Particle Diffusion - Revision history

Bradley Monk: /* Matlab Script */

2015-01-30T04:47:10Z

Matlab Script

← Older revision		Revision as of 21:47, 29 January 2015
Line 32:		Line 32:
	D2 = Dsp; % Diffusion Rate SYN2: LTP		D2 = Dsp; % Diffusion Rate SYN2: LTP

	~~% DpDb = fliplr(linspace(Dsb,Dsp,HiLoLoop));~~
	DpDb = linspace(Dsp,Dsb,HiLoLoop);		DpDb = linspace(Dsp,Dsb,HiLoLoop);
	%=========================================%		%=========================================%
Line 41:		Line 40:
	% DO-DONT SWITCHES		% DO-DONT SWITCHES
	%-----------------------------------------%		%-----------------------------------------%
	~~% ESsz = POLYSz(1)*POLYSz(2);~~
	~~% ESdensity = Ndots/ESsz;~~

	doESreg = 0;		doESreg = 0;
	doAddDots = 1;		doAddDots = 1;
Line 72:		Line 68:
	%-----------------------------------------%		%-----------------------------------------%
	%{		%{
	Sc = Sc; % scale of model (life:model)		% Sc = Sc; % scale of model (life:model)
	dT = dT; % time step (s)		% dT = dT; % time step (s)
	dm = 2; % dimensions		% dm = 2; % dimensions
	% Da = dSbdT/Sc; % Diffusion Rate A (D = LÂ² / 2ddT)		% Da = dSbdT/Sc; % Diffusion Rate A (D = LÂ² / 2ddT)
	% Db = dSp*dT/Sc; % Diffusion Rate B		% Db = dSp*dT/Sc; % Diffusion Rate B
Line 138:		Line 134:
	EssArea = DenArea - SynAreas;		EssArea = DenArea - SynAreas;
	%=========================================%		%=========================================%

Bradley Monk at 04:45, 30 January 2015

2015-01-30T04:45:07Z

← Older revision		Revision as of 21:45, 29 January 2015
Line 326:		Line 326:
	FINALPLOT(EsPn,S1Pn,S2Pn,S1S2r,Des,dSb,dSp)		FINALPLOT(EsPn,S1Pn,S2Pn,S1S2r,Des,dSb,dSp)

			%-------------------------------------------%

	%~~==============================================================~~%
	end %varargout={S1Pn,S2Pn};		end %varargout={S1Pn,S2Pn};
	%==============================================================%		%======================================================================%
			%% MAIN FUNCTION END
			%======================================================================%


Line 338:		Line 338:


			%======================================================================%
	%~~-------------------------------------------~~%
	% ENCLOSE: keep particles inside polygon		% ENCLOSE: keep particles inside polygon
	%-------------------------------------------%		%-------------------------------------------%
Line 353:		Line 352:

	end		end
			%======================================================================%


			%======================================================================%
	%~~-------------------------------------------~~%
	% DUALPLOT: plots diffusion		% DUALPLOT: plots diffusion
	%-------------------------------------------%		%-------------------------------------------%
Line 377:		Line 376:
	drawnow		drawnow


	end		end
			%======================================================================%


	%~~-------------------------------------------~~%
			%======================================================================%
	% FINALPLOT: plots steady-state averages		% FINALPLOT: plots steady-state averages
	%-------------------------------------------%		%-------------------------------------------%
Line 439:		Line 439:
	text(haxes(2)/2.5,haxes(4)/1.05,strcat(s1txt,' : ',s2txt, ' \bullet (um²/s; ES:',estxt,')' ),...		text(haxes(2)/2.5,haxes(4)/1.05,strcat(s1txt,' : ',s2txt, ' \bullet (um²/s; ES:',estxt,')' ),...
	'FontSize',10,'HorizontalAlignment','left');		'FontSize',10,'HorizontalAlignment','left');
	~~%======================================================================%~~

	%------------------------------------------%		%------------------------------------------%
Line 489:		Line 488:
	ylim([0 haxes(4)*1.2 ]);		ylim([0 haxes(4)*1.2 ]);
	% xlim([0 (haxes(2)*.9)]);		% xlim([0 (haxes(2)*.9)]);
	~~%======================================================================%~~
	%%		%%



	end		end
			%======================================================================%


			%======================================================================%
	%~~-------------------------------------------~~%
	% FINALPLOT: plots steady-state averages		% FINALPLOT: plots steady-state averages
	%-------------------------------------------%		%-------------------------------------------%
	function [] = FINALPLOT(EsPn,S1Pn,S2Pn,S1S2r,Des,dSb,dSp)		function [] = FINALPLOT(EsPn,S1Pn,S2Pn,S1S2r,Des,dSb,dSp)



	%%		%%
Line 562:		Line 556:
	ylim([0 haxes(4)*1.2 ]);		ylim([0 haxes(4)*1.2 ]);
	% xlim([0 (haxes(2)*.9)]);		% xlim([0 (haxes(2)*.9)]);
	~~%======================================================================%~~

	%%		%%


	end		end
			%======================================================================%

Bradley Monk at 04:41, 30 January 2015

2015-01-30T04:41:58Z

Show changes

Bradley Monk: Created page with " ==Brownian Motion Matlab Code== function [] = BasicParticleDiffusion() clc; close all; clear all; ..."

2015-01-30T04:37:38Z

Created page with " ==Brownian Motion Matlab Code== <syntaxhighlight lang="matlab" line start="1" highlight="1" enclose="div"> function [] = BasicParticleDiffusion() clc; close all; clear all; ..."

New page

==Brownian Motion Matlab Code==

<syntaxhighlight lang="matlab" line start="1" highlight="1" enclose="div">
function [] = BasicParticleDiffusion()
clc; close all; clear all;

%=========================================%
% USER-ENTERED STARTING PARAMETERS
%-----------------------------------------%

Ndots = 200; % number of particles in ES
NSteps = 500; % number of steps per trial
NLoops = 10; % number of loops to average over
HiLoLoop = 5; % number of diffusion rates to test between hi and low

Sc = 1; % scale of model
dT = .1; % time step (s)

% Diffusion Rates [Choquet: ES= .13 SynBSL= .05 SynLTP= .01]
Des = (Sc*dT)* .1; % D coef ES
Dsb = (Sc*dT)* .05; % D coef Syn Basal
Dsp = (Sc*dT)* .01; % D coef Syn LTP

% Store a Diffusion Rate Copy
D0 = Des; % Diffusion Rate of Surf (D = LÂ² / 2d*dT)
D1 = Dsb; % Diffusion Rate SYN1: BAS
D2 = Dsp; % Diffusion Rate SYN2: LTP

% DpDb = fliplr(linspace(Dsb,Dsp,HiLoLoop));
DpDb = linspace(Dsp,Dsb,HiLoLoop);
%=========================================%

%=========================================%
% DO-DONT SWITCHES
%-----------------------------------------%
% ESsz = POLYSz(1)*POLYSz(2);
% ESdensity = Ndots/ESsz;

doESreg = 0;
doAddDots = 1;
doSubDots = 0;

doTrace=0;
doLiveScatter = 0;
doLiveBar = 0;

% Extra Stuff
NdotsO = Ndots;
%=========================================%

%#############################################################
for OLoop = 1:HiLoLoop
%#############################################################

dSb = DpDb(OLoop);
dSp = Dsp;

%=========================================%
% BASE DIFFUSION RATES EQUATIONS
%-----------------------------------------%
%{
Sc = Sc; % scale of model (life:model)
dT = dT; % time step (s)
dm = 2; % dimensions
% Da = dSb*dT/Sc; % Diffusion Rate A (D = LÂ² / 2d*dT)
% Db = dSp*dT/Sc; % Diffusion Rate B
% Dr = Da/Db; % Ratio of Da:Des (1/Ls)^2;
% Dn = Da/Dr; % new D after scaling L
% k = sqrt(dm*Da); % stdev of D's step size distribution
% L = sqrt(2*dm*Da); % average diagonal (2D) step size
% Lx = L/sqrt(2); % average linear (1D) step size
% Ls = 1/sqrt(Dr); % scales Lx values for Dn
% MSD = 2*dm*Da; % mean squared displacement
%}

dm = 2; % dimensions
k = sqrt(dm*Des); % stdev of Des step size distribution

Lsb1 = 1/sqrt(Des/dSb); % scales Lx values for Dn
Lsb2 = 1/sqrt(Des/dSp); % scales Lx values for Dn

XYL = zeros(2,Ndots); % XY particle locations
XYS = zeros(2,Ndots); % XY particle step sizes
%=========================================%

%=========================================%
% SYNAPTIC LOCATION SETUP
%-----------------------------------------%
POLYSz = [3 6]; % size of ES (XY in Âµm)
BOXwh = 0.8; % size of ES (XY in Âµm)

% ES Size
POLYSz = POLYSz./Sc; % scale enclosures
XWIDE = POLYSz(1)/2; % half X enclosure size (will double below)
YHIGH = POLYSz(2)/2; % half X enclosure size (will double below)
BOARDER = [-POLYSz(1)/2 -POLYSz(2)/2 POLYSz(1) POLYSz(2)];

S1rad = .4;
S2rad = .4;

S1C = [0; YHIGH/2];
S2C = [0; -YHIGH/2];

S1BL = S1C - S1rad;
S2BL = S2C - S2rad;

% Radius from synapse counters
S1G = repmat(S1C,1,numel(XYL(1,:)));
S2G = repmat(S2C,1,numel(XYL(1,:)));

Box1 = sqrt(sum((XYL-S1G).^2)) < S1rad;
Box2 = sqrt(sum((XYL-S2G).^2)) < S2rad;

DenArea = POLYSz(1) * POLYSz(2);
S1Area = (pi*S1rad^2);
S2Area = (pi*S2rad^2);
SynAreas = S1Area + S2Area;
EssArea = DenArea - SynAreas;
%=========================================%

if doLiveScatter
%=========================================%
% FIGURE SETUP
%-----------------------------------------%
Flh = figure(1);
set(Flh,'Units','pixels','OuterPosition',[1e2 1e2 7e2 7e2],'Color',[.95,.95,.95]);
xlim = [-XWIDE*1.01 XWIDE*1.01]; ylim = [-YHIGH*1.01 YHIGH*1.01];
%---
subplot('Position',[.05 .05 .65 .9])
Ph1 = scatter(XYL(1,:),XYL(2,:),5,[0 0 1]);
set(Ph1,'Marker','o','SizeData',60,'LineWidth',.5,...
'MarkerFaceColor',[.95 .1 .1],'MarkerEdgeColor','none')
axis([xlim, ylim]);
% axis off
set(gca,'XTick',[],'YTick',[],'Color',[.8 .8 .8])
hold on

rectangle('Position',BOARDER); hold on;
rectangle('Position',[S1BL(1),S1BL(2),S1rad*2,S1rad*2],'Curvature',[1,1]); hold on;
rectangle('Position',[S2BL(1),S2BL(2),S2rad*2,S2rad*2],'Curvature',[1,1]); hold on;

pause(.5)

Ah3 = subplot('Position',[.75 .05 .22 .9]);
Ph3 = bar([1 1]);
set(Ah3,'Ylim',[0 100])

pause(.5)
%=========================================%
end %if doLiveScatter

%=========================================%
% MEMORY PREALLOCATION
%-----------------------------------------%
%SMxE = zeros(NLoops);
% preallocate for trace dot
XYLp = zeros(2,NSteps);
% preallocate for data saves
DatN = NSteps/100;

SMxE = zeros(fliplr(POLYSz .* 100));
%=========================================%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
for Ln = 1:NLoops
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%==================================================%
for Nt = 1:NSteps
%==================================================%

% generates step sizes
XYS = (k * randn(2,Ndots));

% Sticky Functions
Box1 = sqrt(sum((XYL-S1G).^2)) < S1rad;
Box2 = sqrt(sum((XYL-S2G).^2)) < S2rad;
XYS(:,Box1) = XYS(:,Box1)*(Lsb1);
XYS(:,Box2) = XYS(:,Box2)*(Lsb2);

% adds step to location
XYL = XYL+XYS;

% rebound at enclosure walls
[XYL] = ENCLOSE(Nt,XYL,XWIDE,YHIGH,Ndots);

% counts particles in each roi
if mod(Nt,100)==0
SYN1n(Nt/100) = sum(Box1>0);
SYN2n(Nt/100) = sum(Box2>0);
end

%------------
% PLOTS - Scatter, Bar, Trace, iSc

if doLiveScatter
set(Ph1,'XData',XYL(1,:),'YData',XYL(2,:));
drawnow
end

if doLiveBar
if mod(Nt,100)==0
set(Ph3,'YData',[SYN1n(Nt/100) SYN2n(Nt/100)]);
drawnow
end
end

if doTrace
XYLp(:,Nt) = XYL(:,1); % save step of first dot (for trace)
DUALPLOT(Nt,XYL,Ph1,XYLp,Ph2)
XL(Nt,:) = XYL(1,:);
YL(Nt,:) = XYL(2,:);
end

%------------
if mod(Nt,400)==0
%if Nt >= 400; keyboard; end;
%%

pXYL = XYL;
GR1x = XYL(1,:)+XWIDE;
GR1y = XYL(2,:)+YHIGH;
GR1c = round(GR1x*100);
GR1r = round(GR1y*100);
GR1c(GR1c < 1) = 1;
GR1c(GR1c > (XWIDE*200)) = (XWIDE*200);
GR1r(GR1r < 1) = 1;
GR1r(GR1r > (YHIGH*200)) = (YHIGH*200);
pXYL(1,:) = GR1c;
pXYL(2,:) = GR1r;

G1xy = SMxE;
for xy = 1:numel(GR1c)
G1xy(GR1r(xy),GR1c(xy)) = 1;
end

%%
end
%------------

%if Nt >= 1; keyboard; end;
%==================================================%
end % for Nt = 1:Nsteps
%==================================================%

S1nPD = (SYN1n)./ S1Area;
S2nPD = (SYN2n)./ S2Area;

S1Pn{Ln} = S1nPD;
S2Pn{Ln} = S2nPD;
S1S2r{Ln} = ((SYN1n+1) ./ (SYN2n+1))';
EsPn{Ln} = ((Ndots - (SYN1n+SYN2n))')./ EssArea;

MeanESSn(Ln) = mean(EsPn{Ln});
MeanSYNbN(Ln) = mean(S1Pn{Ln});
MeanSYNpN(Ln) = mean(S2Pn{Ln});
MeanRatio(Ln) = mean(S1S2r{Ln});

if mod(Ln,10)==0;disp(Ln); end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

mESSn(OLoop) = mean(MeanESSn);
mSYNbN(OLoop) = mean(MeanSYNbN);
mSYNpN(OLoop) = mean(MeanSYNpN);
mRATbp(OLoop) = mean(MeanRatio);

DboxD(:,OLoop) = [Des; dSb; dSp];
DboxR(OLoop) = dSp/dSb;

%#############################################################
end % OLoop
%#############################################################

DPLOT(DboxD,DboxR,mRATbp,mESSn,mSYNbN,mSYNpN,NSteps,Des,dSb,dSp)

FINALPLOT(EsPn,S1Pn,S2Pn,S1S2r,Des,dSb,dSp)

%==============================================================%
end %varargout={S1Pn,S2Pn};
%==============================================================%

%-------------------------------------------%
% ENCLOSE: keep particles inside polygon
%-------------------------------------------%
function [XYL] = ENCLOSE(Nt,XYL,XWIDE,YHIGH,Ndots)

for j = 1:Ndots
if XYL(1,j)>(XWIDE) || XYL(1,j)<(-XWIDE)
XYL(1,j) = sign(XYL(1,j))*(XWIDE);
elseif XYL(2,j)>(YHIGH) || XYL(2,j)<(-YHIGH)
XYL(2,j) = sign(XYL(2,j))*(YHIGH);
end
end

end

%===================================%
% inboxfun
%===================================%
% Tests whether particles are in a box polygon
% and returns a logical vector
%===================================%
function [inbox] = inboxfun(LB,RT,xyl)

if LB(1)>RT(1)
LBt=LB;
RTt=RT;
LB(1)=RTt(1);
RT(1)=LBt(1);
end
if LB(2)>RT(2)
LBt=LB;
RTt=RT;
LB(2)=RTt(2);
RT(2)=LBt(2);
end

xylLB1 = xyl(1,:) > LB(1);
xylRT1 = xyl(1,:) < RT(1);
xylLB2 = xyl(2,:) > LB(2);
xylRT2 = xyl(2,:) < RT(2);

inbox = xylLB1 & xylRT1 & xylLB2 & xylRT2;

end
%===================================%

%===================================%
% incircfun
%===================================%
% Tests whether particles are in a box polygon
% and returns a logical vector
%===================================%
function [inbox] = incircfun(S1G,S2G,XYL)

if LB(1)>RT(1)
LBt=LB;
RTt=RT;
LB(1)=RTt(1);
RT(1)=LBt(1);
end
if LB(2)>RT(2)
LBt=LB;
RTt=RT;
LB(2)=RTt(2);
RT(2)=LBt(2);
end

xylLB1 = xyl(1,:) > LB(1);
xylRT1 = xyl(1,:) < RT(1);
xylLB2 = xyl(2,:) > LB(2);
xylRT2 = xyl(2,:) < RT(2);

inbox = xylLB1 & xylRT1 & xylLB2 & xylRT2;

%----------------------------------------
% Location Counters
%----------------------------------------

S1Cv = XYL-S1G;
S2Cv = XYL-S2G;

P1r = sqrt(sum((S1Cv).^2));
P2r = sqrt(sum((S2Cv).^2));

inP1=P1r<S1rad;
inP2=P2r<S2rad;

end
%===================================%

%-------------------------------------------%
% DUALPLOT: plots diffusion
%-------------------------------------------%
function [] = DUALPLOT(Nt,XYL,Ph1,XYLp,SPh2)
%-------------------------------------------%

LLg = 3;
if Nt > LLg
xp = (XYLp(1,(Nt-LLg):Nt));
yp = (XYLp(2,(Nt-LLg):Nt));
else
xp = (XYLp(1,Nt));
yp = (XYLp(2,Nt));
end

set(Ph1,'XData',XYL(1,:),'YData',XYL(2,:));
drawnow

plot(xp,yp,'Parent',SPh2);
drawnow

end

%-------------------------------------------%
% FINALPLOT: plots steady-state averages
%-------------------------------------------%
function [] = DPLOT(DboxD,DboxR,mRATbp,mESSn,mSYNbN,mSYNpN,NSteps,Des,Db1,Db2)

%%
%------------------------------------------%
Fh = figure;
set(Fh,'OuterPosition',[200 200 1400 500])
% Color
neongreen = [.1 .9 .1];
liteblue = [.2 .9 .9];
hotpink=[.9 .1 .9];
%------------------------------------------%
axes('Position',[.07 .14 .4 .78]);
%------------------------------------------%
% [ph1] = line(1:numel(DboxR),DboxR);
[ph1] = plot(DboxR);
legend(ph1, 'D Ratio');
[LEGH,OBJH,OUTH,OUTM] = legend;
hold on
[ph2] = plot(mRATbp);
legend([OUTH;ph2],OUTM{:},'SS Ratio');
[LEGH,OBJH,OUTH,OUTM] = legend;
hold on
%------------------------------------------%
% xt = (get(gca,'XTick'));
% xt = linspace(0,NSteps,numel(xt)); %.* dT./60
% set(gca,'XTickLabel', sprintf('%.0f|',xt))
set(legend,'Location','NorthWest');
%------------------------------------------%
MS1 = 9; c1=neongreen; c2=hotpink; c3=liteblue;
set(ph1,'LineStyle','-','Color',c1,'LineWidth',2,...
'Marker','o','MarkerSize',MS1,'MarkerEdgeColor',c1,'MarkerFaceColor',c1);
set(ph2,'LineStyle',':','Color',c2,'LineWidth',2,...
'Marker','o','MarkerSize',MS1,'MarkerEdgeColor',c2,'MarkerFaceColor',c2);
hTitle = title('Diffusion Coefficient Ratio vs Particle Steady-State Ratio');
hXLabel = xlabel('Trial');
hYLabel = ylabel('D Ratio or Particle-Density Ratio (+/- SEM)');
set(gca,'FontName','Helvetica');
set([hTitle, hXLabel, hYLabel],'FontName','AvantGarde');
set([hXLabel, hYLabel],'FontSize',10);
set( hTitle,'FontSize',12);
set(gca,'Box','off','TickDir','out','TickLength',[.02 .02], ...
'XMinorTick','on','YMinorTick','on','YGrid','on', ...
'XColor',[.3 .3 .3],'YColor',[.3 .3 .3],'LineWidth',1);
haxes=axis;
ylim([0 haxes(4)*1.2 ]);
% xlim([0 (haxes(2)*.9)]);
haxes=axis;
hold on

estxt = horzcat(' ES: ', num2str(Des), ' ');
s1txt = horzcat(' S1: ', num2str(Db1), ' ');
s2txt = horzcat(' S2: ', num2str(Db2), ' ');
text(haxes(2)/2.5,haxes(4)/1.05,strcat(s1txt,' : ',s2txt, ' \bullet (umÂ²/s; ES:',estxt,')' ),...
'FontSize',10,'HorizontalAlignment','left');
%======================================================================%

%------------------------------------------%
axes('Position',[.55 .14 .4 .78]);
%------------------------------------------%
% [ph1] = line(1:numel(DboxR),DboxR);
[ph1] = plot(mSYNbN);
legend(ph1, 'S1');
[LEGH,OBJH,OUTH,OUTM] = legend;
hold on
[ph2] = plot(mSYNpN);
legend([OUTH;ph2],OUTM{:},'S2');
[LEGH,OBJH,OUTH,OUTM] = legend;
hold on
[ph3] = plot(mESSn);
legend([OUTH;ph3],OUTM{:},'ES');
[LEGH,OBJH,OUTH,OUTM] = legend;
hold on
%------------------------------------------%
xt = (get(gca,'XTick')) .* 0;
xt(1:2:end) = DboxR;

clear xtt
xtt{1,numel(xt)} = [];
xtt = num2cell(xt);
xtt(2:2:end) = {[]};

set(gca,'XTickLabel', sprintf('%.2f|',xtt{1,:}))
set(legend,'Location','NorthEast');
%------------------------------------------%
MS1 = 9; c1=neongreen; c2=hotpink; c3=liteblue;
set(ph1,'LineStyle','-','Color',c1,'LineWidth',2,...
'Marker','o','MarkerSize',MS1,'MarkerEdgeColor',c1,'MarkerFaceColor',c1);
set(ph2,'LineStyle',':','Color',c2,'LineWidth',2,...
'Marker','o','MarkerSize',MS1,'MarkerEdgeColor',c2,'MarkerFaceColor',c2);
set(ph3,'LineStyle','-.','Color',c3,'LineWidth',2,...
'Marker','o','MarkerSize',MS1,'MarkerEdgeColor',c3,'MarkerFaceColor',c3);
hTitle = title('Diffusion Rate Effects on Particle Steady-State');
hXLabel = xlabel('S1:S2 Diffusion Coefficient Ratio');
hYLabel = ylabel('Particle Per Square Micron (+/- SEM)');
set(gca,'FontName','Helvetica');
set([hTitle, hXLabel, hYLabel],'FontName','AvantGarde');
set([hXLabel, hYLabel],'FontSize',10);
set( hTitle,'FontSize',12);
set(gca,'Box','off','TickDir','out','TickLength',[.02 .02], ...
'XMinorTick','on','YMinorTick','on','YGrid','on', ...
'XColor',[.3 .3 .3],'YColor',[.3 .3 .3],'LineWidth',1);
haxes=axis;
ylim([0 haxes(4)*1.2 ]);
% xlim([0 (haxes(2)*.9)]);
%======================================================================%
%%

end

%-------------------------------------------%
% FINALPLOT: plots steady-state averages
%-------------------------------------------%
function [] = FINALPLOT(EsPn,S1Pn,S2Pn,S1S2r,Des,dSb,dSp)

%%
Fh = figure;
set(Fh,'OuterPosition',[200 200 650 700])

% Color
neongreen = [.08 .88 .08];
liteblue = [.2 .9 .9];
hotpink=[.9 .1 .9];
%------------------------------------------%
[ph1 hax1 mu1] = CIplot(EsPn,liteblue,5);
legend(ph1, horzcat('ES _{', num2str(Des), ' umÂ²/s}'));
[LEGH,OBJH,OUTH,OUTM] = legend;
hold on
ph11 = plot(mu1);
hold on
[ph2 hax2 mu2] = CIplot(S1Pn,neongreen,5);
legend([OUTH;ph2],OUTM{:},strcat('S1 _{', num2str(dSb), ' umÂ²/s}'));
[LEGH,OBJH,OUTH,OUTM] = legend;
hold on
ph22 = plot(mu2);
hold on
pause(.5)
[ph3 hax3 mu3] = CIplot(S2Pn,hotpink,5);
legend([OUTH;ph3],OUTM{:},strcat('S2 _{', num2str(dSp), ' umÂ²/s}'));
[LEGH,OBJH,OUTH,OUTM] = legend;
hold on
ph33 = plot(mu3);
hold on
%------------------------------------------%
hleg = legend;
set(hleg,'FontSize',14)

xt = (get(gca,'XTick'))*100;
set(gca,'XTickLabel', sprintf('%.0f|',xt))
%------------------------------------------%
MS1 = 9; c1=liteblue; c2=neongreen; c3=hotpink;
% set(ph1,'LineStyle','-','Color',c1,'LineWidth',1,...
% 'Marker','o','MarkerSize',6,'MarkerEdgeColor',c1,'MarkerFaceColor','none');
set(ph11,'LineStyle','none','Color',c1,'LineWidth',2,...
'Marker','o','MarkerSize',MS1,'MarkerEdgeColor',c1,'MarkerFaceColor',c1);
set(ph22,'LineStyle','none','Color',c2,'LineWidth',2,...
'Marker','o','MarkerSize',MS1,'MarkerEdgeColor',c2,'MarkerFaceColor',c2);
set(ph33,'LineStyle','none','Color',c3,'LineWidth',2,...
'Marker','o','MarkerSize',MS1,'MarkerEdgeColor',c3,'MarkerFaceColor',c3);
hTitle = title('Particle Steady-State Density in Dendritic ROIs');
hXLabel = xlabel('Time');
hYLabel = ylabel('Particle Per Square Micron (+/- SEM)');
set(gca,'FontName','Helvetica');
set([hTitle, hXLabel, hYLabel],'FontName','AvantGarde');
set([hXLabel, hYLabel],'FontSize',10);
set( hTitle,'FontSize',12);
set(gca,'Box','off','TickDir','out','TickLength',[.02 .02], ...
'XMinorTick','on','YMinorTick','on','YGrid','on', ...
'XColor',[.3 .3 .3],'YColor',[.3 .3 .3],'LineWidth',1);
haxes=axis;
ylim([0 haxes(4)*1.2 ]);
% xlim([0 (haxes(2)*.9)]);
%======================================================================%

%%

end

%-------------------------------------------%
% FINALPLOT: plots steady-state averages
%-------------------------------------------%
function [] = FINALPLOT2(S1Pn,S2Pn,S1S2r)

doRatFig = 1;
doRawFig = 1;

%%

if doRawFig
Fh = figure;
set(Fh,'OuterPosition',[200 200 900 600])

% Color
neongreen = [.1 .9 .1];
liteblue = [.2 .9 .9];
hotpink=[.9 .1 .9];
%------------------------------------------%
[ph1 hax1 mu1] = CIplot(S1Pn,neongreen,5);
legend(ph1,'Box1');
[LEGH,OBJH,OUTH,OUTM] = legend;
hold on
ph1 = plot(mu1);
hold on
[ph2 hax2 mu2] = CIplot(S2Pn,hotpink,5);
legend([OUTH;ph2],OUTM{:},'Box2');
[LEGH,OBJH,OUTH,OUTM] = legend;
hold on
ph2 = plot(mu2);
hold on
%------------------------------------------%
xt = (get(gca,'XTick'))*100;
set(gca,'XTickLabel', sprintf('%.0f|',xt))
%------------------------------------------%
MS1 = 8; c1=neongreen; c2=hotpink;
set(ph1,'LineStyle','none','Color',c1,'LineWidth',1,...
'Marker','o','MarkerSize',MS1,'MarkerEdgeColor',c1,'MarkerFaceColor',c1);
set(ph2,'LineStyle','none','Color',c2,'LineWidth',1,...
'Marker','o','MarkerSize',MS1,'MarkerEdgeColor',c2,'MarkerFaceColor',c2);
hTitle = title('Distribution of Particles with Brownian Motion');
hXLabel = xlabel('Time');
hYLabel = ylabel('Particles (+/- SEM)');
set(gca,'FontName','Helvetica');
set([hTitle, hXLabel, hYLabel],'FontName','AvantGarde');
set([hXLabel, hYLabel],'FontSize',10);
set( hTitle,'FontSize',12);
set(gca,'Box','off','TickDir','out','TickLength',[.02 .02], ...
'XMinorTick','on','YMinorTick','on','YGrid','on', ...
'XColor',[.3 .3 .3],'YColor',[.3 .3 .3],'LineWidth',1);
haxes=axis;
ylim([0 haxes(4)*1.2 ]);
% xlim([0 (haxes(2)*.9)]);
%======================================================================%
end

if doRatFig
Fh = figure;
set(Fh,'OuterPosition',[200 200 900 600])

% Color
neongreen = [.1 .9 .1];
liteblue = [.2 .9 .9];
hotpink=[.9 .1 .9];
%------------------------------------------%
[ph1 hax1 mu1] = CIplot(S1S2r,neongreen,5);
legend(ph1,'Box1');
[LEGH,OBJH,OUTH,OUTM] = legend;
hold on
ph1 = plot(mu1);
% hold on
% [ph2 hax2 mu2] = CIplot(S2Pn,hotpink,5);
% legend([OUTH;ph2],OUTM{:},'Box2');
% [LEGH,OBJH,OUTH,OUTM] = legend;
% hold on
% ph2 = plot(mu2);
% hold on
%------------------------------------------%
xt = (get(gca,'XTick'))*100;
set(gca,'XTickLabel', sprintf('%.0f|',xt))
%------------------------------------------%
MS1 = 8; c1=neongreen; c2=hotpink;
set(ph1,'LineStyle','none','Color',c1,'LineWidth',1,...
'Marker','o','MarkerSize',MS1,'MarkerEdgeColor',c1,'MarkerFaceColor',c1);
% set(ph2,'LineStyle','none','Color',c2,'LineWidth',1,...
% 'Marker','o','MarkerSize',MS1,'MarkerEdgeColor',c2,'MarkerFaceColor',c2);
hTitle = title('Distribution of Particles with Brownian Motion');
hXLabel = xlabel('Time');
hYLabel = ylabel('Ratio (+/- SEM)');
set(gca,'FontName','Helvetica');
set([hTitle, hXLabel, hYLabel],'FontName','AvantGarde');
set([hXLabel, hYLabel],'FontSize',10);
set( hTitle,'FontSize',12);
set(gca,'Box','off','TickDir','out','TickLength',[.02 .02], ...
'XMinorTick','on','YMinorTick','on','YGrid','on', ...
'XColor',[.3 .3 .3],'YColor',[.3 .3 .3],'LineWidth',1);
haxes=axis;
ylim([1 haxes(4)*1.2 ]);
% xlim([0 (haxes(2)*.9)]);
%======================================================================%
end
%%

%===========================================================%
% FIG1 BOTTOM RIGHT: Branching Events
%===========================================================%
%----------------------------
% Dual Axis Plot
%----------------------------
sbpos = [.55 .09 .38 .35];
subplot('Position',sbpos);
[ph1] = plot(NumArpR,'r');
leg1 = legend(ph1,'Arp Rate');
[LEGH,OBJH,OUTH,OUTM] = legend;
set(legend,'Location','SouthEast');
haxes1 = gca; % handle to axes
%set(haxes1,'XColor','r','YColor','r')
hold on
haxes1_pos = get(haxes1,'Position'); % store position of first axes
haxes2 = axes('Position',haxes1_pos,...
'XAxisLocation','top',...
'YAxisLocation','right',...
'Color','none');
%subplot('Position',sbpos);
[ph2] = line(1:numel(AcTags),AcTags,'Parent',haxes2,'Color','k');
LGh1 = legend([OUTH;ph2],OUTM{:},'Actin Tags');
[LEGH,OBJH,OUTH,OUTM] = legend;
set(LGh1,'Location','SouthEast');
hold on
%------------------------------------------%
xt = (get(haxes1,'XTick')).* dT./60;
set(haxes1,'XTickLabel', sprintf('%.0f|',xt))
%------------------------------------------%
MS1 = 5; MS2 = 2;
set(ph1,'LineStyle','-','Color',c1,'LineWidth',1,...
'Marker','o','MarkerSize',MS1,'MarkerEdgeColor',c1,'MarkerFaceColor',c11);
set(ph2,'LineStyle','-','Color',c2,'LineWidth',1,...
'Marker','o','MarkerSize',MS1,'MarkerEdgeColor',c2,'MarkerFaceColor',c22);
%hTitle = title('Arp Branching Rate');
%hXLabel = xlabel('Time (min)');
hYLabel = ylabel('Branching Events');
set(gca,'FontName','Helvetica');
set([hTitle, hXLabel, hYLabel],'FontName','AvantGarde');
set([hXLabel, hYLabel],'FontSize',10);
set(hTitle,'FontSize',12);
set(gca,'Box','off','TickDir','out','TickLength',[.02 .02], ...
'XMinorTick','on','YMinorTick','on','YGrid','on', ...
'XColor',[.3 .3 .3],'YColor',[.3 .3 .3],'LineWidth',1);
%===========================================================%
%%

end

%-------------------------------------------%
% doESreg
%-------------------------------------------%
function [] = ESREG(Box1,Box2,XYL)

if doESreg
B1N = sum(Box1>0);
B2N = sum(Box2>0);
Ndots = numel(XYL(1,:));
BoxSum = B1N + B2N;
ESn = Ndots - BoxSum;
ESdef = ESn - NdotsO;

if doAddDots
% Add Dots
if ESdef < -10
ADot = (Ndots+1):(Ndots+3);
%ADot = (Ndots+1):(Ndots+abs(ESdef));
XYL(:,ADot) = 0;
XYL(1,ADot) = 20;
end
end

if doSubDots
% Subtract Dots
if ESdef > 10
[B1r B1c] = find(~Box1);
[B2r B2c] = find(~Box2);
inES = intersect(B1c, B2c);
XDot = inES(1:3);
%XDot = inES(1:abs(ESdef));

XYL(:,XDot) = [];
end
end

Ndots = numel(XYL(1,:));
end

end

%-------------------------------------------%
% dopartmx
%-------------------------------------------%
function [G1xy] = dopartmx(XYL,SMxE)

GR1c = round(XYL(1,:))+55;
GR1r = round(XYL(2,:))+55;
% GR1xy(1,:) = GR1c;
% GR1xy(2,:) = GR1r;

G1xy = SMxE;
for xy = 1:numel(GR1c)
G1xy(GR1r(xy),GR1c(xy)) = 1;
end

end

%----------------------------------%
% CircMask
%----------------------------------%
% Creates a kernel mask using a 3D Gaussian
% that can be used for SAP clustering and
% other matrix conv() functions
%----------------------------------%
function [hkMask] = CircMask(GN)
% GN=[4, .18, 9, .1];
% GN=[mu, sd, num, res];

%--------------------
GNpk = GN(1); % hight of peak
GNx0 = 0; % x-axis peak locations
GNy0 = 0; % y-axis peak locations
GNsd = GN(2); % sigma (stdev of slope)

GNnum = GN(3);
GNres = GN(4);
GNspr = ((GNnum-1)*GNres)/2;

a = .5/GNsd^2;
c = .5/GNsd^2;

[X, Y] = meshgrid((-GNspr):(GNres):(GNspr), (-GNspr):(GNres):(GNspr));
Z = GNpk*exp( - (a*(X-GNx0).^2 + c*(Y-GNy0).^2)) ;

hkMask=Z;

%----------------%
% FIGURE: 3D Gaussian Distribution
fh65 = figure(65); %set(fh5,'OuterPosition',(scsz./[2e-3 2e-3 2 2]))
set(fh65,'OuterPosition',[200 200 500 300]);
%----------------%
figure(fh65)
subplot('Position',[.05 .55 .30 .40]);
ph5 = imagesc(hkMask);
axis equal;
%set(gca,'XTick',[],'YTick',[])
subplot('Position',[.04 .08 .32 .42]);
ph7 = surf(X,Y,Z);
axis equal; shading interp; view(90,90);
subplot('Position',[.45 .05 .50 .90]);
ph7 = surf(X,Y,Z);
axis vis3d; shading interp;
view(-45,30);
xlabel('x-axis');ylabel('y-axis');zlabel('z-axis')
%----------------%

end
%----------------------------------%

</syntaxhighlight>

<br /><br />
{{Clear}}