// THESE SCRIPTS DO A COMBINATION OF AUTOMATED AND MANUAL EDITING TO THE
// MORPHOLOGIES, AS OBTAINED FROM ARRAY TOMOGRAPHY.
// A function that flips the X,Y,Z coordinates of a given section, effectively
// reversing the x values of the branch.
// $o1: SectionRef instance to operate on.
// OUTPUT: the x values of the given section are reversed.
proc flipX() {local theNSeg,segLow,segHigh,ii localobj xVals,yVals,zVals,dVals
// Count number of segments; store values.
theNSeg = 0
xVals = new Vector()
yVals = new Vector()
zVals = new Vector()
dVals = new Vector()
$o1.sec {
for ii=0,n3d()-1 {
xVals.append(x3d(theNSeg))
yVals.append(y3d(theNSeg))
zVals.append(z3d(theNSeg))
dVals.append(diam3d(theNSeg))
theNSeg += 1
}
}
// Reverse X, Y, and Z values associated with each segment.
segLow = 0
segHigh = theNSeg - 1
$o1.sec {
for ii=0,n3d()-1 {
pt3dchange(segHigh,xVals.x[segLow],yVals.x[segLow],zVals.x[segLow],dVals.x[segLow])
segLow+=1
segHigh-=1
}
}
}
// A function that operates on a given section by disconnecting it, flipping it
// (if needed), and then reconnecting it to a new parent branch. This is used
// for correcting issues associated with automated reconstructions.
// INPUT:
// $o1: SectionRef instance to operate on.
// $2: variable. Logic gate to flip the X values of the dendrite. [ no flip = 0 ; flip = 1 ]
// $o3: SectionRef instance to append the operated section to.
// $4: variable. Optional. Connect the daugether dendrite somewhere other
// than the terminal (ie x=1) of the parent dendrite? [ default = 1 ; ie
// the daugheter is connected to the terminus ]
proc modConnect() {local xCon
// disconnect section
$o1.sec { disconnect() }
// flip, if selected
if($2){ flipX($o1) }
if(numarg()>3.1){
xCon = $4
}else{
xCon = 1
}
// connect to parent
$o3.sec { connect $o1.sec(0),xCon }
}
// A function that does modConnect, but allows the call to be done in one
// line. This is done just for parsimony of code.
// $1: variable corresponding to SectionRef index to operate on.
// $2: variable corresponding to SectionRef index to add on operated section.
// $3: variable. Logic gate to flip the X values of the dendrite. [ no flip = 0 ; flip = 1 ]
// $4: variable. Optional. Connect the daugether dendrite somewhere other
// than the terminal (ie x=1) of the parent dendrite? [ default = 1 ; ie
// the daugheter is connected to the terminus ]
proc quickConnect() {local conX localobj dendDau,dendPar
Cell[0].dend[$1] { dendDau = new SectionRef() }
Cell[0].dend[$2] { dendPar = new SectionRef() }
if(numarg()>3.1){
conX = $4
}else{
conX = 1
}
modConnect(dendDau,$3,dendPar,conX)
}
// This function clears the properties of a given neurite. It is used as a
// helper function for the splitSection() call, which relies on a preexisting
// section to write to the newly created section.
// $1: index of section to clear.
proc clearSection(){
Cell[0].dend[$1] {
disconnect()
for ii=0,n3d()-1{
pt3dremove(0)
}
}
}
// A function that turns an existing part of a branch into a new branch.
// This is used for inserting bifurcations into sections where they are not
// present in the original morphology. The topology is then adjusted to connect
// this new branch to the old branch, conserving the 0 -> 1 direction of the
// original neurite.
//
// $1: variable. Index of section to be split (e.g., "100" for Cell[0].dend[100])
// $2: variable. Replace terminal part of neurite (ie, start at point n3d()-1 and proceed
// towards parent?) [ if = 0, start at point 0; if = 1, start at point n3d()-1 ]
// $3: variable. Number of segments to switch over.
// $4: variable. Index of new neurite to be created. Should be an index of
// a neurite that exists but would normally be deleted as part of
// proofreading; see note in body of code before.
proc splitSection(){ local ii,curSeg,xx,yy,zz,dd localobj newNeur
// Clear the properties of the neurite to write.
clearSection($4)
// Identify index to be assigned to new neurite. This was previously
// done automatically, but there are issues associated with create
// calls within a function that make this annoying to implement.
// Thus, I've overwritten this, requiring the user to write new
// properties to a preexisting section. This preexisting section
// would normally be one that is delete by proofreading, but instead
// gets coopted to create this new neurite.
ii = $4
Cell[0].dend[ii] { newNeur = new SectionRef() }
// Write geometry to new section, taken from old section.
ii=0
while(ii<($3-0.1)){
// Record point to transfer and delete.
Cell[0].dend[$1] {
if($2>0.1){
curSeg = n3d()-1
}else{
curSeg = 0
}
xx = x3d(curSeg)
yy = y3d(curSeg)
zz = z3d(curSeg)
dd = diam3d(curSeg)
pt3dremove(curSeg)
}
newNeur.sec {
if($2>0.1){
// Inserting in 1 -> 0 direction.
pt3dinsert(0,xx,yy,zz,dd)
}else{
// Inserting in 0 -> 1 direction.
pt3dinsert(n3d(),xx,yy,zz,dd)
}
}
ii+=1
}
// Assign the number of segments.
Cell[0].dend[$1] {
ns=int(L/segL+0.5)
if (ns==0) {
ns=1
}
if ((ns-int(ns/2)*2)==0) {
ns=ns+1
}
nseg = ns
}
newNeur.sec {
ns=int(L/segL+0.5)
if (ns==0) {
ns=1
}
if ((ns-int(ns/2)*2)==0) {
ns=ns+1
}
nseg = ns
}
// Connect.
if ($2>0.1){
// Inserting in 1 -> 0 direction.
quickConnect($4,$1,0)
}else{
// Inserting in 0 -> 1 direction.
quickConnect($1,$4,0)
}
}
// The given (parent) section "absorbs" its daughter section, in that
// it receives all 3D points and connections of the daughter neurite. The
// daughter neurite is then deleted. This is designed to take neurites that
// are unbifurcated (when looking at morphology) but broken up into seperate
// sections (within NEURON) and clean things up so that the whole unbroken
// neurite can be referenced by one section.
//
// The absorbing only occurs if the parent neurite has a single daughter which
// emerges from the terminus.
//
// $1: variable. Index of parent neurite; will do the absorbing.
objref gdSR[2] // needs to be declared outside of proc because array
proc absorbSection(){local nGd,nD,bD,ii,xx,yy,zz,dd,nDel,dL,pL,newX localobj gdX,dSR,pSR
objref gdSR[2] // reset the SectionRefs to granddaughters.
// Initially, determine whether the section associated with the given
// index is a good candidate to absorb its daughther. This requires
// 1) the indexed neurite to have only one daughter, and
// 2) the daughter must stem from the terminal end of the parent.
// Validate this.
Cell[0].dend[$1] {
pSR = new SectionRef()
nD = pSR.nchild()
if(abs(nD-1)>0.001){
// Break if daughter number is not equal to one.
pop_section()
return
}else{
pSR.child[0] {
bD = parent_connection()
if(abs(bD-1)>0.001){
// Break if bifurcation not at terminus.
pop_section()
return
}else{
// Assign daughter section ref.
dSR = new SectionRef()
}
}
}
}
// Store the locations of granddaughters to be reconnections.
dSR.sec {
nGd = dSR.nchild()
dL = L // length of daughter; used for converting x values to connection location
}
gdX = new Vector(nGd) // store x values of granddaughter branches
dSR.sec {
for ii=1,nGd {
gdX.x[ii-1] = parent_connection()
gdSR[ii-1] = new SectionRef()
}
}
// Disconnect granddaughters; will be readded to parent.
dSR.sec {
for ii=1,nGd {
dSR.child[nGd-ii] {
// iterate backwards to disconnect without
// interfering with loop
disconnect()
}
}
}
// Disconnect daughter and record number of points.
dSR.sec {
disconnect()
nDel = n3d()
}
// Move 3D properties from daughter to parent.
for ii=1,nDel {
dSR.sec {
// remove zero indices only because loop updates zero index
// every iteration.
xx = x3d(0)
yy = y3d(0)
zz = z3d(0)
dd = diam3d(0)
pt3dremove(0)
}
Cell[0].dend[$1] {
// connect to 1 end of parent neurite.
pt3dinsert(n3d(),xx,yy,zz,dd)
}
}
// Delete daughter.
dSR.sec { delete_section() }
// Reconnect granddaughters.
Cell[0].dend[$1] { pL = L } // need length of parent for rescaling
for ii=1,nGd {
gdSR[ii-1].sec {
newX = gdX.x[ii-1]
// Convert previous x value to new x value, adjusted
// for the branch rescaling.
if(newX<0.9999){
// Rescale only if connection not at terminal
// part of neurite.
newX = (newX*dL + pL) / (dL + pL)
}
}
Cell[0].dend[$1] {
connect gdSR[ii-1].sec (0),newX
}
}
// Assign the number of segments.
Cell[0].dend[$1] {
ns=int(L/segL+0.5)
if (ns==0) {
ns=1
}
if ((ns-int(ns/2)*2)==0) {
ns=ns+1
}
nseg = ns
}
}
// This procedure takes two neurites (parent and child), flips the orientation
// of the child dendrite, and reaffixes it to the parent dendrite.
// $1: index of parent dendrite
// $2: index of daughter dendrite.
proc disFlipJoin(){local ii localobj parSec,dauSec
Cell[0].dend[$1] { parSec = new SectionRef() }
Cell[0].dend[$2] { dauSec = new SectionRef() }
// detect whether multiple daughters exist
if(dauSec.nchild>1.1){
print "NOTE: multiple daughters; print out secnames:"
for ii=0,dauSec.nchild()-1{
dauSec.child[ii] { print "\t",secname() }
}
}
parSec.sec { disconnect() }
//flipX(dauSec)
flipX(parSec)
parSec.sec {connect dauSec.sec(0),1}
}
// Do morphology-specific cleanup.
absorbSection(107)
absorbSection(110) // does nothing at this time, as has a small child branch in addition to main "bifurcation"
// delete superfluous sections
//Cell[0].dend[0] {delete_section()} // Normally would delete this, but this now holds the terminal part of dend[190]; see splitSection call
//Cell[0].dend[11] {delete_section()} // Normally would delete this, but this now holds the terminal part of dend[72]; see splitSection call
Cell[0].dend[191] {delete_section()}
Cell[0].dend[47] {delete_section()}
Cell[0].dend[48] {delete_section()}
Cell[0].dend[49] {delete_section()}
Cell[0].dend[51] {delete_section()}
Cell[0].dend[20] {delete_section()}
Cell[0].dend[50] {delete_section()}
Cell[0].dend[140] {delete_section()}
Cell[0].dend[168] {delete_section()}
// Break up a basal dendrite that is unbroken at a bifurcation where it should
// break.
// Split up branch 190.
splitSection(190,1,141,0)
// Split up branch 72 (soma) which has some of the apical dendrite as part
// of the annotated section.
splitSection(72,1,8,11)
quickConnect(11,72,0)
quickConnect(142,11,0)
quickConnect(73,11,0)
// disconnect somatic section so that it can be parent.
Cell[0].dend[72] {disconnect()}
// modify connections and orientations
quickConnect(190,72,0,0)
quickConnect(8,190,1)
quickConnect(9,7,0)
quickConnect(7,8,1)
quickConnect(4,7,1)
quickConnect(5,4,0)
quickConnect(3,4,1)
quickConnect(2,3,0)
quickConnect(6,2,0)
quickConnect(1,3,0)
quickConnect(71,72,1,0)
quickConnect(53,71,0)
quickConnect(27,71,1)
quickConnect(26,27,0)
quickConnect(25,27,1)
quickConnect(23,25,0)
quickConnect(22,25,1)
quickConnect(21,22,0)
quickConnect(24,21,0)
quickConnect(18,22,1)
quickConnect(17,18,1)
quickConnect(19,17,0)
quickConnect(16,17,1)
quickConnect(13,16,1)
quickConnect(12,13,0)
quickConnect(15,12,0)
quickConnect(14,16,0)
Cell[0].dend[190] {
for ii=0,3{
pt3dremove(0) // will always be = 0, as removing as we go..
}
}
Cell[0].dend[28] {
for ii=0,3{
pt3dremove(0) // will always be = 0, as removing as we go..
}
}
// deleting a section, and adding the daughters to the new soma.
quickConnect(27,72,0,0)
quickConnect(53,72,0,0)
Cell[0].dend[71] {delete_section()}
Cell[0].dend[72] {
pt3dinsert(0,199,141,4.7,12)
pt3dinsert(0,201,135,4.9,4)
}
Cell[0].dend[194] {
for ii=0,21{
pt3dremove(0)
}
}
quickConnect(194,70,0)
quickConnect(195,70,0)
Cell[0].dend[193] { delete_section() }
