This package implements the model described in Savtchenko et al. (2018, Nature Communications), Figure 5, simulating extracellular K⁺ accumulation and clearance in a network of four fully reconstructed CA1 astrocytes using the ASTRO builder.
- NEURON v7.8 or later (with Python support)
- Python 3.7+
- Install NEURON with Python bindings (see https://nrn.readthedocs.io).
- Clone or unzip this folder into your working directory.
- From within the
mechanisms/directory, compile the MOD files. With recent NEURON versions, you can do this by runningnrnivmodl MOD_filesfrom a terminal in the top-level directory.
Note: Ensure that your
PYTHONPATHor Python virtual environment includes NEURON’slib/pythondirectory.
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Open a terminal in the top-level directory.
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Launch NEURON’s GUI with the initialization script:
nrngui init.hoc -
You will see several windows/panels:
- Located on the left.
- Enter your extracellular K⁺ source parameters:
- X, Y, Z coordinates (µm)
- Input radius (µm)
- Input onset (ms) and end (ms)
- [K⁺]out (mM)
- Click Run simulation once your sphere is positioned.
- Center panel.
- Displays reconstructed astrocyte morphology and the K⁺ source sphere.
- Top-right.
- Two heatmaps:
[K⁺]in (mM)inside the cell[K⁺]o (mM)outside the cell
- Color scale updates in real time.
- Middle-right.
- Membrane voltage (mV) across the morphology.
- Bottom-right.
- Time-series plot of selected variables (e.g., soma [K⁺]in vs. [K⁺]o).
- Bottom panel.
- Lists SEClamp or other point processes; control buttons available here.
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Position your spherical K⁺ source by either:
- Typing new coordinates/radius in the Potassium Input Simulation panel, or
- Clicking and dragging the sphere in the 3D Morphology View (hold Shift to resize).
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Once your stimulus is set, press Run simulation.
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Watch the Potassium, Voltage, and Graph[0] panels update to show how extracellular [K⁺] drives changes in membrane voltage and intracellular [K⁺].