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Single Cell Examples

This page provides examples of how to use the Single Cell module for various analyses.

Python API Examples

The examples below demonstrate how to use the Single Cell module through its Python API:

Basic Setup

All single cell examples require initializing the Profiler:

from bmtool.singlecell import Profiler

# Initialize with paths to templates and mechanisms
profiler = Profiler(template_dir='templates', mechanism_dir='mechanisms', dt=0.1)

Passive Properties Analysis

Calculating passive properties (V-rest, input resistance, and time constant):

from bmtool.singlecell import Passive, run_and_plot
import matplotlib.pyplot as plt

# Create a Passive simulation object
sim = Passive('Cell_Cf', inj_amp=-100., inj_delay=1500., inj_dur=1000., 
              tstop=2500., method='exp2')

# Run the simulation and plot the results
title = 'Passive Cell Current Injection'
xlabel = 'Time (ms)'
ylabel = 'Membrane Potential (mV)'
X, Y = run_and_plot(sim, title, xlabel, ylabel, plot_injection_only=True)

# Plot the double exponential fit
plt.gca().plot(*sim.double_exponential_fit(), 'r:', label='double exponential fit')
plt.legend()
plt.show()

This will output the passive properties: 

Injection location: Cell_Cf[0].soma[0](0.5)
Recording: Cell_Cf[0].soma[0](0.5)._ref_v
Running simulation for passive properties...

V Rest: -70.21 (mV)
Resistance: 128.67 (MOhms)
Membrane time constant: 55.29 (ms)

Current Clamp

Running a current clamp to observe spiking behavior:

from bmtool.singlecell import CurrentClamp, run_and_plot
import matplotlib.pyplot as plt

# Create a CurrentClamp simulation object
sim = CurrentClamp('Cell_Cf', inj_amp=350., inj_delay=1500., inj_dur=1000., 
                   tstop=3000., threshold=-15.)

# Run the simulation and plot the results
X, Y = run_and_plot(sim, title='Current Injection', xlabel='Time (ms)',
                    ylabel='Membrane Potential (mV)', plot_injection_only=True)
plt.show()

FI Curve

Generating a frequency-current (FI) curve:

from bmtool.singlecell import FI, run_and_plot
import matplotlib.pyplot as plt

# Create an FI simulation object
sim = FI('Cell_Cf', i_start=0., i_stop=1000., i_increment=50., 
          tstart=1500., threshold=-15.)

# Run the simulation and plot the results
X, Y = run_and_plot(sim, title='FI Curve', xlabel='Injection (nA)', 
                    ylabel='# Spikes')
plt.show()

ZAP Protocol

Analyzing frequency response using a chirp current (ZAP):

from bmtool.singlecell import ZAP, run_and_plot
import matplotlib.pyplot as plt

# Create a ZAP simulation object
sim = ZAP('Cell_Cf')

# Run the simulation and plot the results
X, Y = run_and_plot(sim)
plt.show()

Jupyter Notebook Tutorials

For more detailed examples with rich output and visualizations, check out our Jupyter notebook tutorials:

Allen Cell Model Tutorial

The Allen Cell Tutorial demonstrates how to use BMTool with Allen Institute cell models. In this tutorial, you'll learn:

  • How to load Allen Institute cell models from SWC and JSON files
  • How to analyze and characterize the cell's electrophysiological properties
  • How to visualize the results of various protocols

Other Examples

You can also access other examples from the command line:

# Cell Tuning via CLI
bmtool util cell tune --builder

# VHalf Segregation
bmtool util cell vhseg