A multilayer cortical model to study seizure propagation across microdomains (Basu et al. 2015)

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Accession:206238
A realistic neural network was used to simulate a region of neocortex to obtain extracellular LFPs from ‘virtual micro-electrodes’ and produce test data for comparison with multisite microelectrode recordings. A model was implemented in the GENESIS neurosimulator. A simulated region of cortex was represented by layers 2/3, 5/6 (interneurons and pyramidal cells) and layer 4 stelate cells, spaced at 25 µm in each horizontal direction. Pyramidal cells received AMPA and NMDA inputs from neighboring cells at the basal and apical dendrites. The LFP data was generated by simulating 16-site electrode array with the help of ‘efield’ objects arranged at the predetermined positions with respect to the surface of the simulated network. The LFP for the model is derived from a weighted average of the current sources summed over all cellular compartments. Cell models were taken from from Traub et al. (2005) J Neurophysiol 93(4):2194-232.
References:
1 . Basu I, Kudela P, Korzeniewska A, Franaszczuk PJ, Anderson WS (2015) A study of the dynamics of seizure propagation across micro domains in the vicinity of the seizure onset zone. J Neural Eng 12:046016 [PubMed]
2 . Basu I, Kudela P, Anderson WS (2014) Determination of seizure propagation across microdomains using spectral measures of causality. Conf Proc IEEE Eng Med Biol Soc 2014:6349-52 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex U1 L5B pyramidal pyramidal tract GLU cell; Thalamus reticular nucleus GABA cell; Neocortex spiking low threshold (LTS) neuron; Neocortex spiking regular (RS) neuron; Neocortex layer 2-3 interneuron; Neocortex layer 5 interneuron;
Channel(s): I Na,p; I Na,t; I K; I A; I M; I h; I K,Ca; I A, slow; I L high threshold; I T low threshold; I Calcium;
Gap Junctions: Gap junctions;
Receptor(s): AMPA; GabaA; NMDA;
Gene(s):
Transmitter(s): Glutamate; Gaba; Amino Acids;
Simulation Environment: GENESIS;
Model Concept(s): Activity Patterns; Epilepsy;
Implementer(s): Anderson, WS ; Kudela, Pawel ;
Search NeuronDB for information about:  Thalamus reticular nucleus GABA cell; Neocortex U1 L5B pyramidal pyramidal tract GLU cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; GabaA; AMPA; NMDA; I Na,p; I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I h; I K,Ca; I Calcium; I A, slow; Amino Acids; Gaba; Glutamate;
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BasuEtAl2015
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ModelDescription.pdf
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P6RSd_P6RSc.g
P6RSd_P6RSd.g
P6RSd_P6RSd_Gap.g
P6RSd_raninput.g
P6RSd_ST4RS.g
P6RSd_synapsedefs.g
P6RSd_TCR.g
P6RSdcell3Dpk.p
P6RSdchanpk.g
P6RSdprotodefs.g
P6RSsyncond.g
pgenesis_command
protodefs.g
protospikeB23FS.g
protospikeB5FS.g
protospikeC23FS.g
protospikeC5FS.g
protospikeI23LTS.g
protospikeI5LTS.g
protospikenRT.g
protospikeP23FRBa.g
protospikeP23RSa.g
protospikeP23RSb.g
protospikeP23RSc.g
protospikeP23RSd.g
protospikeP5IBa.g
protospikeP5IBb.g
protospikeP5IBc.g
protospikeP5IBd.g
protospikeP5RSa.g
protospikeP6RSa.g
protospikeP6RSb.g
protospikeP6RSc.g
protospikeP6RSd.g
protospikeST4RS.g
protospikeTCR.g
randominputdefs.g
spikedefs.g
ST4RS.g
ST4RS_B23FS.g
ST4RS_B5FS.g
ST4RS_C23FS.g
ST4RS_C5FS.g
ST4RS_I23LTS.g
ST4RS_I5LTS.g
ST4RS_P23FRBa.g
ST4RS_P23RSa.g
ST4RS_P23RSb.g
ST4RS_P23RSc.g
ST4RS_P23RSd.g
ST4RS_P5IBa.g
ST4RS_P5IBb.g
ST4RS_P5IBc.g
ST4RS_P5IBd.g
ST4RS_P5RSa.g
ST4RS_P6RSa.g
ST4RS_P6RSb.g
ST4RS_P6RSc.g
ST4RS_P6RSd.g
ST4RS_raninput.g
ST4RS_ST4RS.g
ST4RS_ST4RS_Gap.g
ST4RS_synapsedefs.g
ST4RScell3Dpk.p
ST4RSchanpk.g
ST4RSprotodefs.g
ST4RSsyncond.g
synapticdelays.g *
synapticprobsTraub.g
synchansB23FS.g *
synchansB5FS.g *
synchansC23FS.g *
synchansC5FS.g *
synchansI23LTS.g *
synchansI5LTS.g *
synchansnRT.g *
synchansP23FRBa.g *
synchansP23RSa.g *
synchansP23RSb.g *
synchansP23RSc.g *
synchansP23RSd.g *
synchansP5IBa.g *
synchansP5IBb.g *
synchansP5IBc.g *
synchansP5IBd.g *
synchansP5RSa.g *
synchansP6RSa.g *
synchansP6RSb.g *
synchansP6RSc.g *
synchansP6RSd.g *
synchansSPIKEs.g *
synchansSPIKEs_base.g
synchansST4RS.g
synchansTCR.g *
syncond.g
syncond2.g
TCR.g
TCR_B23FS.g
TCR_B5FS.g
TCR_C23FS.g
TCR_C5FS.g
TCR_nRT.g
TCR_P23FRBa.g
TCR_P23RSa.g
TCR_P23RSb.g
TCR_P23RSc.g
TCR_P23RSd.g
TCR_P5IBa.g
TCR_P5IBb.g
TCR_P5IBc.g
TCR_P5IBd.g
TCR_P5RSa.g
TCR_P6RSa.g
TCR_P6RSb.g
TCR_P6RSc.g
TCR_P6RSd.g
TCR_raninput.g
TCR_ST4RS.g
TCR_synapsedefs.g
TCRcellpk.p
TCRchanpk.g
TCRprotodefs.g
TCRsyncond.g
                            
// netparams.g - defining Network cell spacings and numbers

float SEPX = 25e-6
float SEPY = 25e-6

float NX = 8 
float NY = 8 

float	P23RSa_SEPX = SEPX
float	P23RSa_SEPY = SEPY
float	P23RSa_NX = NX
float	P23RSa_NY = NY

float	P23RSb_SEPX = SEPX
float	P23RSb_SEPY = SEPY
float	P23RSb_NX = NX
float	P23RSb_NY = NY

float	P23RSc_SEPX = SEPX
float	P23RSc_SEPY = SEPY
float	P23RSc_NX = NX
float	P23RSc_NY = NY

float	P23RSd_SEPX = SEPX
float	P23RSd_SEPY = SEPY
float	P23RSd_NX = NX
float	P23RSd_NY = NY

float	B23FS_SEPX = SEPX
float	B23FS_SEPY = SEPY
float	B23FS_NX = NX
float	B23FS_NY = NY

float	P5IBa_SEPX = SEPX
float	P5IBa_SEPY = SEPY
float	P5IBa_NX = NX
float	P5IBa_NY = NY

float	P5IBb_SEPX = SEPX
float	P5IBb_SEPY = SEPY
float	P5IBb_NX = NX
float	P5IBb_NY = NY

float	P5IBc_SEPX = SEPX
float	P5IBc_SEPY = SEPY
float	P5IBc_NX = NX
float	P5IBc_NY = NY

float	P5IBd_SEPX = SEPX
float	P5IBd_SEPY = SEPY
float	P5IBd_NX = NX
float	P5IBd_NY = NY

float	B5FS_SEPX = SEPX
float	B5FS_SEPY = SEPY
float	B5FS_NX = NX
float	B5FS_NY = NY

float	P6RSa_SEPX = SEPX
float	P6RSa_SEPY = SEPY
float	P6RSa_NX = NX
float	P6RSa_NY = NY

float	P6RSb_SEPX = SEPX
float	P6RSb_SEPY = SEPY
float	P6RSb_NX = NX
float	P6RSb_NY = NY

float	P6RSc_SEPX = SEPX
float	P6RSc_SEPY = SEPY
float	P6RSc_NX = NX
float	P6RSc_NY = NY

float	P6RSd_SEPX = SEPX
float	P6RSd_SEPY = SEPY
float	P6RSd_NX = NX
float	P6RSd_NY = NY

float	C23FS_SEPX = SEPX
float	C23FS_SEPY = SEPY
float	C23FS_NX = NX
float	C23FS_NY = NY

float	C5FS_SEPX = SEPX
float	C5FS_SEPY = SEPY
float	C5FS_NX = NX
float	C5FS_NY = NY

float	ST4RS_SEPX = SEPX
float	ST4RS_SEPY = SEPY
float	ST4RS_NX = NX
float	ST4RS_NY = NY

float	I23LTS_SEPX = SEPX
float	I23LTS_SEPY = SEPY
float	I23LTS_NX = NX
float	I23LTS_NY = NY

float	I5LTS_SEPX = SEPX
float	I5LTS_SEPY = SEPY
float	I5LTS_NX = NX
float	I5LTS_NY = NY

float	TCR_SEPX = SEPX
float	TCR_SEPY = SEPY
float	TCR_NX = NX
float	TCR_NY = NY

float	nRT_SEPX = SEPX
float	nRT_SEPY = SEPY
float	nRT_NX = NX
float	nRT_NY = NY

if ({columntype == 0 })

     float	P23FRBa_SEPX = SEPX
     float	P23FRBa_SEPY = SEPY
     float	P23FRBa_NX = NX
     float	P23FRBa_NY = NY

end

if ({columntype == 1 })

     float	P23FRBa_SEPX = {SEPX}*2
     float	P23FRBa_SEPY = {SEPY}*2
     float	P23FRBa_NX = {NX}/2
     float	P23FRBa_NY = {NY}/2

end

float	P5RSa_SEPX = SEPX
float	P5RSa_SEPY = SEPY
float	P5RSa_NX = NX
float	P5RSa_NY = NY

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