function main_spinal_cord_long_sub(simulation_number)
% 13 December 2012
% This is the main routine to generate the Connectome
% This routine additionally contains dendritic field data
% In this version of 24 Oct 2012 a new routine Generalize_data was used
% also probability of synaptic contacts can be change in the main routine:
% low one is universal and high is for synapses from RB to dla and dlc
%
%%
%clear all
close all
%
global cell_colours;
global gap_between_cells;
global dendwidth;
global total_number_of_cells;
global side_shift;
global prob_syn_low;
global prob_syn_high;
prob_syn_low=0.46;% probability of synapse for all cells exceptfrom RB to dl, ususally 0.46
prob_syn_high=0.63;% probability of synapse from RB to dl, usually 0.63
%
%%
% from Bristol
% The RGB values in the current figures are: % divide 255
rb_colour = [255/255,210/255,50/255];
dlc_colour = [255/255,0/255,0/255];
ain_colour = [70/255,70/255,180/255];
cin_colour = [0/255,170/255,220/255];
din_colour = [150/255,80/255,30/255];
mn_colour = [0/255,150/255,60/255];
dla_colour = [255/255,170/255,140/255]; %dla colour code
%
cell_colours(1,1:3) = rb_colour;
cell_colours(2,1:3) = dlc_colour;
cell_colours(3,1:3) = ain_colour;
cell_colours(4,1:3) = cin_colour;
cell_colours(5,1:3) = din_colour;
cell_colours(6,1:3) = mn_colour;
cell_colours(7,1:3) = dla_colour; %dla colour call
%
%%
section_length = 3800; % Length of cord to simulate (in microns) - from 0.6 to 4000
gap_between_cells =1.5; % It is a gap between cells
pos_per_bin=floor(100/gap_between_cells);
dendwidth = 1;
%
%
dorsal_dendrite = [];
ventral_dendrite = [];
%
%%
n_bins=33;
for j=1:7 %we do it for all cell types
for i=1:n_bins % we consider the body from 500 microns till 2000 microns, therefore 34 bins of 100 microns lengths
D=0.6+0.1*(i-1);
switch j
%Distribution of the number of RB cells
case 1
if D<0.9
number_of_cells(i,1)=floor(15.78*D-7.92);
elseif D>=0.9 & D<3.5
number_of_cells(i,1)=floor(7.11*exp(-0.53*D)+1.67);
elseif D>=3.5 & D<3.9
number_of_cells(i,1)=floor(-5.87*D+22.87);
else
number_of_cells(i,1)=0;
end;
%Distribution of the number of dlc cells
case 2
if D<1.9
number_of_cells(i,2)=floor(-142.06*exp(-6.0*D)+4.54);
elseif D>=1.9 & D<3.2
number_of_cells(i,2)=floor(-0.0244*exp(1.665*D)+4.99);
else
number_of_cells(i,2)=0;
end;
%Distribution of the number of aIN cells
case 3
if D<0.8
number_of_cells(i,3)=0;
elseif D>=0.8 & D<3.0
number_of_cells(i,3)=floor(28.58*exp(-1.78*D)+2.94);
elseif D>=3.2 & D<3.5
number_of_cells(i,3)=floor(-5.59*D+19.6);
else
number_of_cells(i,3)=0;
end;
%Distribution of the number of cIN cells
case 4
if D<1.5
number_of_cells(i,4)=floor(-33.45*exp(-2.961*D)+15.816);
else
number_of_cells(i,4)=floor(45.23*exp(-0.3047*D)-13.746);
end;
%Distribution of the number of dIN cells
case 5
% number_of_cells(i,5)=floor(16*exp(-0.8*D))+1;
number_of_cells(i,5)=floor(11.5-3.2*D)+1;
%Distribution of the number of mn cells
case 6
if D<1.2
number_of_cells(i,6)=floor(-40.11*exp(-3.598*D)+13.46);
elseif D<3.2
number_of_cells(i,6)=floor(-0.065*exp(1.665*D)+13.3);
else
number_of_cells(i,6)=0;
end;
%Distribution of the number of dla cells
case 7
if D<1.2
number_of_cells(i,7)=0;
elseif D>=1.2 & D<1.6
number_of_cells(i,7)=floor(-2.74*10^6*exp(-11.8*D)+4.95);
elseif D>=1.6 & D<2.0
number_of_cells(i,7)=floor(-5.87*10^(-8)*exp(9.2*D)+5.04);
else
number_of_cells(i,7)=0;
end;
end;
end;
end;
total_number_of_cells = sum(sum(number_of_cells));% This is a total number of cells on one side
final_cell_number=total_number_of_cells+total_number_of_cells; % this id total number of cells on both left and rigth sides
side_shift=total_number_of_cells; %This is decrement which we will add to cell numbers on the rigt side,
% so, left side cells are numbered as form 1 to the total_number_of_cells and
% right side cells are numbered as form
% total_number_of_cells+1 to
% final_cell_number
%%
% All this stuff for left side
cell_types1(1:n_bins,1:pos_per_bin)=0;
ct(1:7)=randperm(7);%[4 1 2 3 6 7 ];
for i=1:n_bins
% if number_of_cells(i,5)~=0
% del=(pos_per_bin/(number_of_cells(i,5)));
% del_h=(del/2);
% for j1=1:number_of_cells(i,5)
% pos=round(del_h+(j1-1)*del);
% cell_types1(i,pos)=5;
% end;
% end;
for j=1:7
i1=ct(j);
if number_of_cells(i,i1) ~= 0
del=(pos_per_bin/(number_of_cells(i,i1)));
del_h=(del/2);
for j1=1:number_of_cells(i,i1)
pos=round(del_h+(j1-1)*del);
in=pos;%----------------------------empty? if not - adjust and put to in1
in1=in;
emp=cell_types1(i,in);
if (emp~=0)
k=0;
while emp~=0
k=k+1;
in1=in+k;
if in1<pos_per_bin+1
emp=cell_types1(i,in1);
end;
if emp~=0
in1=in-k;
if in1>0
emp=cell_types1(i,in1);
end;
end;
end
end;%------------------------------------
cell_types1(i,in1)=i1;
end;
end;
end
end;
total_positions=n_bins*pos_per_bin;
%%
%
cell_types1=reshape(cell_types1',total_positions,1);
rc_l=find(cell_types1);
cell_types=cell_types1(rc_l);
%rc_l=600+rc_l*gap_between_cells;
rc_l=500+rc_l*gap_between_cells;
%
%%
% Now we repeat the same for the right side
clear cell_types1;
cell_types1(1:n_bins,1:pos_per_bin)=0;
ct(1:7)=randperm(7);%[1 4 2 6 3 7];%[4 1 2 3 6 7 ];
for i=1:n_bins
% if number_of_cells(i,5)~=0
% del=(pos_per_bin/(number_of_cells(i,5)));
% del_h=(del/2);
% for j1=1:number_of_cells(i,5)
% pos=round(del_h+(j1-1)*del);
% cell_types1(i,pos)=5;
% end;
% end;
for j=1:7
i1=ct(j);
if number_of_cells(i,i1) ~= 0
del=(pos_per_bin/(number_of_cells(i,i1)));
del_h=(del/2);
for j1=1:number_of_cells(i,i1)
pos=round(del_h+(j1-1)*del);
in=pos;%----------------------------empty? if not - adjust and put to in1
in1=in;
emp=cell_types1(i,in);
if (emp~=0)
k=0;
while emp~=0
k=k+1;
in1=in+k;
if in1<pos_per_bin+1
emp=cell_types1(i,in1);
end;
if emp~=0
in1=in-k;
if in1>0
emp=cell_types1(i,in1);
end;
end;
end
end;%------------------------------------
cell_types1(i,in1)=i1;
end;
end;
end
end;
total_positions=n_bins*pos_per_bin;
cell_types1=reshape(cell_types1',total_positions,1);
%
rc_r=find(cell_types1);
%
cell_types(1+side_shift:final_cell_number)=cell_types1(rc_r);
% rc_r=600+rc_r*gap_between_cells;
rc_r=500+rc_r*gap_between_cells;
%
rc=[rc_l; rc_r]';
cell_types=cell_types';
%
%%
dorsal_den_exp5=[70.3232 61.2352 77.3632 72.9856 76.672 99.456 97.024 94.9504 66.56 64.896];
ventral_den_exp5=[32.9728 50.0736 51.584 67.2256 61.5168 85.6832 71.5264 74.24 44.8512 40.1664];
%dlc_DSC_DVsize=[78.5152 88.5504 77.3632 91.4688 85.3504 113.8944 109.6448 105.5232 79.3088 79.744];
dorsal_dendrites_dlc=dorsal_den_exp5';%./dlc_DSC_DVsize'*100; %normalized
ventral_dendrites_dlc=ventral_den_exp5';%./dlc_DSC_DVsize'*100; %normalized
%
%
%%
dorsal_den_exp4=[47.2576 54.1696 66.56 37.0176 53.76 50.176 76.8 40.6528 53.76 60.16];
ventral_den_exp4=[1.5104 4.992 4.1216 2.944 8.192 0.256 30.72 2 1.28 12.8];
%aIN_DSC_DVsize=[94.72 86.4 92.16 105.4464 92.16 92.6208 94.72 82.7648 104.96 70.4]; % aIN D-V cord size (from data)'differet # from axon growth'
dorsal_dendrites_aIN=dorsal_den_exp4';%./aIN_DSC_DVsize'*100; %normalized
ventral_dendrites_aIN=ventral_den_exp4';%./aIN_DSC_DVsize'*100; %normalized
%
%
%%
dorsal_den_exp2=[93 79 79 77 76 76 73 73 70 70 69 67 67 65 65 63 58 55 52 52 52 50 50 45 38 38 37 37 36 36 35 35 33 19];
ventral_den_exp2=[50 44 35 41 24 24 22 49 31 36 19 26 33 26 26 45 15 13 12 19 9 12 38 24 24 20 35 35 15 15 26 22 19 14];
%cIN_DSC_DVsize=[101.12 99.84 96 102.4 94.72 89.6 89.6 98.56 93.44 85.76];
dorsal_dendrites_cIN=dorsal_den_exp2';%./cIN_DSC_DVsize'*100; %normalized
ventral_dendrites_cIN=ventral_den_exp2';%./cIN_DSC_DVsize'*100; %normalized
%
%
%%
%
dIN_proby_table=[];
dorsal_den_gr1=[77.7700 105.2300 65.4100 92.6700 94.5700 70.4000 82.5700 48.6100 67.9700 32.7100 91.3600 89.2300 80.6000 75.5200 12.8 61.7600 61.2100 78.1000 54.3900];
ventral_den_gr1=[25.1600 53.2300 0 40.4100 0 19.2000 9.4400 4.1700 30.5300 2.3000 0 38.7000 29.4000 7.6800 5.1 38.3700 35.4900 23.0000 1.2200];
%
dorsal_den_gr2=[34.6000 54.4600 72.9600 72.7600 62.4700 76.8000 52.0000 40.3400 61.4000 54.8400 64.5300 59.9800 49.1700 74.2000 59.8800];
ventral_den_gr2=[2.6000 28.5400 2.5600 56.4300 35.3000 30.7000 20.0000 1.3600 2.6000 16.7000 13.3300 15.2400 24.1700 58.9000 28.7100];
%
dorsal_den_gr3=[87.0000 56.3000 75.5000 64.6000 61.4500 54.4100 35.8000 58.4000 37.1000 74.2000 94.7000 51.2000 32.4200 49.4900 66.6000 89.6000 32.6200 64.0000 69.1000];
ventral_den_gr3=[46.1000 10.2000 52.5000 18.2400 41.9100 37.6900 29.4000 0 24.3000 33.3000 43.5000 48.6000 15.2300 10.9800 35.8000 69.1000 14.5400 33.3000 25.6000];
%
%dIN_DSC_DVsize=[74.0096 93.6704 89.1904 90.5472 96.2304 87.4496 88.3712 78.6432 93.4912 95.2576]; % dIN D-V cord size (from data)'differet # from axon growth'
dorsal_dendrites_dIN_gr1=dorsal_den_gr1';
dorsal_dendrites_dIN_gr2=dorsal_den_gr2';
dorsal_dendrites_dIN_gr3=dorsal_den_gr3';
%
ventral_dendrites_dIN_gr1=ventral_den_gr1';
ventral_dendrites_dIN_gr2=ventral_den_gr2';
ventral_dendrites_dIN_gr3=ventral_den_gr3';
%
%
%%
dorsal_den_exp6=[36.00291 39.40073 51.47927 46.89455 32.60509 55.22618 64.13964 48.2304 23.5008 51.072 45.184];
ventral_den_exp6=[1.536 10.30982 10.40291 12.89309 5.888 10.03055 3.095273 18.8416 1.152 1.9968 1.6128];
%MN_DSC_DVsize=[117.1084 112.8727 105.6582 96.58182 99.88655 114.8509 109.9636 104.32 82.3808 78.72 87.808 ]; %MN D-V cord size (from data)'differet # from axon growth'
dorsal_dendrites_mn=dorsal_den_exp6';%./MN_DSC_DVsize'*100; %normalized
ventral_dendrites_mn=ventral_den_exp6';%./MN_DSC_DVsize'*100; %normalized
%
%%
dorsal_dendrites_dla=[59 71 86 72 68 72 64 64 68];
ventral_dendrites_dla=[46 67 75 54 41 48 61 41 54];
%
%
%% Determine dendritic fields on the left side
%
limiting_factor=5.;
%
for i=1:final_cell_number
ct=cell_types(i);
sd_v=15.; %%%%%% Standard deviation for ventral end. YOU CAN MODIFY THAT!
sd_d=15.; %%%%%% Standard deviation for dorsal end.YOU CAN MODIFY THAT!
ro=0.8;
%
switch ct
case(1)
dorsal_dendrite(i) = 0;
ventral_dendrite(i) = 0;
case{2}
% sd_d=0.;
% dorsal_dendrites_dlc=137;
[dd, vd] = dendrite_allocation_reconst(dorsal_dendrites_dlc,ventral_dendrites_dlc,sd_d,sd_v,ro,limiting_factor);
dorsal_dendrite(i) = 137;
ventral_dendrite(i) = (137-(dd+25))+ vd+25;
case{3}
[dd, vd] = dendrite_allocation_reconst(dorsal_dendrites_aIN,ventral_dendrites_aIN,sd_d,sd_v,ro,limiting_factor);
dorsal_dendrite(i) = dd+25;
ventral_dendrite(i) = vd+25;
case{4}
[dd, vd] = dendrite_allocation_reconst(dorsal_dendrites_cIN,ventral_dendrites_cIN,sd_d,sd_v,ro,limiting_factor);
dorsal_dendrite(i) = dd+25;
ventral_dendrite(i) = vd+25;
case(5)
if rc(i)<=850
[dd, vd] = dendrite_allocation_reconst(dorsal_dendrites_dIN_gr1,ventral_dendrites_dIN_gr1,sd_d,sd_v,ro,limiting_factor);
dorsal_dendrite(i) = dd+25;
ventral_dendrite(i) = vd+25;
end
if rc(i)>850 & rc(i)<=1400
[dd, vd] = dendrite_allocation_reconst(dorsal_dendrites_dIN_gr2,ventral_dendrites_dIN_gr2,sd_d,sd_v,ro,limiting_factor);
dorsal_dendrite(i) = dd+25;
ventral_dendrite(i) = vd+25;
end
if rc(i)>1400
[dd, vd] = dendrite_allocation_reconst(dorsal_dendrites_dIN_gr3,ventral_dendrites_dIN_gr3,sd_d,sd_v,ro,limiting_factor);
dorsal_dendrite(i) = dd+25;
ventral_dendrite(i) = vd+25;
end
case{6}
[dd, vd] = dendrite_allocation_reconst(dorsal_dendrites_mn,ventral_dendrites_mn,sd_d,sd_v,ro,limiting_factor);
dorsal_dendrite(i) = dd+25;
ventral_dendrite(i) = vd+25;
case{7}
%dorsal_dendrites_dla=137;
%sd_d=0.;
[dd, vd] = dendrite_allocation_reconst(dorsal_dendrites_dla,ventral_dendrites_dla,sd_d,sd_v,ro,limiting_factor);
dorsal_dendrite(i) = 137;
ventral_dendrite(i) = (137-(dd+25))+vd+25;
end
end
%
%% Display dendrites on the left side and right side
% %% left side
% %scaling = 1;
% figure(1);
% hold on;
% xlabel('Distance from midbrain (\mum)','FontSize',14);
% ylabel('D-V Axis (\mum)','FontSize',14);
% title('Generated Tadpole Spinal Connectome','FontSize',14);
% caud=3800; % gives caudal extent of graph
% axis([000 caud -145 145]);
% %set(fig2,'OuterPosition',pos2)
% rectangle('Position',[0, -145, caud, 290],'FaceColor',[255/255,255/255,204/255]);
% rectangle('Position',[0, -25, caud, 50],'FaceColor',[25/255,25/255,112/255]);%[153/204 204/204 153/204]);
% rectangle('Position',[700, 125, caud, 2],'FaceColor',[255/255,0/255,0/255]);
% rectangle('Position',[700, -127, caud, 2],'FaceColor',[255/255,0/255,0/255]);
% rectangle('Position',[500, 137, caud, 8],'FaceColor',[255/255,210/255,50/255]);
% rectangle('Position',[500, -145, caud, 8],'FaceColor',[255/255,210/255,50/255]);
% grid off;
% %
% for i=1:total_number_of_cells
% if cell_types(i)> 1
% rectangle('Position',[rc(i)-dendwidth/2, ventral_dendrite(i), dendwidth, dorsal_dendrite(i) - ventral_dendrite(i)],'FaceColor',cell_colours(cell_types(i),1:3));
% end
% end
% %
%% Determine dendritic fields on the right side
for i=side_shift+1:final_cell_number
ct=cell_types(i);
sd_v=15.; %%%%%% Standard deviation for ventral end. YOU CAN MODIFY THAT!
sd_d=15.; %%%%%% Standard deviation for dorsal end.YOU CAN MODIFY THAT!
ro=0.8;
% if cell_types(i)> 1 % No dendrites for RB
switch ct
case(1)
dorsal_dendrite(i) = 0;
ventral_dendrite(i) = 0;
case{2}
% sd_d=0.;
% dorsal_dendrites_dlc=137;
[dd, vd] = dendrite_allocation_reconst(dorsal_dendrites_dlc,ventral_dendrites_dlc,sd_d,sd_v,ro,limiting_factor);
dorsal_dendrite(i) = 137;
ventral_dendrite(i) = (137-(dd+25))+(vd+25);
case{3}
[dd, vd] = dendrite_allocation_reconst(dorsal_dendrites_aIN,ventral_dendrites_aIN,sd_d,sd_v,ro,limiting_factor);
dorsal_dendrite(i) = (dd+25);
ventral_dendrite(i) = (vd+25);
case{4}
[dd, vd] = dendrite_allocation_reconst(dorsal_dendrites_cIN,ventral_dendrites_cIN,sd_d,sd_v,ro,limiting_factor);
dorsal_dendrite(i) = (dd+25);
ventral_dendrite(i) = (vd+25);
case(5)
if rc(i)<=850
[dd, vd] = dendrite_allocation_reconst(dorsal_dendrites_dIN_gr1,ventral_dendrites_dIN_gr1,sd_d,sd_v,ro,limiting_factor);
dorsal_dendrite(i) = (dd+25);
ventral_dendrite(i) = (vd+25);
end
if rc(i)>850 & rc(i)<=1400
[dd, vd] = dendrite_allocation_reconst(dorsal_dendrites_dIN_gr2,ventral_dendrites_dIN_gr2,sd_d,sd_v,ro,limiting_factor);
dorsal_dendrite(i) = (dd+25);
ventral_dendrite(i) = (vd+25);
end
if rc(i)>1400
[dd, vd] = dendrite_allocation_reconst(dorsal_dendrites_dIN_gr3,ventral_dendrites_dIN_gr3,sd_d,sd_v,ro,limiting_factor);
dorsal_dendrite(i) = (dd+25);
ventral_dendrite(i) = (vd+25);
end
case{6}
[dd, vd] = dendrite_allocation_reconst(dorsal_dendrites_mn,ventral_dendrites_mn,sd_d,sd_v,ro,limiting_factor);
dorsal_dendrite(i) = (dd+25);
ventral_dendrite(i) = (vd+25);
case{7}
%dorsal_dendrites_dla=137;
%sd_d=0.;
[dd, vd] = dendrite_allocation_reconst(dorsal_dendrites_dla,ventral_dendrites_dla,sd_d,sd_v,ro,limiting_factor);
dorsal_dendrite(i) = 137;
ventral_dendrite(i) = (137-(dd+25))+ (vd+25);
end
end
%% right side
% %Generate axons and make synapses on the right side
% %
% %scaling = 1;
% % figure(2);
% % hold on;
% % grid off;
% % xlim([0,(total_number_of_cells+1) * gap_between_cells]);
% % ylim([0,100]);
% % axis([500 1700 0 100]);
% % xlabel('Axon Length (micron)');
% % ylabel('D-V Position (%)');
% % title('Spinal cord right');
% for i=side_shift+1:final_cell_number %total_number_of_cells
% if cell_types(i)> 1
% rectangle('Position',[rc(i)-dendwidth/2, -dorsal_dendrite(i), dendwidth, (dorsal_dendrite(i) - ventral_dendrite(i))],'FaceColor',cell_colours(cell_types(i),1:3));
% end
% end
%
%% ***********************************Generate axons & record synapses for both Left and Right **************************
%
%
%
[syn_tab_asc_L syn_tab_desc_L axon_tab_asc_L axon_tab_desc_L] = generate_axons_and_make_synapses_L(cell_types, rc, dorsal_dendrite, ventral_dendrite);
[syn_tab_asc_R syn_tab_desc_R axon_tab_asc_R axon_tab_desc_R] = generate_axons_and_make_synapses_R(cell_types, rc, dorsal_dendrite, ventral_dendrite);
%
%
%
%
%% Data collection
% %% Syanaptic connectivity
% %
%save('D:\tadpole project\AnalysisCon_7ct_ascdIN\synapses_L_ascGrad.txt', 'syn_tab_asc_L', '-ascii', '-tabs');
%save('D:\tadpole project\AnalysisCon_7ct_ascdIN\synapses_L_descGrad.txt', 'syn_tab_desc_L', '-ascii', '-tabs');
% save('D:\tadpole project\AnalysisCon_7ct_ascdIN\synapses_R_ascGrad.txt', 'syn_tab_asc_R', '-ascii', '-tabs');
% save('D:\tadpole project\AnalysisCon_7ct_ascdIN\synapses_R_descGrad.txt', 'syn_tab_desc_R', '-ascii', '-tabs');
%
all_syn=[syn_tab_asc_L;syn_tab_desc_L;syn_tab_asc_R;syn_tab_desc_R];
size(all_syn)
% save('D:\tadpole project\AnalysisCon_7ct_ascdIN\ALL_synapsesGrad.txt','all_syn', '-ascii', '-tabs');
% all_syn=[syn_tab_asc_L;syn_tab_desc_L;syn_tab_asc_R;syn_tab_desc_R];
% save(['ALL_synapsesGrad.txt'],'all_syn', '-ascii', '-tabs');
% %
% save(['axon_L_ascGrad.txt'size(all_syn)], 'axon_tab_asc_L', '-ascii', '-tabs');
% save(['axon_L_descGrad.txt'], 'axon_tab_desc_L', '-ascii', '-tabs');
% save(['axon_R_ascGrad.txt'], 'axon_tab_asc_R', '-ascii', '-tabs');
% save(['axon_R_descGrad.txt'], 'axon_tab_desc_R', '-ascii', '-tabs');
% % %
% % %
% % %
% % %save ('spinal_synapse_connectivity_R.txt', '[syn_tab_asc_R; syn_tab_desc_R]', '-ascii -tabs');
% % %
% % %
% % %
% % %%
% % %
% % % Data collection left
% % %s=[];
% % i=1:1:final_cell_number; %for i=1:final_cell_number
% % s=[i; cell_types(i); rc(i); dorsal_dendrite(i); ventral_dendrite(i)]';
% % save('D:\tadpole project\AnalysisCon_7ct_ascdIN\DendriteGrad.txt', 's', '-ascii', '-tabs');
% i=1:1:final_cell_number; %for i=1:final_cell_number
% s=[i; cell_types(i); rc(i); dorsal_dendrite(i); ventral_dendrite(i)]';
% save(['DendriteGrad.txt'], 's', '-ascii', '-tabs');
%
%
% [q1,q2]=size(all_syn);
% in_con(1:final_cell_number,1:800)=0;
% ks(1:final_cell_number)=-1;
% for i=1:q1
% i_cur=all_syn(i,3);
% i_pre=all_syn(i,1);
% if (i_cur ~= i_pre)
% ks(i_cur)= ks(i_cur)+2;
% in_con(i_cur,ks(i_cur))=all_syn(i,1);
% in_con(i_cur,ks(i_cur)+1)=all_syn(i,2);
% end;
% end;
% for i=1:final_cell_number
% clear q3;
% q3=find(in_con(i,:));
% b(i,1)=length(q3)+1;
% b(i,2:ks(i)+2)=in_con(i,q3);
% end;
% %
% [qq1,maxrow_len]=size(b);
% %
% c=zeros(1,maxrow_len);
% c(1,1)=maxrow_len;
% c=[c;b];
%
% % save ('max_length.txt','maxrow_len','-ASCII','-tabs');
% fid=fopen(['inc_connectGrad.txt'],'wt');
%
% %fid=fopen('D:\tadpole project\AnalysisCon_7ct_ascdIN\inc_connect55.txt','wt');
% [q1,q2]=size(c);
% for i=1:q1
% fprintf(fid,'% 5.0f',c(i,1:q2));
% fprintf(fid,'\n');
% end;
% fclose(fid);
%
%
i=1:1:final_cell_number; %for i=1:final_cell_number
s=[i; cell_types(i); rc(i); dorsal_dendrite(i); ventral_dendrite(i)]';
save(['connectome files/Dendrite' num2str(simulation_number) '.txt'], 's', '-ascii', '-tabs');
[q1,q2]=size(all_syn);
in_con(1:final_cell_number,1:800)=0;
ks(1:final_cell_number)=-1;
for i=1:q1
i_cur=all_syn(i,3);
i_pre=all_syn(i,1);
if (i_cur ~= i_pre)
ks(i_cur)= ks(i_cur)+2;
in_con(i_cur,ks(i_cur))=all_syn(i,1);
in_con(i_cur,ks(i_cur)+1)=all_syn(i,2);
end;
end;
for i=1:final_cell_number
clear q3;
q3=find(in_con(i,:));
b(i,1)=length(q3)+1;
b(i,2:ks(i)+2)=in_con(i,q3);
end;
%
[qq1,maxrow_len]=size(b);
%
c=zeros(1,maxrow_len);
c(1,1)=maxrow_len;
c=[c;b];
% save ('max_length.txt','maxrow_len','-ASCII','-tabs');
fid=fopen(['connectome files/inc_connect' num2str(simulation_number) '.txt'],'wt');
%fid=fopen('D:\tadpole project\AnalysisCon_7ct_ascdIN\inc_connect55.txt','wt');
[q1,q2]=size(c);
for i=1:q1
fprintf(fid,'% 5.0f',c(i,1:q2));
fprintf(fid,'\n');
end;
fclose(fid);
clear all
close all
end