Merge pull request #669 from suny-downstate-medical-center/sd_example

Spreading Depression Example

examples/spreadingDepression/Neuron.py

@@ -0,0 +1,103 @@
+from neuron import h
+from cfg import cfg 
+import numpy as np 
+
+class ENeuron:
+    """ A neuron with soma and dendrite with; fast and persistent sodium
+    currents, potassium currents, passive leak and potassium leak and an
+    accumulation mechanism. """
+    def __init__(self):
+        self.soma = h.Section(name='Esoma', cell=self)
+        # add 3D points to locate the neuron in the ECS  
+        self.soma.pt3dadd(0.0, 0.0, 0.0, 2.0 * cfg.somaR)
+        self.soma.pt3dadd(0.0, 2.0 * cfg.somaR, 0.0, 2.0 * cfg.somaR)
+        if cfg.epas:
+            self.soma.insert('pas')
+            self.soma(0.5).pas.e = cfg.epas
+            self.soma(0.5).pas.g = cfg.gpas
+
+class E2Neuron:
+    """ A neuron with soma and dendrite with; fast and persistent sodium
+    currents, potassium currents, passive leak and potassium leak and an
+    accumulation mechanism. """
+    def __init__(self):
+        self.soma = h.Section(name='E2soma', cell=self)
+        # add 3D points to locate the neuron in the ECS  
+        self.soma.pt3dadd(0.0, 0.0, 0.0, 2.0 * cfg.somaR)
+        self.soma.pt3dadd(0.0, 2.0 * cfg.somaR, 0.0, 2.0 * cfg.somaR)
+        if cfg.epas:
+            self.soma.insert('pas')
+            self.soma(0.5).pas.e = cfg.epas
+            self.soma(0.5).pas.g = cfg.gpas
+
+class I2Neuron:
+    """ A neuron with soma and dendrite with; fast and persistent sodium
+    currents, potassium currents, passive leak and potassium leak and an
+    accumulation mechanism. """
+    def __init__(self):
+        self.soma = h.Section(name='I2soma', cell=self)
+        # add 3D points to locate the neuron in the ECS  
+        self.soma.pt3dadd(0.0, 0.0, 0.0, 2.0 * cfg.somaR)
+        self.soma.pt3dadd(0.0, 2.0 * cfg.somaR, 0.0, 2.0 * cfg.somaR)
+        if cfg.epas:
+            self.soma.insert('pas')
+            self.soma(0.5).pas.e = cfg.epas
+            self.soma(0.5).pas.g = cfg.gpas
+
+class E4Neuron:
+    """ A neuron with soma and dendrite with; fast and persistent sodium
+    currents, potassium currents, passive leak and potassium leak and an
+    accumulation mechanism. """
+    def __init__(self):
+        self.soma = h.Section(name='E4soma', cell=self)
+        # add 3D points to locate the neuron in the ECS  
+        self.soma.pt3dadd(0.0, 0.0, 0.0, 2.0 * cfg.somaR)
+        self.soma.pt3dadd(0.0, 2.0 * cfg.somaR, 0.0, 2.0 * cfg.somaR)
+        if cfg.epas:
+            self.soma.insert('pas')
+            self.soma(0.5).pas.e = cfg.epas
+            self.soma(0.5).pas.g = cfg.gpas
+
+class I4Neuron:
+    """ A neuron with soma and dendrite with; fast and persistent sodium
+    currents, potassium currents, passive leak and potassium leak and an
+    accumulation mechanism. """
+    def __init__(self):
+        self.soma = h.Section(name='I4soma', cell=self)
+        # add 3D points to locate the neuron in the ECS  
+        self.soma.pt3dadd(0.0, 0.0, 0.0, 2.0 * cfg.somaR)
+        self.soma.pt3dadd(0.0, 2.0 * cfg.somaR, 0.0, 2.0 * cfg.somaR)
+        if cfg.epas:
+            self.soma.insert('pas')
+            self.soma(0.5).pas.e = cfg.epas
+            self.soma(0.5).pas.g = cfg.gpas
+
+class E5Neuron:
+    """ A neuron with soma and dendrite with; fast and persistent sodium
+    currents, potassium currents, passive leak and potassium leak and an
+    accumulation mechanism. """
+    def __init__(self):
+        self.soma = h.Section(name='E5soma', cell=self)
+        # add 3D points to locate the neuron in the ECS  
+        self.soma.pt3dadd(0.0, 0.0, 0.0, 2.0 * cfg.somaR)
+        self.soma.pt3dadd(0.0, 2.0 * cfg.somaR, 0.0, 2.0 * cfg.somaR)
+        if cfg.epas:
+            self.soma.insert('pas')
+            self.soma(0.5).pas.e = cfg.epas
+            self.soma(0.5).pas.g = cfg.gpas
+
+class I5Neuron:
+    """ A neuron with soma and dendrite with; fast and persistent sodium
+    currents, potassium currents, passive leak and potassium leak and an
+    accumulation mechanism. """
+    def __init__(self):
+        self.soma = h.Section(name='I5soma', cell=self)
+        # add 3D points to locate the neuron in the ECS  
+        self.soma.pt3dadd(0.0, 0.0, 0.0, 2.0 * cfg.somaR)
+        self.soma.pt3dadd(0.0, 2.0 * cfg.somaR, 0.0, 2.0 * cfg.somaR)
+        if cfg.epas:
+            self.soma.insert('pas')
+            self.soma(0.5).pas.e = cfg.epas
+            self.soma(0.5).pas.g = cfg.gpas
+
+# v0.00 - classes for each cell type in network

examples/spreadingDepression/README.md

@@ -0,0 +1,38 @@
+# RxD Spreading Depression/Depiolarization
+## Overview
+A tissue-scale model of spreading depolarization (SD) in brain slices
+ported to NetPyNE from [Kelley et al. 2022](https://github.com/suny-downstate-medical-center/SDinSlice).
+
+We use NetPyNE to interface with the NEURON simulator's reaction-diffusion framework to embed thousands of neurons 
+(based on the the model from Wei et al. 2014)
+in the extracellular space of a brain slice, which is itself embedded in an bath solution.
+![model schematic](./schematic.png)
+We initiate SD in the slice by elevating extracellular K+ in a spherical region at the center of the slice.
+Effects of hypoxia and propionate on the slice were modeled by appropriate changes to the volume fraction 
+and tortuosity of the extracellular space and oxygen/chloride concentrations.
+
+In this example, we use NetPyNE to define the cells, extracellular space,
+ion/oxygen dynamics, and channel/cotransporter/pump dynamics, but we use  
+calls to NEURON to handle running the simulation and interval saving. 
+
+## Setup and execution
+Requires NEURON with RxD and Python. We recommend using [MPI](https://www.open-mpi.org/) to parallelize simulations.  Simulations, especially without 
+multiple cores, may take upwards of thiry minutes.
+
+To run the simulation on a sinle core:
+```
+python3 init.py
+```
+To run on (for instance) 6 cores with MPI:
+```
+mpiexec -n 6 nrniv -python -mpi init.py
+```
+
+Parameters like slice oxygenation, radius and concentration of the K+ bolus used 
+to initiate SD, neuronal density, etc. can be changed by editing **cfg.py**.
+
+## References
+Craig Kelley, Adam J. H. Newton, Sabina Hrabetova, Robert A. McDougal, and William W. Lytton. 2022. “Multiscale Computer Modeling of Spreading Depolarization in Brain Slices.” bioRxiv. https://doi.org/10.1101/2022.01.20.477118.
+
+Yina Wei, Ghanim Ullah, and Steven J. Schiff. "Unification of neuronal spikes, seizures, and spreading depression." Journal of Neuroscience 34, no. 35 (2014): 11733-11743.
+https://doi.org/10.1523/JNEUROSCI.0516-14.2014