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Point process not located in a section
Posted: Tue Nov 20, 2018 6:35 am
by Krishna Chaitanya
Hi,
When I use integrate and fire model template in NetPyNE through importing class, and when I try to simulate it, I get an error "Point process not located in a section".
This typically happens during association of gid to a pointer i.e., NetCon(pointer, None).
However, I used to do the same in NEURON using h.NetCon(pointer, None, sec=<sec>). There's no error in this case.
I do not understand why NetPyNE throws an error when using the same template.
Re: Point process not located in a section
Posted: Thu Nov 22, 2018 1:41 pm
by salvadord
Hi Krishna,
Could you please share your code so we can look at the details? If it's not too long you can post it here. Alternatively you can share the link to a repo (eg. in Github) or send it to me by email (
salvadordura@gmail.com).
Thanks
Re: Point process not located in a section
Posted: Fri Nov 23, 2018 10:37 am
by Krishna Chaitanya
Hello,
Here's the script I used to simulate
Code: Select all
from netpyne import specs, sim
# Network parameters
netParams = specs.NetParams() # object of class NetParams to store the network parameters
netParams.popParams['Izhi03a_pop'] = {'cellType': 'PYR', 'numCells': 100, 'cellModel': 'Izhike'}
cellRule = netParams.importCellParams(label='PYR_Izhi03a_rule', conds={'cellType': 'PYR', 'cellModel':'Izhike'},
fileName='GrCTemp.py', cellName='granule')
netParams.renameCellParamsSec('PYR_Izhi03a_rule', 'sec', 'soma') # rename imported section 'sec' to 'soma'
cellRule['secs']['soma']['pointps']['Granule_0']['vref'] = 'vv' # specify that uses its own voltage V
# Stimulation parameters
netParams.stimSourceParams['bkg'] = {'type': 'NetStim', 'rate': 50, 'noise': 0.1}
netParams.stimTargetParams['bg2'] = {'source': 'bkg', 'conds': {'cellType': 'PYR', 'cellModel': ['Izhike']},
'weight': 9, 'delay': 5, 'sec': 'soma'}
## Connectivity params
# Simulation options
simConfig = specs.SimConfig() # object of class SimConfig to store simulation configuration
simConfig.duration = 1*1e3 # Duration of the simulation, in ms
simConfig.dt = 0.025 # Internal integration timestep to use
simConfig.verbose = 0 # Show detailed messages
simConfig.threshold=-42
simConfig.recordTraces = {'V_soma':{'sec':'soma', 'loc':0.5, 'var':'vv'}} # Dict with traces to record
simConfig.recordStep = 0.1 # Step size in ms to save data (eg. V traces, LFP, etc)
simConfig.filename = 'model_output' # Set file output name
simConfig.savePickle = True # Save params, network and sim output to pickle file
simConfig.analysis['plotRaster'] = True#{True, 'saveFig': 'tut_import_raster.png'} # Plot a raster
simConfig.analysis['plotTraces'] = {'include': [1], 'saveFig':'plotvoltage.png'} # Plot recorded traces for this list of cells
My model has a internal threshold of -42, which means if the voltage crosses the threshold -42, it should generate a spike.
After simulation, the raster plot doesn't show anything because there are no spikes recorded.
I don't understand where I am going wrong.
Kindly let me know if there are any errors in the script I have used.
Thank you.
Re: Point process not located in a section
Posted: Thu Nov 29, 2018 11:26 am
by salvadord
Thanks Krishna. I need the GrCTemp.py to actually test the model. You can paste it here or email to
salvadordura@gmail.com
Re: Point process not located in a section
Posted: Fri Nov 30, 2018 1:46 am
by Krishna Chaitanya
Hi,
I have sent an email with the cell template.
The template is for a detailed model. Is there a possibility to export cell positions from hdf5 and set it in the model? I have predefined cell positions in hdf5.
Kindly let me know.
Thank you.