Mouse oct

.gitignore

@@ -22,7 +22,8 @@ cnmodel.egg*
 .cache*
 .pytest*
 Figure6*
-
-
+cnmodel/cells/tests/cell_data/*
+cnmode/synapses/tests/test_data/*
+*.dll
 
 

cnmodel/cells/octopus.py

@@ -181,6 +181,7 @@ def __init__(self, morphology=None, decorator=None, nach=None,
                 modelName = 'XM13'
             if modelName == 'XM13':
                 dataset = 'XM13_channels'
+                temp = 34.0
             elif modelName  == 'XM13nacncoop':
                 dataset = 'XM13_channels_nacncoop'
             else:
@@ -206,17 +207,18 @@ def __init__(self, morphology=None, decorator=None, nach=None,
             self.e_h = -38. # from McGinley et al. 
             self.R_a = 195  # McGinley et al. 
             if self.status['species'] == 'mouse':
-                self.mechanisms = ['klt', 'kht', 'hcnobo', 'leak', self.pars.natype]
+                # self.mechanisms = ['klt', 'kht', 'hcnobo', 'leak', self.pars.natype]
+                self.mechanisms = ['klt', 'kht', 'ihvcn', 'leak', self.pars.natype]
             elif self.status['species'] == 'guineapig':
                 self.mechanisms = ['klt', 'kht', 'ihvcn', 'leak', self.pars.natype]
             for mech in self.mechanisms:
                 self.soma.insert(mech)
             self.soma.ek = self.e_k
             self.soma.ena = self.e_na
-            if self.status['species'] == 'mouse':
-                self.soma().hcnobo.eh = self.e_h
-            else:
-                self.soma().ihvcn.eh = self.e_h
+            # if self.status['species'] == 'mouse':
+            #     self.soma().hcnobo.eh = self.e_h
+            # else:
+            self.soma().ihvcn.eh = self.e_h
             self.soma().leak.erev = self.e_leak
             self.soma.Ra = self.R_a
             self.species_scaling(silent=True)  # set the default type II cell parameters
@@ -253,7 +255,7 @@ def get_cellpars(self, dataset, species='guineapig', modelType='I-c'):
                 pars.additem(g,  data.get(dataset, species=species, model_type=modelType,
                     field=g))
         elif self.status['modelName'] == 'XM13':
-            for g in ['%s_gbar' % pars.natype, 'kht_gbar', 'ka_gbar', 'ihvcn_gbar', 'leak_gbar', 'leak_erev', 'ih_eh', 'e_k', 'e_na']:
+            for g in ['%s_gbar' % pars.natype,'klt_gbar', 'kht_gbar', 'ka_gbar', 'ihvcn_gbar', 'leak_gbar', 'leak_erev', 'ih_eh', 'e_k', 'e_na']:
                 pars.additem(g,  data.get(dataset, species=species, model_type=modelType,
                     field=g))
         # elif self.status['modelName'] == 'mGBC':
@@ -310,15 +312,16 @@ def species_scaling(self, silent=True):
         elif self.status['species'] == 'mouse' and self.status['modelType'] =='II-o':
             self.i_test_range = {'pulse': (-4.0, 4.0, 0.2)}
             self.vrange = [-70., -57.]  # set a default vrange for searching for rmp
-            self.set_soma_size_from_Cm(25.0)
+            self.set_soma_size_from_Cm(self.pars.cap)
             self._valid_temperatures = (34., )
             if self.status['temperature'] is None:
                 self.set_temperature(34.)
             self.adjust_na_chans(soma, sf=1.0)
-            soma().kht.gbar = nstomho(150.0, self.somaarea)  # 6.1 mmho/cm2
-            soma().klt.gbar = nstomho(3196.0, self.somaarea)  #  40.7 mmho/cm2
-            soma().hcnobo.gbar = nstomho(40.0, self.somaarea)  # 7.6 mmho/cm2, cf. Bal and Oertel, Spencer et al. 25 u dia cell
-            soma().leak.gbar = nstomho(2.0, self.somaarea)
+            soma().kht.gbar = nstomho(self.pars.kht_gbar, self.somaarea)  # 6.1 mmho/cm2
+            soma().klt.gbar = nstomho(self.pars.klt_gbar, self.somaarea)  #  40.7 mmho/cm2
+            # soma().hcnobo.gbar = nstomho(40.0, self.somaarea)  # 7.6 mmho/cm2, cf. Bal and Oertel, Spencer et al. 25 u dia cell
+            soma().ihvcn.gbar = nstomho(self.pars.ihvcn_gbar, self.somaarea)  # 7.6 mmho/cm2, cf. Bal and Oertel, Spencer et al. 25 u dia cell 40ns?
+            soma().leak.gbar = nstomho(self.pars.leak_gbar, self.somaarea)
             self.axonsf = 1.0
         else:
             raise ValueError('Species "%s" or species-type "%s" is not recognized for octopus cells' %  (species, type))

cnmodel/cells/tests/test_cells.py

@@ -56,6 +56,11 @@ def test_octopus():
     cell = cells.Octopus.create(species='guineapig', modelType='II-o')
     CellTester('octopus_guineapig-typeII-o', cell)
 
+def test_octopus_mouse():
+    reset(raiseError=False)
+    cell = cells.Octopus.create(species='mouse', modelType='II-o')
+    CellTester('octopus_mouse-typeII-o', cell)
+
 def test_pyramidal():
     reset(raiseError=False)
     cell = cells.Pyramidal.create(species='rat', model='POK', modelType='I')

cnmodel/data/ionchannels.py

@@ -65,24 +65,24 @@
 that can be accessed.
 
 -----------------------------------------------------------------------------------------------------------------------------------
-               II             II-I           I-c           I-II          I-t       
+               II             II-I           I-c           I-II          I-t           II-o       
 
-nav11_gbar     1000.  [4]     0000.  [4]     800.   [4]    800.   [4]    1000.  [4] 
-nacn_gbar      2300.  [1]     1000.  [1]     3000.  [1]    0000.  [2]    0000.  [1] 
-na_gbar        0000.  [1]     0000.  [1]     3000.  [1]    1800.  [2]    0000.  [1] 
-kht_gbar       58.0   [1]     58.0   [1]     500.0  [1]    150.0  [2]    500.0  [1] 
-klt_gbar       80.0   [1]     20.0   [1]     0.0    [1]    14.0   [3]    0.0    [1] 
-ka_gbar        0.0    [1]     0.0    [1]     0.0    [1]    0.0    [2]    125.0  [1] 
-ihvcn_gbar     30.0   [1]     30.0   [1]     18.0   [1]    2.0    [2]    18.0   [1] 
-leak_gbar      2.0    [1]     2.0    [1]     8.0    [1]    2.0    [2]    8.0    [1] 
-leak_erev      -65    [1]     -65    [1]     -65    [1]    -65    [2]    -65    [1] 
-na_type        nacn   [1]     nacn   [1]     nacn   [1]    na     [3]    nav11  [1] 
-ih_type        ihvcn  [1]     ihvcn  [1]     ihvcn  [1]    ihvcn  [2]    ihvcn  [1] 
-soma_Cap       26.0   [1]     26.0   [1]     25.0   [1]    25.0   [2]    25.0   [1] 
-nav11_vshift   4.3    [1]     4.3    [1]     4.3    [1]    4.3    [1]    4.3    [1]
-e_k            -84    [1]     -84    [1]     -84    [1]    -70    [3]    -84    [1] 
-e_na           50.    [1]     50.    [1]     50.    [1]    55.    [3]    50.    [1] 
-ih_eh          -43    [1]     -43    [1]     -43    [1]    -43    [2]    -43    [1] 
+nav11_gbar     1000.  [4]     0000.  [4]     800.   [4]    800.   [4]    1000.  [4]    1000.  [4]             
+nacn_gbar      2300.  [1]     1000.  [1]     3000.  [1]    0000.  [2]    0000.  [1]    2300.  [1]
+na_gbar        0000.  [1]     0000.  [1]     3000.  [1]    1800.  [2]    0000.  [1]    0000.  [1]
+kht_gbar       58.0   [1]     58.0   [1]     500.0  [1]    150.0  [2]    500.0  [1]    58.0   [1]
+klt_gbar       80.0   [1]     20.0   [1]     0.0    [1]    14.0   [3]    0.0    [1]    450.0  [5]
+ka_gbar        0.0    [1]     0.0    [1]     0.0    [1]    0.0    [2]    125.0  [1]    0.0    [1]
+ihvcn_gbar     30.0   [1]     30.0   [1]     18.0   [1]    2.0    [2]    18.0   [1]    130.0  [5]
+leak_gbar      2.0    [1]     2.0    [1]     8.0    [1]    2.0    [2]    8.0    [1]    2.0    [1]
+leak_erev      -65    [1]     -65    [1]     -65    [1]    -65    [2]    -65    [1]    -65    [1]
+na_type        nacn   [1]     nacn   [1]     nacn   [1]    na     [3]    nav11  [1]    nacn   [1]
+ih_type        ihvcn  [1]     ihvcn  [1]     ihvcn  [1]    ihvcn  [2]    ihvcn  [1]    ihvcn  [1]
+soma_Cap       26.0   [1]     26.0   [1]     25.0   [1]    25.0   [2]    25.0   [1]    40.0   [6]
+nav11_vshift   4.3    [1]     4.3    [1]     4.3    [1]    4.3    [1]    4.3    [1]    4.3    [1]
+e_k            -84    [1]     -84    [1]     -84    [1]    -70    [3]    -84    [1]    -84    [1]
+e_na           50.    [1]     50.    [1]     50.    [1]    55.    [3]    50.    [1]    50.    [1]
+ih_eh          -43    [1]     -43    [1]     -43    [1]    -43    [2]    -43    [1]    -43    [1]
 
 -----------------------------------------------------------------------------------------------------------------------------------
 
@@ -104,6 +104,10 @@
     used for mice in the master distribution of cnmodel, which used only the nacn
     channels. The channel type can be overridden however.
 
+[5] Table 1 of Cao and Oertel. 2017. Hearing Research 345: 57–68. 
+
+[6] McGinley et al. 2012. Journal of Neuroscience 32 (27): 9301–11.
+
 """)
 
 add_table_data('XM13_channels_compartments', row_key='parameter', col_key='compartment', 
@@ -240,7 +244,7 @@
 nav11_gbar     1600.  [1]     1600.  [1]     3000.  [1]    1600.  [2]    3000.  [1] 
 kht_gbar       58.0   [1]     58.0   [1]     500.0  [1]    150.0  [2]    500.0  [1] 
 klt_gbar       80.0   [1]     14.0   [1]     0.0    [1]    20.0   [2]    0.0    [1] 
-ka_gbar        0.0    [1]     0.0    [1]     0.0    [1]    0.0    [2]    125.0    [1] 
+ka_gbar        0.0    [1]     0.0    [1]     0.0    [1]    0.0    [2]    125.0  [1] 
 ihvcn_gbar     30.0   [1]     30.0   [1]     18.0   [1]    2.0    [2]    18.0   [1] 
 leak_gbar      2.0    [1]     2.0    [1]     8.0    [1]    2.0    [2]    8.0    [1] 
 leak_erev      -65    [1]     -65    [1]     -65    [1]    -65    [2]    -65    [1] 

examples/toy_model.py

@@ -167,6 +167,10 @@ def run(self):
                     "Octopus, II-o",
                     (cells.Octopus, "II-o", "guineapig", (-2.5, 2.5, 11), 22),
                 ),
+                (
+                    "Octopus, II-o",
+                    (cells.Octopus, "II-o", "mouse", (-4, 4, 15),34),
+                ),
                 ("Bushy, II, Mouse", (cells.Bushy, "II", "mouse", (-1, 1.2, 13), 34)),
                 (
                     "TStellate, I-c, Mouse",