## -*- coding: utf-8 -*-
__author__ = "Zafeirios Fountas"
__credits__ = ["Murray Shanahan", "Mark Humphries", "Rob Leech", "Jeanette Hellgren Kotaleski"]
__license__ = "GPLv3"
__version__ = "0.1"
__maintainer__ = "Zafeirios Fountas"
__email__ = "fountas@outlook.com"
__status__ = "Published"
# NOTES:
# vr is the resting potential & vt the instantaneous threshold potential!
# The MSN model was taken from Humphries 2014 and the parameters were adjusted
# using various sources
from brian import mV, pF, ms, pA
data = dict()
data["MSN"] = {
"a" : { "value" : 0.01/ms, "source" : "Mahon etal 2000b, Izhikevich 2007", "unit" : ""},
"b" : { "value" : -20/ms, "source" : "Izhikevich 2007", "unit" : ""},
"c" : { "value" : -55*mV, "source" : "Izhikevich 2007", "unit" : ""},
"d" : { "value" : 91*mV/ms, "source" : "Humphries 2009B", "unit" : ""},
"vpeak" : { "value" : 40 * mV, "source" : "Izhikevich 2007", "unit" : "mV"},
"vr" : { "value" : -80 * mV, "source" : "Izhikevich 2007", "unit" : "mV"},
"vt" : { "value" : -29.7 * mV,"source" : "Humphries 2009B", "unit" : "mV"},
"k" : { "value" : 1.0, "source" : "Izhikevich 2007", "unit" : ""},
"C" : { "value" : 15.2*pF, "source" : "Humphries 2009B", "unit" : "pF"},
"v" : { "value" : -80.0 * mV,"source" : "resting (Vr)", "unit" : "mV"},
"u" : { "value" : 0.0 * mV, "source" : "??", "unit" : "mV"},
"Ispon" : { "value" : 0.0 * mV, "source" : "??", "unit" : "mV"},
"K" : { "value" : 0.0289, "source" : "Humphries 2009B", "unit" : ""},
"L" : { "value" : 0.331, "source" : "Humphries 2009B", "unit" : ""},
"alpha" : { "value" : 0.032, "source" : "Humphries 2009B", "unit" : ""},
#"bita1" : { "value" : 6.3, "source" : "Humphries 2009B", "unit" : ""},
#"bita2" : { "value" : 0.215, "source" : "Humphries 2009B", "unit" : ""}
"bita1" : { "value" : 0.5, "source" : "Humphries 2014", "unit" : ""},
"bita2" : { "value" : 0.3, "source" : "Humphries 2014", "unit" : ""}
}
data["FSI"] = {
"a" : { "value" : 0.2/ms, "source" : "Izhikevich 2007", "unit" : ""},
"b" : { "value" : 0.025/ms, "source" : "Izhikevich 2007", "unit" : ""},
"c" : { "value" : -60.0*mV, "source" : "Tetano 2004 - Humphries 2014", "unit" : ""},
"d" : { "value" : 0.0*mV/ms, "source" : "Izhikevich 2007", "unit" : ""},
"vpeak" : { "value" : 25.0*mV, "source" : "Izhikevich 2007", "unit" : "mV"},
"vr" : { "value" : -70.0*mV, "source" : "Tetano 2004 - Humphries 2014", "unit" : "mV"},
"vt" : { "value" : -50.0*mV, "source" : "Tetano 2004 - Humphries 2014", "unit" : "mV"},
"k" : { "value" : 1.0, "source" : "Izhikevich 2007", "unit" : "none"},
"C" : { "value" : 80.0*pF, "source" : "Tetano 2004 - Humphries 2014", "unit" : "pF"},
"v" : { "value" : -70.0*mV, "source" : "resting (Vr)", "unit" : "mV"},
"u" : { "value" : 0.0*mV, "source" : "??", "unit" : "mV"},
"Ispon" : { "value" : 0.0*mV, "source" : "??", "unit" : "mV"},
"vb" : { "value" : -55.0*mV, "source" : "Izhikevich 2007", "unit" : "mV"},
"hta" : { "value" : 0.1, "source" : "Humphries 2014", "unit" : ""},
"epsilon" : { "value" : 0.625*mV, "source" : "Humphries 2014", "unit" : ""},
}
# -- Fountas 2014 --------------------------------------------------------------
data["GPe-typeA"] = {
"a" : { "value" : 0.29 / ms, "source" : "GA", "unit" : ""},
"b" : { "value" : 4.26 / ms, "source" : "GA", "unit" : ""},
"c" : { "value" : -57.4 * mV, "source" : "GA", "unit" : ""},
"d" : { "value" : 110.0 * mV/ms, "source" : "GA", "unit" : ""},
"vpeak" : { "value" : 38.0 * mV, "source" : "", "unit" : "mV"},
"vr" : { "value" : -50.7 * mV, "source" : "", "unit" : "mV"},
"vt" : { "value" : -42.0 * mV, "source" : "", "unit" : "mV"},
"k" : { "value" : 0.06 , "source" : "GA", "unit" : ""},
"C" : { "value" : 70.0, "source" : "GA", "unit" : "pF"},
"Cfig" : { "value" : 55.0, "source" : "GA", "unit" : "pF"},
"C_var" : { "value" : 20.0, "source" : "manual", "unit" : "pF"},
"C_var_real" : { "value" : 20.0, "source" : "manual", "unit" : "pF"},
"v" : { "value" : -50.7 * mV, "source" : "", "unit" : "mV"},
"u" : { "value" : 0.0 * mV, "source" : "", "unit" : "mV"},
# NOTE: Although Ivivo was 117 in the final tuning experiment, we need 15pA
# more to make the spontaneous activation (10Hz) to be consistent among GPes.
"Ivivo" : { "value" : (107.0+60.0)*pA, "source" : "Manual tuning", "unit" : "pA"},
"Ivitro" : { "value" : 107.0 * pA, "source" : "GA", "unit" : "pA"},
"sigma_vivo" : { "value" : 0.7, "source" : "manual", "unit" : ""},
"sigma_vitro" :{ "value" : 0.0, "source" : "manual", "unit" : ""},
"density" : { "value" : 0.0405, "source" : "From Bugaysen and Delong (15% LFB)", "unit" : ""}
}
data["GPe-typeB"] = {
"a" : { "value" : 0.0045 / ms, "source" : "GA", "unit" : ""},
"b" : { "value" : 3.895 / ms, "source" : "GA", "unit" : ""},
"c" : { "value" : -58.36 * mV, "source" : "GA", "unit" : ""},
"d" : { "value" : 0.353 * mV/ms, "source" : "GA", "unit" : ""},
"vpeak" : { "value" : 25.0 * mV, "source" : "", "unit" : "mV"},
"vr" : { "value" : -53.0 * mV, "source" : "", "unit" : "mV"},
"vt" : { "value" : -44.0 * mV, "source" : "", "unit" : "mV"},
"k" : { "value" : 0.943 , "source" : "GA", "unit" : ""},
"C" : { "value" : 68.0, "source" : "GA", "unit" : "pF"},
"Cfig" : { "value" : 68.0, "source" : "GA", "unit" : "pF"},
"C_var" : { "value" : 20.0, "source" : "manual", "unit" : "pF"},
"C_var_real" : { "value" : 20.0, "source" : "manual", "unit" : "pF"},
"v" : { "value" : -53.0 * mV, "source" : "", "unit" : "mV"},
"u" : { "value" : 0.0 * mV, "source" : "", "unit" : "mV"},
"Ivivo" : { "value" : 64.0 * pA, "source" : "Manual tuning", "unit" : "pA"}, # Because I deleted Istim
"Ivitro" : { "value" : 52.0 * pA, "source" : "GA", "unit" : "pA"},
"sigma_vivo" : { "value" : 1.6, "source" : "manual", "unit" : ""},
"sigma_vitro" :{ "value" : 0.0, "source" : "manual", "unit" : ""},
"density" : { "value" : 0.85, "source" : "From Delong (85% HFP)", "unit" : ""}
}
data["GPe-typeC"] = {
"a" : { "value" : 0.42 / ms, "source" : "GA", "unit" : ""},
"b" : { "value" : 7.0 / ms, "source" : "GA", "unit" : ""},
"c" : { "value" : -52.0 * mV, "source" : "GA", "unit" : ""},
"d" : { "value" : 166.0 * mV/ms, "source" : "GA", "unit" : ""},
"vpeak" : { "value" : 34.5 * mV, "source" : "", "unit" : "mV"},
"vr" : { "value" : -54.0 * mV, "source" : "", "unit" : "mV"},
"vt" : { "value" : -43.0 * mV, "source" : "", "unit" : "mV"},
"k" : { "value" : 0.099 , "source" : "GA", "unit" : ""},
"C" : { "value" : 65.0, "source" : "GA", "unit" : "pF"},
"Cfig" : { "value" : 57.0, "source" : "GA", "unit" : "pF"},
"C_var" : { "value" : 20.0, "source" : "manual", "unit" : "pF"},
"C_var_real" : { "value" : 20.0, "source" : "manual", "unit" : "pF"},
"v" : { "value" : -54.0 * mV, "source" : "", "unit" : "mV"},
"u" : { "value" : 0.0 * mV, "source" : "", "unit" : "mV"},
#"Ivivo" : { "value" : 328.5 * pA, "source" : "cGA2-2", "unit" : "pA"},
#"Ivivo" : { "value" : 197.5 * pA, "source" : "Manual tuning", "unit" : "pA"},
"Ivivo" : { "value" : (187.5+50.0)* pA,"source" : "Manual tuning", "unit" : "pA"},
"Ivitro" : { "value" : 187.5 * pA, "source" : "GA", "unit" : "pA"},
"sigma_vivo" : { "value" : 1.3, "source" : "manual", "unit" : ""},
"sigma_vitro" :{ "value" : 0.0, "source" : "manual", "unit" : ""},
"density" : { "value" : 0.1095, "source" : "Bugaysen and Delong (15% LFB)", "unit" : ""}
}
data["SNr"] = {
"a" : { "value" : 0.113 / ms, "source" : "GA", "unit" : ""},
"b" : { "value" : 11.057 / ms, "source" : "GA", "unit" : ""},
"c" : { "value" : -62.7 * mV, "source" : "GA", "unit" : ""},
"d" : { "value" : 138.4 * mV/ms, "source" : "GA", "unit" : ""},
"vpeak" : { "value" : 9.8 * mV, "source" : "", "unit" : "mV"},
"vr" : { "value" : -64.58 * mV, "source" : "", "unit" : "mV"},
"vt" : { "value" : -51.8 * mV, "source" : "", "unit" : "mV"},
"k" : { "value" : 0.7836 , "source" : "GA", "unit" : ""},
"C" : { "value" : 200.0, "source" : "GA", "unit" : "pF"},
"Cfig" : { "value" : 172.1, "source" : "GA", "unit" : "pF"},
"C_var" : { "value" : 50.0, "source" : "manual", "unit" : "pF"},
"C_var_real" : { "value" : 50.0, "source" : "manual", "unit" : "pF"},
"v" : { "value" : -64.58 * mV, "source" : "", "unit" : "mV"},
"u" : { "value" : 0.0 * mV, "source" : "", "unit" : "mV"},
"IvivoC" : { "value" : 150.0 * pA, "source" : "GA", "unit" : "pA"},
"Ivivo" : { "value" : 235.0 * pA, "source" : "Manual tuning - This gives us 14.36Hz without STN connections which is consistent with Lindahl2013, Féger&Robledo 1991", "unit" : "pA"},
"Ivitro" : { "value" : 206.0 * pA, "source" : "GA", "unit" : "pA"},
"sigma_vivo" : { "value" : 0.3, "source" : "GA", "unit" : ""},
"sigma_vitro" :{ "value" : 0.3, "source" : "GA", "unit" : ""}
}
data["STN-typeA"] = {
"a1" : { "value" : 0.021 / ms, "source" : "GA", "unit" : ""},
"b1" : { "value" : 4.0 / ms, "source" : "GA", "unit" : ""},
"c" : { "value" : -47.7 * mV, "source" : "GA", "unit" : ""},
"d1" : { "value" : 17.1 * mV/ms, "source" : "GA", "unit" : ""},
"vpeak" : { "value" : 15.4 * mV, "source" : "", "unit" : "mV"},
"vr" : { "value" : -56.2 * mV, "source" : "", "unit" : "mV"},
"vt" : { "value" : -41.4 * mV, "source" : "", "unit" : "mV"},
"k" : { "value" : 0.439 , "source" : "GA", "unit" : ""},
"C" : { "value" : 23.0, "source" : "GA", "unit" : "pF"},
"Cfig" : { "value" : 23.0, "source" : "GA", "unit" : "pF"},
"C_var" : { "value" : 10.0, "source" : "manual", "unit" : "pF"},
"C_var_real" :{ "value" : 10.0, "source" : "manual", "unit" : "pF"},
"vr2" : { "value" : -60.0 * mV, "source" : "", "unit" : "mV"},
"b_thres" : { "value" : -60.0 * mV, "source" : "", "unit" : "mV"},
"a2" : { "value" : 0.123 / ms, "source" : "GA", "unit" : ""},
"b2" : { "value" : 0.015 / ms, "source" : "GA", "unit" : ""},
"d2" : { "value" : -68.4 * mV/ms, "source" : "GA", "unit" : ""},
"w1" : { "value" : 0.1, "source" : "", "unit" : ""},
"w2" : { "value" : 0.0, "source" : "", "unit" : ""},
"v" : { "value" : -56.2 * mV, "source" : "", "unit" : "mV"},
"u1" : { "value" : 0.0, "source" : "", "unit" : ""},
"u2" : { "value" : 0.0, "source" : "", "unit" : ""},
"Ivivo" : { "value" : 56.1 * pA, "source" : "GA", "unit" : "pA"},
"Ivitro" : { "value" : 56.1 * pA, "source" : "GA", "unit" : "pA"},
"sigma_vivo" :{ "value" : 1.5, "source" : "GA", "unit" : ""},
"sigma_vitro":{ "value" : 1.5, "source" : "GA", "unit" : ""},
"density" : { "value" : 0.6, "source" : "Bevan 2000", "unit" : ""}
}
data["STN-typeB"] = {
"a1" : { "value" : 0.05 / ms, "source" : "GA", "unit" : ""},
"b1" : { "value" : 0.2 / ms, "source" : "GA", "unit" : ""},
"c" : { "value" : -60.0 * mV, "source" : "GA", "unit" : ""},
"d1" : { "value" : 1.0 * mV/ms, "source" : "GA", "unit" : ""},
"vpeak" : { "value" : 15.4 * mV, "source" : "", "unit" : "mV"},
"vr" : { "value" : -56.2 * mV, "source" : "", "unit" : "mV"},
"vt" : { "value" : -50.0 * mV, "source" : "", "unit" : "mV"},
"k" : { "value" : 0.3 , "source" : "GA", "unit" : ""},
"C" : { "value" : 40.0, "source" : "GA", "unit" : "pF"},
"Cfig" : { "value" : 40.0, "source" : "GA", "unit" : "pF"},
"C_var" : { "value" : 10.0, "source" : "manual", "unit" : "pF"},
"C_var_real" :{ "value" : 10.0, "source" : "manual", "unit" : "pF"},
"vr2" : { "value" : -60.0 * mV, "source" : "", "unit" : "mV"},
"b_thres" : { "value" : -60.0 * mV, "source" : "", "unit" : "mV"},
"a2" : { "value" : 0.001 / ms, "source" : "GA", "unit" : ""},
"b2" : { "value" : 0.3 / ms, "source" : "GA", "unit" : ""},
"d2" : { "value" : 10.0 * mV/ms, "source" : "GA", "unit" : ""},
"w1" : { "value" : 0.01, "source" : "", "unit" : ""},
"w2" : { "value" : 0.0, "source" : "", "unit" : ""},
"v" : { "value" : -56.2 * mV, "source" : "", "unit" : "mV"},
"u1" : { "value" : 0.0, "source" : "", "unit" : ""},
"u2" : { "value" : 0.0, "source" : "", "unit" : ""},
"Ivivo" : { "value" : 8.0 * pA, "source" : "GA", "unit" : "pA"},
"Ivitro" : { "value" : 25.0 * pA, "source" : "GA", "unit" : "pA"},
"sigma_vivo" :{ "value" : 1.5, "source" : "GA", "unit" : ""},
"sigma_vitro":{ "value" : 1.5, "source" : "GA", "unit" : ""},
"density" : { "value" : 0.25, "source" : "Bevan 2000", "unit" : ""}
}
data["STN-typeC"] = {
"a1" : { "value" : 0.44 / ms, "source" : "GA", "unit" : ""},
"b1" : { "value" : -1.35 / ms, "source" : "GA", "unit" : ""},
"c" : { "value" : -52.34 * mV, "source" : "GA", "unit" : ""},
"d1" : { "value" : 17.65 * mV/ms, "source" : "GA", "unit" : ""},
"vpeak" : { "value" : 15.4 * mV, "source" : "", "unit" : "mV"},
"vr" : { "value" : -58.5 * mV, "source" : "", "unit" : "mV"},
"vt" : { "value" : -43.75 * mV, "source" : "", "unit" : "mV"},
"k" : { "value" : 0.105 , "source" : "GA", "unit" : ""},
"C" : { "value" : 30.0, "source" : "GA", "unit" : "pF"},
"Cfig" : { "value" : 23.0, "source" : "GA", "unit" : "pF"},
"C_var" : { "value" : 20.0, "source" : "manual", "unit" : "pF"},
"C_var_real" :{ "value" : 20.0, "source" : "manual", "unit" : "pF"},
"vr2" : { "value" : -43.2 * mV, "source" : "", "unit" : "mV"},
"b_thres" : { "value" : 1000.0 * mV, "source" : "", "unit" : "mV"},
"a2" : { "value" : 0.32 / ms, "source" : "GA", "unit" : ""},
"b2" : { "value" : 3.13 / ms, "source" : "GA", "unit" : ""},
"d2" : { "value" : 92.0 * mV/ms, "source" : "GA", "unit" : ""},
"w1" : { "value" : 0.001, "source" : "", "unit" : ""},
"w2" : { "value" : 1.0, "source" : "", "unit" : ""},
"v" : { "value" : -58.5 * mV, "source" : "", "unit" : "mV"},
"u1" : { "value" : 0.0, "source" : "", "unit" : ""},
"u2" : { "value" : 0.0, "source" : "", "unit" : ""},
"Ivivo" : { "value" : -18.0 * pA, "source" : "GA", "unit" : "pA"},
"Ivitro" : { "value" : -1.0 * pA, "source" : "GA", "unit" : "pA"},
"sigma_vivo" :{ "value" : 1.5, "source" : "GA", "unit" : ""},
"sigma_vitro":{ "value" : 0.5, "source" : "GA", "unit" : ""},
"density" : { "value" : 0.15, "source" : "Bevan 2000", "unit" : ""}
}