Region-specific atrophy in dendrites (Narayanan, Narayan, Chattarji, 2005)

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Accession:147756
...in this study, we develop an algorithm that uses statistics from precise morphometric analyses to systematically remodel neuronal reconstructions. We use the distribution function of the ratio of two normal distributed random variables to specify the probabilities of remodeling along various regions of the dendritic arborization. We then use these probabilities to drive an iterative algorithm for manipulating the dendritic tree in a region-specific manner. As a test, we apply this framework to a well characterized example of dendritic remodeling: stress-induced dendritic atrophy in hippocampal CA3 pyramidal cells. We show that our pruning algorithm is capable of eliciting atrophy that matches biological data from rodent models of chronic stress. <br>
Reference:
1 . Narayanan R, Narayan A, Chattarji S (2005) A probabilistic framework for region-specific remodeling of dendrites in three-dimensional neuronal reconstructions. Neural Comput 17:75-96 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Dendrite;
Brain Region(s)/Organism: Hippocampus;
Cell Type(s): Hippocampus CA3 pyramidal cell;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: C or C++ program;
Model Concept(s): Influence of Dendritic Geometry;
Implementer(s): Narayanan, Rishikesh [rishi at iisc.ac.in];
Search NeuronDB for information about:  Hippocampus CA3 pyramidal cell;
#include"Prune.h"

/*****************************************************************/

void Prune :: initialize()
{
	int i;
	isRead();
	ShollAnalysis();

	npc=ncomp;
	PruCom=new SWCData[npc];
	for(i=0; i<npc; i++)
		PruCom[i]=Comptmt[i];


	delete(Comptmt);

	getSoma();
	getStems();
	getBP();
	getTP();



	Children=new Subset[npc] ;
	for(i=0; i<npc; i++){
		Children[i].npts=0;
		Children[i].Pts=new int [3];	// Maximum is trifurcation
	}	

	findChildren();

 	//generateSpecs(); exit(1);

	abpprune=new double[sdata.na]; bbpprune=new double[sdata.nb];
	adlprune=new double[sdata.na]; bdlprune=new double[sdata.nb];
	abpP    =new double[sdata.na]; bbpP    =new double[sdata.nb];
	adlP    =new double[sdata.na]; bdlP    =new double[sdata.nb];

	for(i=0; i<sdata.na; i++)		// Amount of initial pruning is zero
		adlprune[i]=abpprune[i]=0;
	for(i=0; i<sdata.nb; i++)
		bdlprune[i]=bbpprune[i]=0;

	cmr=0;	// Reduction in number of compartments
	dlr=0;	// Reduction in dl.

	setZeta(basefilename);
	//setBasalMaxZeta(basefilename);
	setProbabilities();

/* findTPBP requires probabilities to be initialized and hence is called
 * after setProbabilities() */

	TPBP=new int[TP.npts];
	bpPruneP=new double[TP.npts];
	findTPBP();
}

/*****************************************************************/

void Prune :: PruneTree()
{
	int i;
	initialize();
	prune();
//	cerr << "\nNo. of Soma Pts: " << Soma.npts ;
//	cerr << "\nNo. of Stems: " << Stems.npts ;
//	cerr << "\nNo. of BP's: " << BP.npts ;
//	cerr << "\nNo. of TP's: " << TP.npts << endl ;
	char  * filename=new char[35];
	sprintf(filename,"%s_final.swc",outfilename);
	cerr << "\nFinal save in " << filename << " after pruning " 
		<< dlr << " micron of length" << endl ;
	saveSWC(filename);
	
	//printStatus();
}

/*****************************************************************/

void Prune :: prune()
{
	int i;
	struct timeval tv;
	struct timezone tz;
	gettimeofday(&tv,&tz);
	int SEED=tv.tv_usec;
	srand48(SEED);

	int count =0;
	int scount = 1000; // Save for every 1000 um reduction in DL.
	char  * filename=new char[35];

	//while(convmeasure()>0.05){
	while(dlr<dlred){
	//while(dlr<dlsum){
	//while (count < 5000000){
		if(TP.npts==0){
			cerr << "\nNo more to Prune...\n";
			break;
		}	
		for(i=0; i<TP.npts; i++){
			bpPrune(i);
			tpPrune(i);
		}	
		//cerr << count << "\t" << cmr << "\t" << dlr << "\t" 
		//	 << convmeasure() << endl ;
		count ++;
		if(dlr>scount){
			sprintf(filename,"%s_%d.swc",outfilename,scount);
			cerr << "\nSaving file " << filename << " after pruning " 
				<< dlr << " micron of length" << endl ;
			saveSWC(filename);
			scount += 1000;
		}
	}	

	//cerr << "\nReduction in DL: " << dlr ;
	//cerr << "\nReduction in Cmptmt: " << cmr << endl ;
}

/*****************************************************************/
// Prunes TP[i]

void Prune :: tpPrune(int i)
{
	double dist;
	int l;
	int sn;	// Segment number
	int cn;		// Compartment number
	int PRUNE;

	/* BP has been pruned and the number of TP's has been reduced.
	 * So, the value of i will be greater than what is allowed. We
	 * just return back without bothering much as it does not mean
	 * anything */ 

	if(i>(TP.npts-1)){
		return;
	}	

	cn    = TP.Pts[i];
	dist  = 0.0;
	dist += (somax-PruCom[cn].x)*(somax-PruCom[cn].x);
	dist += (somay-PruCom[cn].y)*(somay-PruCom[cn].y);
	dist += (somaz-PruCom[cn].z)*(somaz-PruCom[cn].z);
	dist  = sqrt(dist);
	sn   = (int)(dist/(double)STLENGTH); // Segment where TP[i] belongs
	PRUNE=0;
	if (PruCom[cn].tc==4){	// Apical
		if(drand48()*maxdlP<adlP[sn]) PRUNE=1;
	}
	else if (PruCom[cn].tc==3){	// Basal
		if(drand48()*maxdlP<bdlP[sn]) PRUNE=1;
	}
	else{
		cerr << "\ntpP :: Terminal point is not dendrite!!!\n\n";
		checkTPs();
		cerr <<  i << endl << PruCom[cn] ;
		cerr <<  Children[cn].npts << endl  ;
		for(l=0; l<Children[cn].npts; l++){
			cerr << PruCom[Children[cn].Pts[l]];
		}
		exit(1);
	}	

	if(PRUNE){
		pruneTP(cn,sn);
		//setProbabilities();		// Update probability
		findChildren();			// Update children list
		findTPBP();				// Update TPBP list
	}	
}	

/*****************************************************************/
// Prunes TPBP[i]

void Prune :: bpPrune(int i)
{
	double dist;
	int sn;	// Segment number
	int cn;		// Compartment number
	int PRUNE;
	cn    = TPBP[i];
	
	if(cn==-2) return; // Case where the TP does not end on a BP.
	
	dist  = 0.0;
	dist += (somax-PruCom[cn].x)*(somax-PruCom[cn].x);
	dist += (somay-PruCom[cn].y)*(somay-PruCom[cn].y);
	dist += (somaz-PruCom[cn].z)*(somaz-PruCom[cn].z);
	dist  = sqrt(dist);
	sn   = (int)(dist/(double)STLENGTH); // Segment where TP[i] belongs
	PRUNE=0;
	if (PruCom[cn].tc==4){	// Apical
		//if(drand48()*maxdlP<(bpPruneP[i]*abpP[sn])) PRUNE=1;
		if(drand48()*maxdlP<bpPruneP[i]) PRUNE=1;
	}
	else if (PruCom[cn].tc==3){	// Basal
		//if(drand48()*maxdlP<(bpPruneP[i]*bbpP[sn])) PRUNE=1;
		if(drand48()*maxdlP<bpPruneP[i]) PRUNE=1;
	}
	else{
		cerr << "\nBranching point is not dendrite!!!\n\n";
		//cerr << j << " " << i << " "<< PruCom[cn] ;
		exit(1);
	}	
	if(PRUNE){
		pruneBP(i);
		//setProbabilities();		// Update probability
		findChildren();
		findTPBP();
	}	
}

/*****************************************************************/
// Convergence measure.

double Prune :: convmeasure()
{
	double cm=0.0;
	int i;
	
/* If the percentage reduction is negative it is not considered. Can be
 * reviewed at a later stage. TEST */

	for(i=0; i<sdata.na; i++){
		if((adlzeta[i]-adlprune[i])/adlzeta[i]>cm)
			cm=fabs((adlzeta[i]-adlprune[i])/adlzeta[i]);
		if((abpzeta[i]-abpprune[i])/abpzeta[i]>cm)
			cm=fabs((abpzeta[i]-abpprune[i])/abpzeta[i]);
	}		

	for(i=0; i<sdata.nb; i++){
		if((bdlzeta[i]-bdlprune[i])/bdlzeta[i]>cm)
			cm=fabs((bdlzeta[i]-bdlprune[i])/bdlzeta[i]);
		if((bbpzeta[i]-bbpprune[i])/bbpzeta[i]>cm)
			cm=fabs((bbpzeta[i]-bbpprune[i])/bbpzeta[i]);
	}		

	return cm;
}

/*****************************************************************/

void Prune :: saveSWC(char * filename)
{
	char fname[35];
	if(!filename) strcpy (fname,outfilename);
	else strcpy(fname,filename);

   	ofstream outfile (fname);
   	for(int i=0; i<npc; i++)
       	outfile << PruCom[i] ;
   	outfile.close();
}

/*****************************************************************/

void Prune :: checkTPs()
{
	int cn;
	for (int i=0; i<TP.npts; i++){
		cn=TP.Pts[i];
		if((PruCom[cn].tc != 3) && (PruCom[cn].tc != 4)){
    		cerr << "\ncheckTPs :: TP not dendrite\n";
			exit(1);
		}
	}
}

/*****************************************************************/


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