Olfactory bulb mitral and granule cell column formation (Migliore et al. 2007)

 Download zip file   Auto-launch 
Help downloading and running models
Accession:114665
In the olfactory bulb, the processing units for odor discrimination are believed to involve dendrodendritic synaptic interactions between mitral and granule cells. There is increasing anatomical evidence that these cells are organized in columns, and that the columns processing a given odor are arranged in widely distributed arrays. Experimental evidence is lacking on the underlying learning mechanisms for how these columns and arrays are formed. We have used a simplified realistic circuit model to test the hypothesis that distributed connectivity can self-organize through an activity-dependent dendrodendritic synaptic mechanism. The results point to action potentials propagating in the mitral cell lateral dendrites as playing a critical role in this mechanism, and suggest a novel and robust learning mechanism for the development of distributed processing units in a cortical structure.
Reference:
1 . Migliore M, Inzirillo C, Shepherd GM (2007) Learning mechanism for column formation in the olfactory bulb. Front Integr Neurosci 1:12 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
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): AMPA; NMDA; Gaba;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Activity Patterns; Dendritic Action Potentials; Active Dendrites; Detailed Neuronal Models; Synaptic Plasticity; Long-term Synaptic Plasticity; Action Potentials; Learning; Olfaction;
Implementer(s): Migliore, Michele [Michele.Migliore at Yale.edu];
Search NeuronDB for information about:  Olfactory bulb main mitral GLU cell; Olfactory bulb main interneuron granule MC GABA cell; AMPA; NMDA; Gaba; I Na,t; I A; I K; Gaba; Glutamate;
/
plast
readme.html
kamt.mod *
kdrmt.mod *
naxn.mod *
nmdanetOB.mod *
2mc-w05-w00-e2i3-int220.hoc
2mt-s1-w05-w00-e2i3-int220.txt
2mt-s2-w05-w00-e2i3-int220.txt
2mt-s4-w05-w00-e2i3-int220.txt
gc-plast.hoc
mitral-plast-2.hoc
mosinit.hoc
plasticity-disp.hoc
screenshot.jpg
trace-gc0dend0-w05-w00-e2i3-int220.txt
trace-gc33dend0-w05-w00-e2i3-int220.txt
trace-mt0dend066-w05-w00-e2i3-int220.txt
trace-mt0soma05-w05-w00-e2i3-int220.txt
trace-time-w05-w00-e2i3-int220.txt
                            
load_file("nrngui.hoc")

objref b,b2,s1,f,b3,b4,b5,tr,tr1,tr2,tr3,e,final,ats1,ats2,ats4,b6,b7
objref tracetime,tracemt0,tracegc0,tracegc33,tracemt0dend066
objref outfile1, outfile2, outfile4, outtrace1, outtrace2,outtrace3,outtrace4,outtrace5
objref index1,index2,index4,times1,times2,times4,timespikeints1,timespikeints2,timespikeints4,sinweights1,sinweights2,sinweights4,sigmoidmt0,sigmoidmt1,sigmoid,sigmoida

objref distrs1,distrs2,distrs4,distryf,distrx,distrxs1, distrys1, distrxs2, distrys2, distrxs4, distrys4,distrts1,distrts2,distrts4
objref sinindex,sinie,sintime,sin1,sin2,sin4,temp,temp1
double nc[300],nc1[300],nct1[300],nct2[300],nct3[300],nct4[300]
objref distrs1,distrs2,distrs4
objref temptime,tracetimetemp,tracemt0temp,tracegc0temp,tracemt0d66temp,tracegc33temp
objref obj


obj=new StringFunctions()

outfile1 = new File()
outfile2 = new File()
outfile4 = new File()

outtrace1 = new File()
outtrace2 = new File()
outtrace3 = new File()
outtrace4 = new File()
outtrace5 = new File()



index1 = new Vector()
index2 = new Vector()
index4 = new Vector()

times1 = new Vector()
times2 = new Vector()
times4 = new Vector()

timespikeints1 =new Vector()
timespikeints2 =new Vector()
timespikeints4 =new Vector()

sigmoidmt0=new Vector()
sigmoidmt1=new Vector()
sigmoid=new Vector()

sinweights1= new Vector()
sinweights2= new Vector()
sinweights4= new Vector()





distrx = new Vector(50)
distryf = new Vector()
distrs1 = new Vector(50)
distrs2 = new Vector(50)
distrs4 = new Vector(50)

distrxs1 = new Vector()
distrys1 = new Vector()
distrxs2 = new Vector()
distrys2 = new Vector()
distrxs4 = new Vector()
distrys4 = new Vector()
distrts1 = new Vector()
distrts2 = new Vector()
distrts4 = new Vector()

func plast() {
	return (1-(1/(1+exp(($1-25)/3))))
}

proc loadsyn(){
	
	strdef pt,pths1,pths2,pths4,ptht1,ptht2,ptht3,ptht4,ptht5,sig,pthin,pthres,pths1r,pths2r,pths4r,ptht1r,ptht2r,ptht3r,ptht4r,ptht5r
	sig="sig"
	
	for (k=0;k<50;k=k+1){
		nc1[1+k*6]=0
		nc1[2+k*6]=0
		nc1[4+k*6]=0
		nc[1+k*6]=0
		nc[2+k*6]=0
		nc[4+k*6]=0
		
	}
	
	pthres=$s1
	obj.right($s1,7)
	
	
	obj.left($s1,obj.len($s1)-4)
	pt=$s1
	if(obj.substr(pthres,"r.") != -1){
		print "restart"
		obj.left($s1,obj.len($s1)-1)
	}
	print $s1
	sprint(pths1,"2mt-s1-%s.txt",$s1)
	sprint(pths2,"2mt-s2-%s.txt",$s1)
	sprint(pths4,"2mt-s4-%s.txt",$s1)
	sprint(ptht1,"trace-time-%s.txt",$s1)
	sprint(ptht2,"trace-mt0soma05-%s.txt",$s1)
	sprint(ptht3,"trace-gc0dend0-%s.txt",$s1)
	sprint(ptht4,"trace-mt0dend066-%s.txt",$s1)
	sprint(ptht5,"trace-gc33dend0-%s.txt",$s1)
	

	if(obj.substr($s1,"sig") != -1){
		print "sig"
		sprint(pthin,"%sinit.txt",$s1)
		
		dispin(pthin)
		doNotify()
		
	}
	
	trace(ptht1,ptht2,ptht3,ptht4,ptht5)
	load(pths1,pths2,pths4)
	
}

proc trace(){
	outtrace1.ropen($s1)
	outtrace2.ropen($s2)
	outtrace3.ropen($s3)
	outtrace4.ropen($s4)
	outtrace5.ropen($s5)
	
	
	print "reading"
	
	tracesize=outtrace1.scanvar()
	
	temptime= new Vector()
	tracetimetemp= new Vector()
	tracemt0temp= new Vector()
	tracegc0temp=new Vector()
	tracemt0d66temp=new Vector()
	tracegc33temp=new Vector()
	
	tracetime = new Vector(tracesize)
	tracemt0 = new Vector(tracesize)
	tracegc0 = new Vector(tracesize)
	tracemt0dend066 = new Vector(tracesize)
	tracegc33= new Vector(tracesize)
	
	tracetime.scanf(outtrace1,tracesize)
	print "loaded trace1"
	tracemt0.scanf(outtrace2,tracesize)
	print "loaded trace2"
	tracegc0.scanf(outtrace3,tracesize)
	print "loaded trace3"
	tracemt0dend066.scanf(outtrace4,tracesize)
	print "loaded trace4"
	tracegc33.scanf(outtrace5,tracesize)
	print "loaded trace5"
	print "loaded"
	start=0
}

proc load(){
	print " reading ...\n",$s1,"...\n",$s2,"...\n",$s3,"...\n"
	outfile1.ropen($s1)
	outfile2.ropen($s2)
	outfile4.ropen($s3)
	if (!outfile1.eof()){
		outfile1.ropen($s1)
		index1.scanf(outfile1, 1, 5)
		outfile1.close()
		outfile1.ropen($s1)
		times1.scanf(outfile1, 2, 5)
		outfile1.close()
		outfile1.ropen($s1)
		timespikeints1.scanf(outfile1, 3, 5)
		outfile1.close()
		outfile1.ropen($s1)
		sigmoidmt0.scanf(outfile1, 4, 5)
		outfile1.close()
		outfile1.ropen($s1)
		sinweights1.scanf(outfile1, 5, 5)
		sigmoidmt0.apply("plast")
		sigmoidmt0.mul(1.e-3)
		sigmoidmt0.mul(synstr)
		sigmoidmt0.div(2e-3)
		print "loaded syn1"
	} else {
		index1.resize(0)
		times1.resize(0)
		timespikeints1.resize(0)
		sinweights1.resize(0)
		sigmoidmt0.resize(0)
	}
	if (!outfile2.eof()){
		outfile2.ropen($s2)
		index2.scanf(outfile2, 1, 5)
		outfile2.close()
		outfile2.ropen($s2)
		times2.scanf(outfile2, 2, 5)
		outfile2.close()
		outfile2.ropen($s2)
		timespikeints2.scanf(outfile2, 3, 5)
		outfile2.close()
		outfile2.ropen($s2)
		sigmoid.scanf(outfile2, 4, 5)
		outfile2.close()
		outfile2.ropen($s2)
		sinweights2.scanf(outfile2, 5, 5)
		sigmoid.apply("plast")
		sigmoid.mul(1.e-3)
		sigmoid.mul(inh)
		sigmoid.div(3e-3)
		print "loaded syn2"
	}else {
		index2.resize(0)
		times2.resize(0)
		timespikeints2.resize(0)
		sinweights2.resize(0)
		sigmoid.resize(0)
	}
	if (!outfile4.eof()){
		outfile4.ropen($s3)
		index4.scanf(outfile4, 1, 5)
		outfile4.close()
		outfile4.ropen($s3)
		times4.scanf(outfile4, 2, 5)
		outfile4.close()
		outfile4.ropen($s3)
		timespikeints4.scanf(outfile4, 3, 5)
		outfile4.close()
		outfile4.ropen($s3)
		sigmoidmt1.scanf(outfile4, 4, 5)
		outfile4.close()
		outfile4.ropen($s3)
		sinweights4.scanf(outfile4, 5, 5)
		sigmoidmt1.apply("plast")
		sigmoidmt1.mul(1.e-3)
		sigmoidmt1.mul(synstr)
		print "loaded syn4"
	} else {
		index4.resize(0)
		times4.resize(0)
		timespikeints4.resize(0)
		sinweights4.resize(0)
		sigmoidmt1.resize(0)
	}
	sinsize=index1.size()+index2.size()+index4.size()
	sin1=new Vector(index1.size())
	sin2=new Vector(index2.size())
	sin4=new Vector(index4.size())
	sinie=new Vector()
	sin1.add(1)
	sin2.add(2)
	sin4.add(4)
	sinie.append(sin1)
	sinie.append(sin2)
	sinie.append(sin4)
	sigmoida=new Vector()
	sigmoida.append(sigmoidmt0)
	sigmoida.append(sigmoid)
	sigmoida.append(sigmoidmt1)
	sinindex= new Vector()
	sintime= new Vector()
	
	sinindex.append(index1)
	sinindex.append(index2)
	sinindex.append(index4)
	sintime.append(times1)
	sintime.append(times2)
	sintime.append(times4)
	temp=new Vector(sinsize)
	temp=sintime.sortindex()
	temp1=new Vector()
	ind=0
	for(i=0;i<temp.size();i=i+1){
		while (tracetime.x[ind]<=sintime.x[temp.x[i]]){
					ind=ind+1
				}
				temp1.append(ind)
				
		
	}
	print "loaded"
}






proc disp(){
	
	closeAll()
	distrys1.resize(0)
	distrxs1.resize(0)
	distrts1.resize(0)
	distrys2.resize(0)
	distrxs2.resize(0)
	distrts2.resize(0)
	distrys4.resize(0)
	distrxs4.resize(0)
	distrts4.resize(0)
	
	
	
	b2= new VBox()
	b2.intercept(1)
	
	
	
	xpanel("")
	
	xvalue("synapse")
	
	xbutton("display synapse", "disp1()")
	
	xpanel()
	//xpanel("",1)
	
	
	
	s1 = new Graph()
	
	b2.intercept(0)
	b2.map(pt, 0, 0, 240, 620)
        disp1()
}


proc disp1(){	
        
	
	s1.erase()
	distrys1.resize(0)
	distrxs1.resize(0)
	distrts1.resize(0)
	distrys2.resize(0)
	distrxs2.resize(0)
	distrts2.resize(0)
	distrys4.resize(0)
	distrxs4.resize(0)
	distrts4.resize(0)
	
	
	s1.size(0,10000, 0,1)
	s1.xaxis(1)
	s1.exec_menu("10% Zoom out")
	s1.label(0.5,0.75," mitral->GC (exc)",2,1,0.4,0.4,1)
	s1.label(0.5,0.70," GC->mitral (inh)",2,1,0.4,0.4,3)

	for (i=0;i<index1.size();i=i+1){ 
		
		if (index1.x[i] == synapse){
			
			distrys1.append(sigmoidmt0.x[i])
			distrxs1.append(times1.x[i])
			
		}
	}
	for (i=0;i<index2.size();i=i+1){ 
			
	
		if (index2.x[i] == synapse){
			
			
			distrys2.append(sigmoid.x[i])
			distrxs2.append(times2.x[i])
			
			
		}
	}
	for (i=0;i<index4.size();i=i+1){ 
		if (index4.x[i] == synapse){
			distrys4.append(sigmoidmt1.x[i])
			distrxs4.append(times4.x[i])
		}
		
	}
	
	distrys1.line(s1,distrxs1,1,2)
	distrys2.line(s1,distrxs2,3,2)
//	distrys4.mark(s1,distrxs4,"O",6,2)
	s1.flush()
	
}



proc evolution(){
	closeAll()
	for k=0,49{
		distrs1.x[k]=nc1[1+k*6]
		distrs2.x[k]=nc1[2+k*6]
		distrs4.x[k]=nc1[4+k*6]
		
		
		distrx.x[k]=k*10
	}
	go=0
	bool=0
	bool1=0
        start=0
	skip=30
	b4=new VBox()
	b4.intercept(1)
	tr=new Graph()
	
	b4.intercept(0)
	b4.map("mt soma (Fig.2b)",0,0,300,200)
	
	b6=new VBox()
	b6.intercept(1)
	tr2=new Graph()
	
	b6.intercept(0)
	b6.map("mt0 dend (Fig.2c)",820,0,300,200)
	
	
	b3 = new VBox()
	b3.intercept(1)
	
	
	tr.size(0,10000,-70, 50)
	
	xpanel("",1)
	e = new Graph()
	e.size(0,50,0,1)
	e.erase()
	
	interval=500
	time=0
	xvalue("time")
	xvalue("skip")
	xvalue("time window", "interval")
        xbutton("play", "play()")
	xbutton("pause", "pause()")
        xbutton("close", "closeEvol()")
	xpanel()
	b3.intercept(0)
	b3.map(pt)
	b5=new HBox()
	b5.intercept(1)
	tr1=new Graph()
	
	
	
	b5.intercept(0)
	b5.map("gc (Fig.2b)",0,540,300,200)
	
	b7=new HBox()
	b7.intercept(1)
	
	tr3=new Graph()
	
	
	b7.intercept(0)
	b7.map("gc (Fig.2c)",820,540,300,200)
	tr1.size(0,10000,-70, 50)
	tr.label(5000, 30, "mt0")
	tr2.label(5000, 30, "mt0dend66")
	tr1.label(5000, 30, "gc0")
	tr3.label(5000, 30, "gc33")
	tr2.size(0,10000,-70, 50)
	tr3.size(0,10000,-70, 50)
	tr.xaxis(3)
	tr1.xaxis(3)
	tr2.xaxis(3)
	tr3.xaxis(3)

	distrs1.mark(e,distrx,"S",9,1)
	distrs2.mark(e,distrx,"O",6,3)
	play()
}

proc pause(){
	
	bool=1
	bool1=0
	
}

proc play(){

bool1=bool1+1
if (bool1 < 2 && bool == 0){

	
	

for (i=go;i<sintime.size();i=i+1){
		
		time=sintime.x[temp.x[i]]
		
		if (sinie.x[temp.x[i]]==1){
			index=sinindex.x[temp.x[i]]
			peso=sigmoida.x[temp.x[i]]
			
			distrs1.x[index]=peso
			
			
		}
		if (sinie.x[temp.x[i]]==2){
			index=sinindex.x[temp.x[i]]
			peso=sigmoida.x[temp.x[i]]
			
			distrs2.x[index]=peso
			
		}
		if (sinie.x[temp.x[i]]==4){
			index=sinindex.x[temp.x[i]]
			peso=sigmoida.x[temp.x[i]]
		
			distrs4.x[index]=peso
			
		}
		 

		if ((i-(int(i/skip)*skip)) == 0 ){
	
		tracedisp(i)
		dispevol()
		doNotify()
		} 
		
		if(i==sintime.size()-1){
			dispevol()
			doNotify()
			for k=0,49{
				distrs1.x[k]=nc1[1+k*6]
				distrs2.x[k]=nc1[2+k*6]
				distrs4.x[k]=nc1[4+k*6]
				start=0
			    tracetimetemp.resize(0)
				tracemt0temp.resize(0)
	
				tracemt0temp.resize(0)
				tracegc0temp.resize(0)
				tracemt0d66temp.resize(0)
				tracegc33temp.resize(0)
			}
			go=0
                        bool1=0
			print go
		}
		if(bool==1){
			bool=0
                        
			go=i
			i=sintime.size()-1
			print go
		}

	}
	}

}

proc tracedisp() {	
	
	
	
	
	tr.size(tracetime.x[start]-interval,tracetime.x[temp1.x[$1]], -70,50)
	tr1.size(tracetime.x[start]-interval,tracetime.x[temp1.x[$1]], -70,50)
	tr2.size(tracetime.x[start]-interval,tracetime.x[temp1.x[$1]], -70,50)
	tr3.size(tracetime.x[start]-interval,tracetime.x[temp1.x[$1]], -70,50)
	
	tr.flush
	tr1.flush
	tr2.flush
	tr3.flush
	
	tracetimetemp=tracetime.at(start,temp1.x[$1])
	tracemt0temp=tracemt0.at(start,temp1.x[$1])
	tracetimetemp=tracetime.at(start,temp1.x[$1])
	tracemt0temp=tracemt0.at(start,temp1.x[$1])
	tracegc0temp=tracegc0.at(start,temp1.x[$1])
	tracemt0d66temp=tracemt0dend066.at(start,temp1.x[$1])
	tracegc33temp=tracegc33.at(start,temp1.x[$1])
	
	
	tracemt0temp.line(tr,tracetimetemp,1,0)
	tracegc0temp.line(tr1,tracetimetemp,1,0)
	tracemt0d66temp.line(tr2,tracetimetemp,1,0)
	tracegc33temp.line(tr3,tracetimetemp,1,0)
	
	start=temp1.x[$1]
	
}

proc dispevol() {
	
	e.size(0,500,0,1)
	e.erase()
	e.mark(0,0.0005, "T", 15, 2, 2)
//	e.mark(500,0.0005, "T", 15, 2, 2)
	e.color(2)
	e.beginline()
	e.line(0, 0.0005)
	e.line(500, 0.2)
//	e.beginline()
//	e.line(500, 0.0005)
//	e.line(-5, 0.001)

	distrs1.mark(e,distrx,"S",9,1)
	distrs2.mark(e,distrx,"O",6,3)
	
	e.flush
	
}

proc dispfinal(){
	closeAll()
	j=0
	end=0
	end1=0
	end2=0
	end3=0
	while(end<3){
		if(j<index1.size()){
			
			nc[1+index1.x[j]*6]=sigmoidmt0.x[j]
			
		}else{
			end1=1
		}
		if (j<index2.size()){
			
			nc[2+index2.x[j]*6]=sigmoid.x[j]
			
		}else{
			end2=1
		}
		if (j<index4.size()){
			
			nc[4+index4.x[j]*6]=sigmoidmt1.x[j]
			
		}else{
			end3=1
		}
		end=end1+end2+end3
		j=j+1
	}
	final = new Graph()
	final.size(0,500,0,1)
	final.erase()
	final.mark(0,0.0005, "T", 15, 2, 2)
	final.mark(500,0.0005, "T", 15, 2, 2)
	final.color(2)
	final.beginline()
	final.line(0, 0.0005)
	final.line(500, 0.2)
	final.beginline()
	final.line(500, 0.0005)
	final.line(-5, 0.001)
	
   
	distryf.resize(0)
	
	for k=0, 49 {
		distryf.append(nc[1+k*6])
		distrx.x[k]=k*10
	}
	distryf.mark(final,distrx,"S",9,1)
	final.flush()

	
	distryf.resize(0)
	for k=0, 49 {distryf.append(nc[4+k*6]) }
	distryf.mark(final,distrx,"O",6,2)
	final.flush()
	
	
	distryf.resize(0)
	for k=0, 49 {distryf.append(nc[2+k*6])}
	distryf.mark(final,distrx,"O",6,3)
	final.flush()
    
	
	
	
	
}

proc closeAll(){
	objref b2,b3,b4,b5,b6,b7,final
	
}

proc closeEvol(){

	b3.unmap()
	b4.unmap()
	b5.unmap()
	b6.unmap()
	b7.unmap()

}

func max(){
	if ($1 >= $2){
		return ($1)
	}else{
		return ($2)
	}

}

weight=0.5
amp=.03
rel=0.2
inh=3
synstr=2
nmdafactor=0.0035
tracesize=0
b = new VBox()
b.intercept(1)

strdef path1
	
loadsyn("2mt-s1-w05-w00-e2i3-int220.txt")

xpanel("")
xvarlabel(pths1)
xvarlabel(pths2)
xvarlabel(pths4)

go=0
synapse=33
box=-1
xvalue("synapse")
xbutton("synapse time course ", "disp()")
xbutton("traces and weights, Fig. 2b-c","evolution()")
xbutton("final weights", "dispfinal()")

xpanel()



b.intercept(0)
b.map(pt)
//evolution()

outfile1.close()
outfile2.close()
outfile4.close()



Loading data, please wait...