(270.5 / stf.get_sampling_interval()) +
(50 / stf.get_sampling_interval()) * i)
stf.measure()
pk.append(stf.get_peak() - stf.get_base())
# Create table of results
dictlist = [("Peak 1", pk[0])]
dictlist += [("Peak 2", pk[1])]
dictlist += [("Peak 3", pk[2])]
dictlist += [("Peak 4", pk[3])]
dictlist += [("Peak 5", pk[4])]
retval = dict(dictlist)
stf.show_table(retval,
"peaks, Section #%i" % float(stf.get_trace_index() + 1))
# Create table of results
dictlist = [("Peak 1", pk[0] / pk[0] * 100)]
dictlist += [("Peak 2", pk[1] / pk[0] * 100)]
dictlist += [("Peak 3", pk[2] / pk[0] * 100)]
dictlist += [("Peak 4", pk[3] / pk[0] * 100)]
dictlist += [("Peak 5", pk[4] / pk[0] * 100)]
retval = dict(dictlist)
stf.show_table(
retval, "norm peaks, Section #%i" % float(stf.get_trace_index() + 1))
return
def Train10AP():
"""
An example function to perform peak measurements of a train of
evoked fluorescence signals in the active window
"""
# Setup
offset = 40
stf.set_base_start(0)
stf.set_peak_start(offset - 2)
stf.measure()
base = stf.get_base()
stf.set_peak_mean(1)
stf.set_peak_direction("up")
peak = []
# Get peak measurements
for i in range(10):
stf.set_peak_start(offset + (i * 4) - 2)
stf.set_peak_end(offset + (i * 4) + 2)
stf.measure()
peak.append(stf.get_peak())
# Plot fit in a new window
matrix = np.zeros((2, stf.get_size_trace())) * np.nan
matrix[0, :] = stf.get_trace()
for i in range(10):
matrix[1, offset + (i * 4) - 1:offset + (i * 4) + 2] = peak[i]
stf.new_window_matrix(matrix)
# Create table of results
retval = []
for i in range(10):
retval += [("Peak %d" % (i), peak[i] - base)]
retval = dict(retval)
stf.show_table(retval,
"Train10AP, Section #%i" % float(stf.get_trace_index() + 1))
return
def fit_experiment(params, pulse_length, function_to_fit):
num_sweeps = stf.get_size_channel()
stf.set_channel(0)
stf.set_trace(0)
#jjm_analysis.set_params(params);
#stf.measure();
#this is in samples
#peak_index = stf.peak_index();
#stf.set_fit_start(peak_index, is_time=False);
#fit_start_time = peak_index*stf.get_sampling_interval();
#stf.set_fit_end(fit_start_time+pulse_length-(10*stf.get_sampling_interval()), is_time=True);
#fit_func = stf.leastsq(function_to_fit);
#fit_func['Baseline(pA)']=stf.get_base();
#fit_df = pd.DataFrame(fit_func, index=[0]);
fits = []
traces = []
for x in range(0, num_sweeps):
stf.set_trace(x)
jjm_analysis.set_params(params)
stf.measure()
#this is in samples
peak_index = stf.peak_index()
stf.set_fit_start(peak_index, is_time=False)
fit_start_time = peak_index * stf.get_sampling_interval()
stf.set_fit_end(fit_start_time + pulse_length -
(10 * stf.get_sampling_interval()),
is_time=True)
sweep_fit = stf.leastsq(function_to_fit)
sweep_fit['Baseline(pA)'] = stf.get_base()
fits.append(sweep_fit)
traces.append(x)
fit_df = pd.DataFrame(fits)
return (fit_df)
def timeconstants(fitwindow, pulsewindow, ichannel=0, vchannel=1):
"""
Compute and plot decay time constants
Parameters
----------
fitwindow : (float, float), optional
Window for fitting time constant (time in ms from beginning of sweep)
None for current cursor settings. Default: None
pulsewindow : (float, float), optional
Window for voltage pulse measurement (time in ms from beginning of sweep)
None for current cursor settings. Default: None
ichannel : int, optional
current channel number. Default: 0
vchannel : int, optional
voltage channel number. Default: 1
Returns
-------
v_commands : numpy.ndarray
Command voltages
taus : numpy.ndarray
Time constants
"""
import stf
if not stf.check_doc():
return None
nchannels = stf.get_size_recording()
if nchannels < 2:
sys.stderr.write(
"Function requires 2 channels (0: current; 1: voltage)\n")
return
dt = stf.get_sampling_interval()
v_commands = []
taus = []
fig = stf.mpl_panel(figsize=(12, 8)).fig
fig.clear()
gs = gridspec.GridSpec(4, 8)
ax_currents = stfio_plot.StandardAxis(fig,
gs[:3, :4],
hasx=False,
hasy=False)
ax_voltages = stfio_plot.StandardAxis(fig,
gs[3:, :4],
hasx=False,
hasy=False,
sharex=ax_currents)
for ntrace in range(stf.get_size_channel()):
stf.set_trace(ntrace)
stf.set_channel(ichannel)
trace = stf.get_trace()
ax_currents.plot(np.arange(len(trace)) * dt, trace)
if fitwindow is not None:
stf.fit.cursor_time = fitwindow
res = stf.leastsq(0, False)
taus.append(res['Tau_0'])
# Measure pulse amplitude
stf.set_channel(vchannel)
trace = stf.get_trace()
ax_voltages.plot(np.arange(len(trace)) * dt, trace)
stf.set_peak_direction("up")
stf.set_peak_mean(-1)
if pulsewindow is not None:
stf.peak.cursor_time = pulsewindow
stf.measure()
v_commands.append(stf.peak.value)
stfio_plot.plot_scalebars(ax_currents,
xunits=stf.get_xunits(),
yunits=stf.get_yunits(channel=ichannel))
stfio_plot.plot_scalebars(ax_voltages,
xunits=stf.get_xunits(),
yunits=stf.get_yunits(channel=vchannel))
v_commands = np.array(v_commands)
taus = np.array(taus)
ax_taus = plot_iv(taus, v_commands, "ms", stf.get_yunits(channel=vchannel),
fig, 122)
# Reset peak computation to single sampling point
stf.set_peak_mean(1)
# Reset active channel
stf.set_channel(ichannel)
# Compute conductances:
stf.show_table_dictlist({
"Voltage ({0})".format(stf.get_yunits(channel=vchannel)):
v_commands.tolist(),
"Taus (ms)":
taus.tolist(),
})
return v_commands, taus
def iv(peakwindow=None, basewindow=None, pulsewindow=None,
erev=None, peakmode="both", ichannel=0, vchannel=1,
exclude=None):
"""
Compute and plot an IV curve for currents
Parameters
----------
peakwindow : (float, float), optional
Window for peak measurement (time in ms from beginning of sweep)
None for current cursor settings. Default: None
basewindow : (float, float), optional
Window for baseline measurement (time in ms from beginning of sweep)
None for current cursor settings. Default: None
pulsewindow : (float, float), optional
Window for voltage pulse measurement (time in ms from beginning of sweep)
None for current cursor settings. Default: None
erev : float, optional
End of v clamp pulse in ms or None to determine automatically.
Default: None
peakmode : string, optional
Peak direction - one of "up", "down", "both" or "mean". Default: "up"
ichannel : int, optional
current channel number. Default: 0
vchannel : int, optional
voltage channel number. Default: 1
exclude : list of ints, optional
List of trace indices to be excluded from the analysis. Default: None
Returns
-------
v_commands : numpy.ndarray
Command voltages
ipeaks : numpy.ndarray
Peak currents
gpeaks : numpy.ndarray
Peak normalized conductances
g_fit : numpy.ndarray
Half-maximal voltage and slope of best-fit Boltzmann function
"""
import stf
if not stf.check_doc():
return None
nchannels = stf.get_size_recording()
if nchannels < 2:
sys.stderr.write(
"Function requires 2 channels (0: current; 1: voltage)\n")
return
dt = stf.get_sampling_interval()
olddirection = stf.get_peak_direction()
v_commands = []
ipeaks = []
if basewindow is not None:
stf.base.cursor_time = basewindow
fig = stf.mpl_panel(figsize=(12, 8)).fig
fig.clear()
gs = gridspec.GridSpec(4, 8)
ax_currents = stfio_plot.StandardAxis(
fig, gs[:3, :4], hasx=False, hasy=False)
ax_voltages = stfio_plot.StandardAxis(
fig, gs[3:, :4], hasx=False, hasy=False, sharex=ax_currents)
for ntrace in range(stf.get_size_channel()):
if exclude is not None:
if ntrace in exclude:
continue
stf.set_trace(ntrace)
stf.set_channel(ichannel)
trace = stf.get_trace()
ax_currents.plot(np.arange(len(trace))*dt, trace)
# Measure only downward peaks (inward currents)
if peakmode is "mean":
stf.set_peak_direction("up")
stf.set_peak_mean(-1)
else:
stf.set_peak_direction(peakmode)
# Set peak computation to single sampling point
stf.set_peak_mean(1)
if peakwindow is not None:
stf.peak.cursor_time = peakwindow
stf.measure()
if basewindow is not None:
ipeaks.append(stf.peak.value-stf.base.value)
else:
ipeaks.append(stf.peak.value)
# Measure pulse amplitude
stf.set_channel(vchannel)
trace = stf.get_trace()
ax_voltages.plot(np.arange(len(trace))*dt, trace)
stf.set_peak_direction("up")
stf.set_peak_mean(-1)
if pulsewindow is not None:
stf.peak.cursor_time = pulsewindow
stf.measure()
v_commands.append(stf.peak.value)
stfio_plot.plot_scalebars(
ax_currents, xunits=stf.get_xunits(), yunits=stf.get_yunits(channel=0))
stfio_plot.plot_scalebars(
ax_voltages, xunits=stf.get_xunits(), yunits=stf.get_yunits(channel=1))
v_commands = np.array(v_commands)
ipeaks = np.array(ipeaks)
if erev is None:
# Find first zero crossing in ipeaks:
for npulse in range(ipeaks.shape[0]-1):
if np.sign(ipeaks[npulse]) != np.sign(ipeaks[npulse+1]):
# linear interpolation
m1 = (ipeaks[npulse+1]-ipeaks[npulse]) / (
v_commands[npulse+1]-v_commands[npulse])
c1 = ipeaks[npulse] - m1*v_commands[npulse]
erev = -c1/m1
break
if erev is None:
sys.stderr.write(
"Could not determine reversal potential. Aborting now\n")
return None
# Reset peak computation to single sampling point
stf.set_peak_mean(1)
stf.set_peak_direction(olddirection)
# Reset active channel
stf.set_channel(ichannel)
# Compute conductances:
gpeaks, g_fit = gv(ipeaks, v_commands, erev)
ax_ipeaks = plot_iv(
ipeaks, v_commands, stf.get_yunits(channel=ichannel),
stf.get_yunits(channel=1), fig, 222)
ax_ipeaks.set_title("Peak current")
ax_gpeaks = plot_gv(
gpeaks, v_commands, stf.get_yunits(channel=vchannel),
g_fit, fig, 224)
ax_gpeaks.set_title("Peak conductance")
stf.show_table_dictlist({
"Voltage ({0})".format(
stf.get_yunits(channel=vchannel)): v_commands.tolist(),
"Peak current ({0})".format(
stf.get_yunits(channel=ichannel)): ipeaks.tolist(),
"Peak conductance (g/g_max)": gpeaks.tolist(),
})
return v_commands, ipeaks, gpeaks, g_fit
def EPSPtrains(latency=200,
numStim=4,
intvlList=[1, 0.8, 0.6, 0.4, 0.2, 0.1, 0.08, 0.06, 0.04, 0.02]):
# Initialize
numTrains = len(intvlList) # Number of trains
intvlArray = np.array(intvlList) * 1000 # Units in ms
si = stf.get_sampling_interval() # Units in ms
# Background subtraction
traceBaselines = []
subtractedTraces = []
k = 1e-4
x = [i * stf.get_sampling_interval() for i in range(stf.get_size_trace())]
for i in range(numTrains):
stf.set_trace(i)
z = x
y = stf.get_trace()
traceBaselines.append(y)
ridx = []
if intvlArray[i] > 500:
for j in range(numStim):
ridx += range(
int(round(((intvlArray[i] * j) + latency - 1) / si)),
int(round(
((intvlArray[i] * (j + 1)) + latency - 1) / si)) - 1)
else:
ridx += range(
int(round((latency - 1) / si)),
int(
round(((intvlArray[i] *
(numStim - 1)) + latency + 500) / si)) - 1)
ridx += range(int(round(4999 / si)), int(round(5199 / si)))
z = np.delete(z, ridx, 0)
y = np.delete(y, ridx, 0)
yi = np.interp(x, z, y)
yf = signal.symiirorder1(yi, (k**2), 1 - k)
traceBaselines.append(yf)
subtractedTraces.append(stf.get_trace() - yf)
stf.new_window_list(traceBaselines)
stf.new_window_list(subtractedTraces)
# Measure depolarization
# Initialize variables
a = []
b = []
# Set baseline start and end cursors
stf.set_base_start(np.round(
(latency - 50) / si)) # Average during 50 ms period before stimulus
stf.set_base_end(np.round(latency / si))
# Set fit start cursor
stf.set_fit_start(np.round(latency / si))
stf.set_fit_end(
np.round(((intvlArray[1] * (numStim - 1)) + latency + 1000) /
si)) # Include a 1 second window after last stimulus
# Start AUC calculations
for i in range(numTrains):
stf.set_trace(i)
stf.measure()
b.append(stf.get_base())
n = int(stf.get_fit_end() + 1 - stf.get_fit_start())
x = np.array([k * stf.get_sampling_interval() for k in range(n)])
y = stf.get_trace()[int(stf.get_fit_start()):int(stf.get_fit_end() +
1)]
a.append(np.trapz(y - b[i], x)) # Units in V.s
return a
def wcp(V_step=-5, step_start=10, step_duration=20):
"""
Measures whole cell properties. Specifically, this function returns the
voltage clamp step estimates of series resistance, input resistance, cell
membrane resistance, cell membrane capacitance, cell surface area and
specific membrane resistance.
The series (or access) resistance is obtained my dividing the voltage step
by the peak amplitude of the current transient (Ogden, 1994): Rs = V / Ip
The input resistance is obtained by dividing the voltage step by the average
amplitude of the steady-state current (Barbour, 2014): Rin = V / Iss
The cell membrane resistance is calculated by subtracting the series
resistance from the input resistance (Barbour, 1994): Rm = Rin - Rs
The cell membrane capacitance is estimated by dividing the transient charge
by the size of the voltage-clamp step (Taylor et al. 2012): Cm = Q / V
The cell surface area is estimated by dividing the cell capacitance by the
specific cell capacitance, c (1.0 uF/cm^2; Gentet et al. 2000; Niebur, 2008):
Area = Cm / c
The specific membrane resistance is calculated by multiplying the cell
membrane resistance with the cell surface area: rho = Rm * Area
Users should be aware of the approximate nature of determining cell
capacitance and derived parameters from the voltage-clamp step method
(Golowasch, J. et al., 2009)
References:
Barbour, B. (2014) Electronics for electrophysiologists. Microelectrode
Techniques workshop tutorial.
www.biologie.ens.fr/~barbour/electronics_for_electrophysiologists.pdf
Gentet, L.J., Stuart, G.J., and Clements, J.D. (2000) Direct measurement
of specific membrane capacitance in neurons. Biophys J. 79(1):314-320
Golowasch, J. et al. (2009) Membrane Capacitance Measurements Revisited:
Dependence of Capacitance Value on Measurement Method in Nonisopotential
Neurons. J Neurophysiol. 2009 Oct; 102(4): 2161-2175.
Niebur, E. (2008), Scholarpedia, 3(6):7166. doi:10.4249/scholarpedia.7166
www.scholarpedia.org/article/Electrical_properties_of_cell_membranes
(revision #13938, last accessed 30 April 2018)
Ogden, D. Chapter 16: Microelectrode electronics, in Ogden, D. (ed.)
Microelectrode Techniques. 1994. 2nd Edition. Cambridge: The Company
of Biologists Limited.
Taylor, A.L. (2012) What we talk about when we talk about capacitance
measured with the voltage-clamp step method J Comput Neurosci.
32(1):167-175
"""
# Error checking
if stf.get_yunits() != "pA":
raise ValueError('The recording is not voltage clamp')
# Prepare variables from input arguments
si = stf.get_sampling_interval()
t0 = step_start / si
l = step_duration / si
# Set cursors and update measurements
stf.set_base_start((step_start - 1) / si)
stf.set_base_end(t0 - 1)
stf.set_peak_start(t0)
stf.set_peak_end((step_start + 1) / si)
stf.set_fit_start(t0)
stf.set_fit_end(t0 + l - 1)
stf.set_peak_direction("both")
stf.measure()
# Calculate series resistance (Rs) from initial transient
b = stf.get_base()
Rs = 1000 * V_step / (stf.get_peak() - b) # in Mohm
# Calculate charge delivered during the voltage clamp step
n = int(stf.get_fit_end() + 1 - stf.get_fit_start())
x = [i * stf.get_sampling_interval() for i in range(n)]
y = stf.get_trace()[int(stf.get_fit_start()):int(stf.get_fit_end() + 1)]
Q = np.trapz(y - b, x)
# Set cursors and update measurements
stf.set_base_start(t0 + l - 1 - (step_duration / 4) / si)
stf.set_base_end(t0 + l - 1)
stf.measure()
# Measure steady state current and calculate input resistance
I = stf.get_base() - b
Rin = 1000 * V_step / I # in Mohm
# Calculate cell membrane resistance
Rm = Rin - Rs # in Mohm
# Calculate voltage-clamp step estimate of the cell capacitance
t = x[-1] - x[0]
Cm = (Q - I * t) / V_step # in pF
# Estimate membrane surface area, where the capacitance per unit area is 1.0 uF/cm^2
A = Cm * 1e-06 / 1.0 # in cm^2
# Calculate specific membrane resistance
rho = 1e+03 * Rm * A # in kohm.cm^2; usually 10 at rest
# Create table of results
retval = []
retval += [("Holding current (pA)", b)]
retval += [("Series resistance (Mohm)", Rs)]
retval += [("Input resistance (Mohm)", Rin)]
retval += [("Cell resistance (Mohm)", Rm)]
retval += [("Cell capacitance (pF)", Cm)]
retval += [("Surface area (um^2)", A * 1e+04**2)]
retval += [("Membrane resistivity (kohm.cm^2)", rho)]
retval = dict(retval)
stf.show_table(retval, "Whole-cell properties")
return retval
def glu_iv(pulses=13, subtract_base=True):
"""Calculates an iv from a repeated series of fast application and
voltage pulses.
Keyword arguments:
pulses -- Number of pulses for the iv.
subtract_base -- If True (default), baseline will be subtracted.
Returns:
True if successful.
"""
# Some ugly definitions for the time being
# Cursors are in ms here.
gFitEnd = 330.6 # fit end cursor is variable
gFSelect = 0 # Monoexp
gDictSize = stf.leastsq_param_size(
gFSelect) + 2 # Parameters, chisqr, peak value
gBaseStart = 220.5 # Start and end of the baseline before the control pulse, in ms
gBaseEnd = 223.55
gPeakStart = 223.55 # Start and end of the peak cursors for the control pulse, in ms
gPeakEnd = 253.55
if (gDictSize < 0):
print('Couldn\'t retrieve function id=%d, aborting now.' % gFSelect)
return False
if (not (stf.check_doc())):
print('Couldn\'t find an open file; aborting now.')
return False
# analyse iv, subtract baseline if requested:
ivtools.analyze_iv(pulses)
if (subtract_base == True):
if (not (stf.set_base_start(gBaseStart, True))): return False
if (not (stf.set_base_end(gBaseEnd, True))): return False
stf.measure()
stf.select_all()
stf.subtract_base()
# set cursors:
if (not (stf.set_peak_start(gPeakStart, True))): return False
if (not (stf.set_peak_end(gPeakEnd, True))): return False
if (not (stf.set_base_start(gBaseStart, True))): return False
if (not (stf.set_base_end(gBaseEnd, True))): return False
if (not (stf.set_fit_end(gFitEnd, True))): return False
if (not (stf.set_peak_mean(3))): return False
if (not (stf.set_peak_direction("both"))): return False
# A list for dictionary keys and values:
dict_keys = []
dict_values = np.empty((gDictSize, stf.get_size_channel()))
firstpass = True
for n in range(0, stf.get_size_channel()):
if (stf.set_trace(n) == False):
print('Couldn\'t set a new trace; aborting now.')
return False
print('Analyzing trace %d of %d' % (n + 1, stf.get_size_channel()))
# set the fit window cursors:
if (not (stf.set_fit_start(stf.peak_index()))): return False
# Least-squares fitting:
p_dict = stf.leastsq(gFSelect)
if (p_dict == 0):
print('Couldn\'t perform a fit; aborting now.')
return False
# Create an empty list:
tempdict_entry = []
row = 0
for k, v in p_dict.iteritems():
if (firstpass == True):
dict_keys.append(k)
dict_values[row][n] = v
row = row + 1
if (firstpass):
dict_keys.append("Peak amplitude")
dict_values[row][n] = stf.get_peak() - stf.get_base()
firstpass = False
retDict = dict()
# Create the dictionary for the table:
entry = 0
for elem in dict_keys:
retDict[elem] = dict_values[entry].tolist()
entry = entry + 1
return stf.show_table_dictlist(retDict)
def glu_iv( pulses = 13, subtract_base=True ):
"""Calculates an iv from a repeated series of fast application and
voltage pulses.
Keyword arguments:
pulses -- Number of pulses for the iv.
subtract_base -- If True (default), baseline will be subtracted.
Returns:
True if successful.
"""
# Some ugly definitions for the time being
# Cursors are in ms here.
gFitEnd = 330.6 # fit end cursor is variable
gFSelect = 0 # Monoexp
gDictSize = stf.leastsq_param_size( gFSelect ) + 2 # Parameters, chisqr, peak value
gBaseStart = 220.5 # Start and end of the baseline before the control pulse, in ms
gBaseEnd = 223.55
gPeakStart = 223.55 # Start and end of the peak cursors for the control pulse, in ms
gPeakEnd = 253.55
if ( gDictSize < 0 ):
print('Couldn\'t retrieve function id=%d, aborting now.'%gFSelect)
return False
if ( not(stf.check_doc()) ):
print('Couldn\'t find an open file; aborting now.')
return False
# analyse iv, subtract baseline if requested:
ivtools.analyze_iv( pulses )
if ( subtract_base == True ):
if ( not(stf.set_base_start( gBaseStart, True )) ): return False
if ( not(stf.set_base_end( gBaseEnd, True )) ): return False
stf.measure()
stf.select_all()
stf.subtract_base()
# set cursors:
if ( not(stf.set_peak_start( gPeakStart, True )) ): return False
if ( not(stf.set_peak_end( gPeakEnd, True )) ): return False
if ( not(stf.set_base_start( gBaseStart, True )) ): return False
if ( not(stf.set_base_end( gBaseEnd, True )) ): return False
if ( not(stf.set_fit_end( gFitEnd, True )) ): return False
if ( not(stf.set_peak_mean( 3 )) ): return False
if ( not(stf.set_peak_direction( "both" )) ): return False
# A list for dictionary keys and values:
dict_keys = []
dict_values = np.empty( (gDictSize, stf.get_size_channel()) )
firstpass = True
for n in range( 0, stf.get_size_channel() ):
if ( stf.set_trace( n ) == False ):
print('Couldn\'t set a new trace; aborting now.')
return False
print('Analyzing trace %d of %d'%( n+1, stf.get_size_channel() ) )
# set the fit window cursors:
if ( not(stf.set_fit_start( stf.peak_index() )) ): return False
# Least-squares fitting:
p_dict = stf.leastsq( gFSelect )
if ( p_dict == 0 ):
print('Couldn\'t perform a fit; aborting now.')
return False
# Create an empty list:
tempdict_entry = []
row = 0
for k, v in p_dict.iteritems():
if ( firstpass == True ):
dict_keys.append( k )
dict_values[row][n] = v
row = row+1
if ( firstpass ):
dict_keys.append( "Peak amplitude" )
dict_values[row][n] = stf.get_peak()-stf.get_base()
firstpass = False
retDict = dict()
# Create the dictionary for the table:
entry = 0
for elem in dict_keys:
retDict[ elem ] = dict_values[entry].tolist()
entry = entry+1
return stf.show_table_dictlist( retDict )
def timeconstants(fitwindow, pulsewindow, ichannel=0, vchannel=1):
"""
Compute and plot decay time constants
Parameters
----------
fitwindow : (float, float), optional
Window for fitting time constant (time in ms from beginning of sweep)
None for current cursor settings. Default: None
pulsewindow : (float, float), optional
Window for voltage pulse measurement (time in ms from beginning of sweep)
None for current cursor settings. Default: None
ichannel : int, optional
current channel number. Default: 0
vchannel : int, optional
voltage channel number. Default: 1
Returns
-------
v_commands : numpy.ndarray
Command voltages
taus : numpy.ndarray
Time constants
"""
import stf
if not stf.check_doc():
return None
nchannels = stf.get_size_recording()
if nchannels < 2:
sys.stderr.write(
"Function requires 2 channels (0: current; 1: voltage)\n")
return
dt = stf.get_sampling_interval()
v_commands = []
taus = []
fig = stf.mpl_panel(figsize=(12, 8)).fig
fig.clear()
gs = gridspec.GridSpec(4, 8)
ax_currents = stfio_plot.StandardAxis(
fig, gs[:3, :4], hasx=False, hasy=False)
ax_voltages = stfio_plot.StandardAxis(
fig, gs[3:, :4], hasx=False, hasy=False, sharex=ax_currents)
for ntrace in range(stf.get_size_channel()):
stf.set_trace(ntrace)
stf.set_channel(ichannel)
trace = stf.get_trace()
ax_currents.plot(np.arange(len(trace))*dt, trace)
if fitwindow is not None:
stf.fit.cursor_time = fitwindow
res = stf.leastsq(0, False)
taus.append(res['Tau_0'])
# Measure pulse amplitude
stf.set_channel(vchannel)
trace = stf.get_trace()
ax_voltages.plot(np.arange(len(trace))*dt, trace)
stf.set_peak_direction("up")
stf.set_peak_mean(-1)
if pulsewindow is not None:
stf.peak.cursor_time = pulsewindow
stf.measure()
v_commands.append(stf.peak.value)
stfio_plot.plot_scalebars(
ax_currents, xunits=stf.get_xunits(),
yunits=stf.get_yunits(channel=ichannel))
stfio_plot.plot_scalebars(
ax_voltages, xunits=stf.get_xunits(),
yunits=stf.get_yunits(channel=vchannel))
v_commands = np.array(v_commands)
taus = np.array(taus)
ax_taus = plot_iv(
taus, v_commands, "ms",
stf.get_yunits(channel=vchannel), fig, 122)
# Reset peak computation to single sampling point
stf.set_peak_mean(1)
# Reset active channel
stf.set_channel(ichannel)
# Compute conductances:
stf.show_table_dictlist({
"Voltage ({0})".format(
stf.get_yunits(channel=vchannel)): v_commands.tolist(),
"Taus (ms)": taus.tolist(),
})
return v_commands, taus
def iv(peakwindow=None,
basewindow=None,
pulsewindow=None,
erev=None,
peakmode="both",
ichannel=0,
vchannel=1,
exclude=None):
"""
Compute and plot an IV curve for currents
Parameters
----------
peakwindow : (float, float), optional
Window for peak measurement (time in ms from beginning of sweep)
None for current cursor settings. Default: None
basewindow : (float, float), optional
Window for baseline measurement (time in ms from beginning of sweep)
None for current cursor settings. Default: None
pulsewindow : (float, float), optional
Window for voltage pulse measurement (time in ms from beginning of sweep)
None for current cursor settings. Default: None
erev : float, optional
End of v clamp pulse in ms or None to determine automatically.
Default: None
peakmode : string, optional
Peak direction - one of "up", "down", "both" or "mean". Default: "up"
ichannel : int, optional
current channel number. Default: 0
vchannel : int, optional
voltage channel number. Default: 1
exclude : list of ints, optional
List of trace indices to be excluded from the analysis. Default: None
Returns
-------
v_commands : numpy.ndarray
Command voltages
ipeaks : numpy.ndarray
Peak currents
gpeaks : numpy.ndarray
Peak normalized conductances
g_fit : numpy.ndarray
Half-maximal voltage and slope of best-fit Boltzmann function
"""
import stf
if not stf.check_doc():
return None
nchannels = stf.get_size_recording()
if nchannels < 2:
sys.stderr.write(
"Function requires 2 channels (0: current; 1: voltage)\n")
return
dt = stf.get_sampling_interval()
olddirection = stf.get_peak_direction()
v_commands = []
ipeaks = []
if basewindow is not None:
stf.base.cursor_time = basewindow
fig = stf.mpl_panel(figsize=(12, 8)).fig
fig.clear()
gs = gridspec.GridSpec(4, 8)
ax_currents = stfio_plot.StandardAxis(fig,
gs[:3, :4],
hasx=False,
hasy=False)
ax_voltages = stfio_plot.StandardAxis(fig,
gs[3:, :4],
hasx=False,
hasy=False,
sharex=ax_currents)
for ntrace in range(stf.get_size_channel()):
if exclude is not None:
if ntrace in exclude:
continue
stf.set_trace(ntrace)
stf.set_channel(ichannel)
trace = stf.get_trace()
ax_currents.plot(np.arange(len(trace)) * dt, trace)
# Measure only downward peaks (inward currents)
if peakmode is "mean":
stf.set_peak_direction("up")
stf.set_peak_mean(-1)
else:
stf.set_peak_direction(peakmode)
# Set peak computation to single sampling point
stf.set_peak_mean(1)
if peakwindow is not None:
stf.peak.cursor_time = peakwindow
stf.measure()
if basewindow is not None:
ipeaks.append(stf.peak.value - stf.base.value)
else:
ipeaks.append(stf.peak.value)
# Measure pulse amplitude
stf.set_channel(vchannel)
trace = stf.get_trace()
ax_voltages.plot(np.arange(len(trace)) * dt, trace)
stf.set_peak_direction("up")
stf.set_peak_mean(-1)
if pulsewindow is not None:
stf.peak.cursor_time = pulsewindow
stf.measure()
v_commands.append(stf.peak.value)
stfio_plot.plot_scalebars(ax_currents,
xunits=stf.get_xunits(),
yunits=stf.get_yunits(channel=0))
stfio_plot.plot_scalebars(ax_voltages,
xunits=stf.get_xunits(),
yunits=stf.get_yunits(channel=1))
v_commands = np.array(v_commands)
ipeaks = np.array(ipeaks)
if erev is None:
# Find first zero crossing in ipeaks:
for npulse in range(ipeaks.shape[0] - 1):
if np.sign(ipeaks[npulse]) != np.sign(ipeaks[npulse + 1]):
# linear interpolation
m1 = (ipeaks[npulse + 1] - ipeaks[npulse]) / (
v_commands[npulse + 1] - v_commands[npulse])
c1 = ipeaks[npulse] - m1 * v_commands[npulse]
erev = -c1 / m1
break
if erev is None:
sys.stderr.write(
"Could not determine reversal potential. Aborting now\n")
return None
# Reset peak computation to single sampling point
stf.set_peak_mean(1)
stf.set_peak_direction(olddirection)
# Reset active channel
stf.set_channel(ichannel)
# Compute conductances:
gpeaks, g_fit = gv(ipeaks, v_commands, erev)
ax_ipeaks = plot_iv(ipeaks, v_commands, stf.get_yunits(channel=ichannel),
stf.get_yunits(channel=1), fig, 222)
ax_ipeaks.set_title("Peak current")
ax_gpeaks = plot_gv(gpeaks, v_commands, stf.get_yunits(channel=vchannel),
g_fit, fig, 224)
ax_gpeaks.set_title("Peak conductance")
stf.show_table_dictlist({
"Voltage ({0})".format(stf.get_yunits(channel=vchannel)):
v_commands.tolist(),
"Peak current ({0})".format(stf.get_yunits(channel=ichannel)):
ipeaks.tolist(),
"Peak conductance (g/g_max)":
gpeaks.tolist(),
})
return v_commands, ipeaks, gpeaks, g_fit