Add <spikeThresh> to core examples

OpenSourceBrain · May 14, 2024 · ee658bb · ee658bb
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commit ee658bb
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diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472450023.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472450023.cell.nml
@@ -6907,6 +6907,7 @@ Electrophysiology on which this model is based: http://celltypes.brain-map.org/m
                 <channelDensity id="pas_dend" ionChannel="pas" condDensity="0.00012046511053782884 S_per_cm2" erev="-80.97549438476562 mV" segmentGroup="dend" ion="non_specific"/>
                 <channelDensityNernst id="Ca_HVA_soma" ionChannel="Ca_HVA" condDensity="5.857401378883121e-05 S_per_cm2" segmentGroup="soma" ion="ca"/>
                 <channelDensityNernst id="Ca_LVA_soma" ionChannel="Ca_LVA" condDensity="0.009555960646307055 S_per_cm2" segmentGroup="soma" ion="ca"/>
+                <spikeThresh value="10mV"/>
                 <specificCapacitance value="2.207587481 uF_per_cm2" segmentGroup="soma"/>
                 <specificCapacitance value="2.207587481 uF_per_cm2" segmentGroup="axon"/>
                 <specificCapacitance value="2.207587481 uF_per_cm2" segmentGroup="dend"/>

diff --git a/CellTypesDatabase/models/NeuroML2/Cell_483108201.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_483108201.cell.nml
@@ -24659,6 +24659,7 @@ Electrophysiology on which this model is based: http://celltypes.brain-map.org/m
                 <channelDensity id="pas_apic" ionChannel="pas" condDensity="0.0009041788650989756 S_per_cm2" erev="-88.22792053222656 mV" segmentGroup="apic" ion="non_specific"/>
                 <channelDensityNernst id="Ca_HVA_soma" ionChannel="Ca_HVA" condDensity="0.000645323135868344 S_per_cm2" segmentGroup="soma" ion="ca"/>
                 <channelDensityNernst id="Ca_LVA_soma" ionChannel="Ca_LVA" condDensity="0.004712369819164053 S_per_cm2" segmentGroup="soma" ion="ca"/>
+                <spikeThresh value="10mV"/>
                 <specificCapacitance value="1.0 uF_per_cm2" segmentGroup="soma"/>
                 <specificCapacitance value="1.0 uF_per_cm2" segmentGroup="axon"/>
                 <specificCapacitance value="4.3300862052082865 uF_per_cm2" segmentGroup="dend"/>

diff --git a/CellTypesDatabase/models/NeuroML2/Cell_486556811.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_486556811.cell.nml
@@ -21298,6 +21298,7 @@ Electrophysiology on which this model is based: http://celltypes.brain-map.org/m
                 <channelDensity id="pas_apic" ionChannel="pas" condDensity="9.365286537058084e-06 S_per_cm2" erev="-84.25226783752441 mV" segmentGroup="apic" ion="non_specific"/>
                 <channelDensityNernst id="Ca_HVA_soma" ionChannel="Ca_HVA" condDensity="0.0003425366456967047 S_per_cm2" segmentGroup="soma" ion="ca"/>
                 <channelDensityNernst id="Ca_LVA_soma" ionChannel="Ca_LVA" condDensity="0.00642497815758423 S_per_cm2" segmentGroup="soma" ion="ca"/>
+                <spikeThresh value="10mV"/>
                 <specificCapacitance value="1.0 uF_per_cm2" segmentGroup="soma"/>
                 <specificCapacitance value="1.0 uF_per_cm2" segmentGroup="axon"/>
                 <specificCapacitance value="2.621448263075259 uF_per_cm2" segmentGroup="dend"/>

diff --git a/CellTypesDatabase/models/NeuroML2/Cell_497232312.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_497232312.cell.nml
@@ -18761,6 +18761,7 @@ Electrophysiology on which this model is based: http://celltypes.brain-map.org/m
                 <channelDensityNernst id="Ca_LVA_axon" ionChannel="Ca_LVA" condDensity="0.00196838 S_per_cm2" segmentGroup="axon" ion="ca"/>
                 <channelDensityNernst id="Ca_HVA_soma" ionChannel="Ca_HVA" condDensity="2.05006e-05 S_per_cm2" segmentGroup="soma" ion="ca"/>
                 <channelDensityNernst id="Ca_LVA_soma" ionChannel="Ca_LVA" condDensity="0.00456603 S_per_cm2" segmentGroup="soma" ion="ca"/>
+                <spikeThresh value="10mV"/>
                 <specificCapacitance value="8.51603 uF_per_cm2" segmentGroup="soma"/>
                 <specificCapacitance value="9.34469 uF_per_cm2" segmentGroup="axon"/>
                 <specificCapacitance value="0.965264 uF_per_cm2" segmentGroup="apic"/>

diff --git a/CellTypesDatabase/models/ParseAll.py b/CellTypesDatabase/models/ParseAll.py
@@ -211,6 +211,10 @@
 
     membrane_properties = neuroml.MembraneProperties()
 
+    # 10mV is default for Neuron spike threshold in NetCon
+    # https://www.neuron.yale.edu/neuron/static/py_doc/modelspec/programmatic/network/netcon.html
+    membrane_properties.spike_threshes.append(neuroml.SpikeThresh(value="10mV", segment_groups='all'))
+
     if all_active:
         for sc in cell_info["genome"]:
             if sc["name"] == "cm":