Merge pull request #3 from Traps128/master

Possibility to split the GPe in two parts (results of Gregoire Berthelon's internship).
benoit-girard · Jun 13, 2018 · 7e9d5a3 · 7e9d5a3
2 parents ea13aec + 7249c6a
commit 7e9d5a3
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Showing 9 changed files with 1,181 additions and 152 deletions.
diff --git a/LGneurons.py b/LGneurons.py
diff --git a/baseParams.py b/baseParams.py
@@ -6,30 +6,79 @@
 ####################################################################################
 
 params = {
+'splitGPe':                  False,
 'nbCh':                          1, # number of concurrent channels to simulate
 'LG14modelID':                   9, # LG 2014 parameterization used (default: model #9)
+
 'nbMSN':                     2644., # population size (default: 1/1000 of the BG)
 'nbFSI':                       53., # ^
 'nbSTN':                        8., # ^
 'nbGPe':                       25., # ^
+'nbArky':                       5., # part of the GPe which projects to the striatum
+'nbProt':                      20., # part of the GPe which projects to the STN and GPi/SNr
 'nbGPi':                       14., # ^
 'nbCSN':                     3000., # ^
 'nbPTN':                      100., # ^
 'nbCMPf':                       9., # ^
-'GMSN':                         1., # gain on all synapses (default: no gain)
-'GFSI':                         1., # ^
-'GSTN':                         1., # ^
-'GGPe':                         1., # ^
-'GGPi':                         1., # ^
+
+'GCSNMSN':           1., # defining connection types for channel-based models (focused or diffuse) based on LG14 - refer to this paper for justification
+'GPTNMSN':           1., # ^
+'GCMPfMSN':          1., # ^
+'GMSNMSN':           1., # ^
+'GFSIMSN':           1., # ^
+'GSTNMSN':           1., # ^
+'GGPeMSN':           1., # ^
+'GArkyMSN':          1., # ^
+
+'GCSNFSI':           1., # ^
+'GPTNFSI':           1., # ^
+'GCMPfFSI':          1., # ^
+'GFSIFSI':           1., # ^
+'GSTNFSI':           1., # ^
+'GGPeFSI':           1., # ^
+'GArkyFSI':          1., # ^
+
+'GPTNSTN':           1., # ^
+'GCMPfSTN':          1., # ^
+'GGPeSTN':           1., # ^
+'GProtSTN':          1., # ^
+
+'GCMPfGPe':          1., # ^
+'GMSNGPe':           1., # ^
+'GSTNGPe':           1., # ^
+'GGPeGPe':           1., # ^
+
+'GCMPfArky':         1., # ^
+'GMSNArky':          1., # ^
+'GSTNArky':          1., # ^
+'GArkyArky':         1/5., # ^
+'GProtArky':         4/5., # ^
+
+'GCMPfProt':         1., # ^
+'GMSNProt':          1., # ^
+'GSTNProt':          1., # ^
+'GArkyProt':         1/5., # ^
+'GProtProt':         4/5., # ^
+
+'GCMPfGPi':          1., # ^
+'GMSNGPi':           1., # ^
+'GSTNGPi':           1., # ^
+'GGPeGPi':           1., # LG14: no data available to decide; setting to diffuse improve selection properties
+'GProtGPi':          1., #
+
 'IeMSN':                        0., # tonic input currents (default: no input current)
 'IeFSI':                        0., # ^
 'IeSTN':                        0., # ^
 'IeGPe':                        0., # ^
+'IeArky':                       0., # ^
+'IeProt':                       0., # ^
 'IeGPi':                        0., # ^
+
 # There are 3 different format for setting the inDegreeXY (=number of different incoming neurons from X that target one neuron in Y)
 # - 'inDegreeAbs': specify the absolute number of different input neurons from X that target one neuron of Y --- be careful when using this setting, as the population size varies widly between the striatum and the downstream nuclei
 # - 'outDegreeAbs': specify the absolute number of contacts between an axon from X to each dendritic tree in Y
 # - 'outDegreeCons': specify the constrained number of contacts between an axon from X to each dendritic tree in Y as a fraction between 0 (minimal number of contacts to achieve required axonal bouton counts) and 1 (maximal number of contacts with respect to population numbers)
+
 'RedundancyType':   'outDegreeAbs', # by default all axons are hypothesized to target each dendritic tree at 3 different locations
 'redundancyCSNMSN':              3, # ^
 'redundancyPTNMSN':              3, # ^
@@ -38,47 +87,89 @@
 'redundancyFSIMSN':              3, # ^
 'redundancySTNMSN':              3, # ^
 'redundancyGPeMSN':              3, # ^
+'redundancyArkyMSN':             3, # ^
+
 'redundancyCSNFSI':              3, # ^
 'redundancyPTNFSI':              3, # ^
-'redundancySTNFSI':              3, # ^
-'redundancyGPeFSI':              3, # ^
 'redundancyCMPfFSI':             3, # ^
 'redundancyFSIFSI':              3, # ^
+'redundancySTNFSI':              3, # ^
+'redundancyGPeFSI':              3, # ^
+'redundancyArkyFSI':             3, # ^
+
 'redundancyPTNSTN':              3, # ^
 'redundancyCMPfSTN':             3, # ^
 'redundancyGPeSTN':              3, # ^
+'redundancyProtSTN':              3, # ^
+
 'redundancyCMPfGPe':             3, # ^
 'redundancySTNGPe':              3, # ^
 'redundancyMSNGPe':              3, # ^
 'redundancyGPeGPe':              3, # ^
+
+'redundancyCMPfArky':            3, # ^
+'redundancySTNArky':             3, # ^
+'redundancyMSNArky':             3, # ^
+'redundancyArkyArky':            3, # ^
+'redundancyProtArky':            3, # ^
+
+'redundancyCMPfProt':            3, # ^
+'redundancySTNProt':             3, # ^
+'redundancyMSNProt':             3, # ^
+'redundancyArkyProt':            3, # ^
+'redundancyProtProt':            3, # ^
+
+'redundancyCMPfGPi':             3, # ^
 'redundancyMSNGPi':              3, # ^
 'redundancySTNGPi':              3, # ^
 'redundancyGPeGPi':              3, # ^
-'redundancyCMPfGPi':             3, # ^
+'redundancyProtGPi':             3, # ^
+
 'cTypeCSNMSN':           'focused', # defining connection types for channel-based models (focused or diffuse) based on LG14 - refer to this paper for justification
 'cTypePTNMSN':           'focused', # ^
 'cTypeCMPfMSN':          'diffuse', # ^
 'cTypeMSNMSN':           'diffuse', # ^
 'cTypeFSIMSN':           'diffuse', # ^
 'cTypeSTNMSN':           'diffuse', # ^
 'cTypeGPeMSN':           'diffuse', # ^
+'cTypeArkyMSN':          'diffuse', # ^
+
 'cTypeCSNFSI':           'focused', # ^
 'cTypePTNFSI':           'focused', # ^
 'cTypeCMPfFSI':          'diffuse', # ^
 'cTypeFSIFSI':           'diffuse', # ^
 'cTypeSTNFSI':           'diffuse', # ^
 'cTypeGPeFSI':           'diffuse', # ^
+'cTypeArkyFSI':          'diffuse', # ^
+
 'cTypePTNSTN':           'focused', # ^
 'cTypeCMPfSTN':          'diffuse', # ^
 'cTypeGPeSTN':           'focused', # ^
+'cTypeProtSTN':          'focused', # ^
+
 'cTypeCMPfGPe':          'diffuse', # ^
 'cTypeMSNGPe':           'focused', # ^
 'cTypeSTNGPe':           'diffuse', # ^
 'cTypeGPeGPe':           'diffuse', # ^
+
+'cTypeCMPfArky':         'diffuse', # ^
+'cTypeMSNArky':          'focused', # ^
+'cTypeSTNArky':          'diffuse', # ^
+'cTypeArkyArky':         'diffuse', # ^
+'cTypeProtArky':         'diffuse', # ^
+
+'cTypeCMPfProt':         'diffuse', # ^
+'cTypeMSNProt':          'focused', # ^
+'cTypeSTNProt':          'diffuse', # ^
+'cTypeArkyProt':         'diffuse', # ^
+'cTypeProtProt':         'diffuse', # ^
+
 'cTypeCMPfGPi':          'diffuse', # ^
 'cTypeMSNGPi':           'focused', # ^
 'cTypeSTNGPi':           'diffuse', # ^
 'cTypeGPeGPi':           'diffuse', # LG14: no data available to decide; setting to diffuse improve selection properties
+'cTypeProtGPi':          'diffuse', #
+
 'parrotCMPf' :                True, # Should the CMPf be simulated using parrot neurons?
 'stochastic_delays':          None, # If specified, gives the relative sd of a clipped Gaussian distribution for the delays
 # For convenience, a few simulator variables are also set here
@@ -88,5 +179,6 @@
 'nbcpu':                         1, # number of CPUs to be used by nest
 'durationH':                  '08', # max duration of a simulation, used by Sango cluster
 'nbnodes':                     '1', # number of nodes, used by K computer
+'tSimu':                     5000., # time duration of one simulation
 }
 
diff --git a/baseParams.pyc b/baseParams.pyc