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"SWC.h"


/*****************************************************************/
// Overloading SWCData for I/0
/*****************************************************************/

ostream & operator << (ostream & tmp, SWCData swcd)
{
	tmp << swcd.pi << " " ;
	tmp << swcd.tc << " " ;
	tmp << swcd.x << " " ;
	tmp << swcd.y << " " ;
	tmp << swcd.z << " " ;
	tmp << swcd.r << " " ;
	tmp << swcd.ppi << endl ;
	return tmp;
}	

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

istream & operator >> (istream & tmp, SWCData & swcd)
{
	tmp >> swcd.pi ;
	tmp >> swcd.tc ;
	tmp >> swcd.x  ;
	tmp >> swcd.y  ;
	tmp >> swcd.z  ;
	tmp >> swcd.r  ;
	tmp >> swcd.ppi;
	return tmp;
}	


/*****************************************************************/
// SWC Class Files 
/*****************************************************************/

SWC :: SWC ()
{
	ncomp=0;
}

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

void SWC :: ReadSWC(char * filename)
{
	char * flname=new char [35];
	if(!filename){
		cout << "\nGive input SWC filename : ";
		cin >> flname ;
	}
	else strcpy(flname,filename);

	ifstream swcfile (flname);
	if(!swcfile){
		cerr << "\nFile " << flname << " does not exist.\n";
		exit(1);
	}	

 	char c;
    char * buffer=new char[80];
	streampos crps;
	int i;


	swcfile.get(c);
	if (c=='#'){

		// Skip through header...

		while (c == '#'){
			swcfile.getline(buffer,80);
			swcfile.get(c);
		}	

		crps=swcfile.tellg();
	}
	else crps=0;

	// Browse through the end of file to get the number of points....

	ncomp=0;
	while(!swcfile.eof()){
		swcfile.getline(buffer,80);
		ncomp ++;
	}

	ncomp --;
	Comptmt=new SWCData[ncomp];
	
	// Read all points...

	swcfile.close();

	ifstream swc1file;
	swc1file.open(flname);
	if(!swc1file){
		cerr << "\nFile " << flname << " does not exist.\n";
		exit(1);
	}	
	swc1file.seekg(crps);
	
	for(i=0; i<ncomp; i++){
		swc1file >> Comptmt[i];
		if(Comptmt[i].tc==-1)
			cerr << "\nWarning: Undefined compartment type at " 
				 << Comptmt[i] ;
	}		

	delete(buffer);
	delete(flname);
}
	
/*****************************************************************/

void SWC :: isRead()
{
	if(!ncomp){
		cerr << "\nSWC file has been read.\n";
		exit(1);
	}	
}

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

void SWC :: WriteSWC(char * filename)
{
	isRead ();

	char * flname=new char [35];
	if(!filename){
		cout << "\nGive output SWC filename : ";
		cin >> flname ;
	}
	else strcpy(flname,filename);     

	ofstream outfile (flname);
	int i;
	
	for(i=0; i<ncomp; i++)
		outfile << Comptmt[i] ;

	delete(flname);
}	
	
/*****************************************************************/

void SWC :: SetComptmt(SWCData * Cpts, int npts)
{
	int i;
	ncomp=npts;
	Comptmt=new SWCData[ncomp];
	for(i=0; i<ncomp; i++)
		Comptmt[i]=Cpts[i];
}
/*****************************************************************/

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