3D model of the olfactory bulb (Migliore et al. 2014)

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Accession:151681
This entry contains a link to a full HD version of movie 1 and the NEURON code of the paper: "Distributed organization of a brain microcircuit analysed by three-dimensional modeling: the olfactory bulb" by M Migliore, F Cavarretta, ML Hines, and GM Shepherd.
Reference:
1 . Migliore M, Cavarretta F, Hines ML, Shepherd GM (2014) Distributed organization of a brain microcircuit analyzed by three-dimensional modeling: the olfactory bulb. Front Comput Neurosci 8:50 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Channel/Receptor; Dendrite;
Brain Region(s)/Organism: Olfactory bulb;
Cell Type(s): Olfactory bulb main mitral GLU cell; Olfactory bulb main interneuron granule MC GABA cell;
Channel(s): I Na,t; I A; I K;
Gap Junctions:
Receptor(s): NMDA; Glutamate; Gaba;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Pattern Recognition; Activity Patterns; Bursting; Temporal Pattern Generation; Oscillations; Synchronization; Active Dendrites; Detailed Neuronal Models; Synaptic Plasticity; Action Potentials; Synaptic Integration; Unsupervised Learning; Olfaction;
Implementer(s): Hines, Michael [Michael.Hines at Yale.edu]; Migliore, Michele [Michele.Migliore at Yale.edu]; Cavarretta, Francesco [francescocavarretta at hotmail.it];
Search NeuronDB for information about:  Olfactory bulb main mitral GLU cell; Olfactory bulb main interneuron granule MC GABA cell; NMDA; Glutamate; Gaba; I Na,t; I A; I K;
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bulb3d
readme.html
ampanmda.mod *
distrt.mod *
fi.mod *
kamt.mod *
kdrmt.mod *
naxn.mod *
ThreshDetect.mod *
all2all.py *
balance.py *
bindict.py
BulbSurf.py
colors.py *
common.py
complexity.py *
custom_params.py *
customsim.py
destroy_model.py *
determine_connections.py
distribute.py *
fig7.py
fixnseg.hoc *
getmitral.py
gidfunc.py *
glom.py
granule.hoc *
granules.py
input-odors.txt *
loadbalutil.py *
lpt.py *
mayasyn.py
mgrs.py
misc.py
mitral.hoc *
mitral_dend_density.py
mkmitral.py
modeldata.py *
multisplit_distrib.py *
net_mitral_centric.py
odordisp.py *
odors.py *
odorstim.py
params.py
parrun.py
realgloms.txt *
runsim.py
split.py *
util.py *
weightsave.py *
                            
begintemplate GranuleSpine
public head, neck, all
create head, neck
objref all
proc init() {
	all = new SectionList()
	head all.append()
	neck all.append()
	connect head(0), neck(1)
	neck { L = 2  diam = .2 }
	head { L = 1  diam = 1 }
	memb()
}
proc memb() {
	forsec all {
		insert pas 
		insert kamt gbar_kamt=0.008 ek=-90
		insert nax gbar_nax=0.02 sh_nax=15 ena=60
		Ra = 80
		cm = 1
		g_pas = 1/30000
		e_pas = -65
		ek = -90
	}
}
endtemplate GranuleSpine

begintemplate Granule

public soma, priden, priden2, external_syn
public prilist
public position, x, y, z
objref external_syn

//create soma, priden2[3], priden
create soma, priden2[1], priden

objref prilist

proc init() {
	npri = 1
	create priden2[npri]
	prilist = new SectionList()
	priden prilist.append()
	for i=0, npri-1 priden2[i] { prilist.append() }
topol()
geometry()
segments()
memb()
	x = y = z = 0 // only change via position
}


proc topol() {local i
	connect priden(0), soma(1)
	for i=0, npri-1 {connect priden2[i](0), priden(.8)}
}

proc segments() {local i
	soma.nseg= 1
	forsec "priden" nseg = 10
}

proc geometry() {local i
	basic_shape()
	soma { L = 8  diam = 8}
	priden {L=150 diam=.5}
	for i=0, npri-1 {priden2[i] {L=100 diam=.4}}
//	define_shape()
}
	
proc basic_shape() {local i
  soma {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(0, 1, 0, 1)}
  priden {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(0, 1, 0, 1)}
  for i=0,npri-1 {
	priden2[i] {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(i/npri, 1, 0, 1)}
  }
}

proc memb() {
	forall {
		insert pas 
		insert kamt gbar_kamt=0.008 ek=-90
		insert nax gbar_nax=0.02 sh_nax=15 ena=60
		Ra = 80
		cm = 1
		g_pas = 1/30000
		e_pas = -65
		ek = -90
	}

	soma {
		gbar_nax=0.04
       		insert kdrmt gbar_kdrmt=0.006
		gbar_kamt = 0.004
		cm = 4
		g_pas = cm/30000
	}

	forsec prilist {
		cm = 4
		g_pas = cm/30000
	}
	 soma {
                external_syn = new Exp2Syn(.5)
                external_syn.e=0
                external_syn.tau1 = 5
                external_syn.tau2 = 50  
            }
	
}

proc position() { local i
  soma for i = 0, n3d()-1 {
    pt3dchange(i, $1-x+x3d(i), $2-y+y3d(i), $3-z+z3d(i), diam3d(i))
  }
  x = $1  y = $2  z = $3
}

endtemplate Granule

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