function CM = simConn_L4toL23_FsPVtoAll(ADO_Mat, postIND, postType, AxonRatio, DendRatio, DMs)
% ADO_Mat: axon-dendritic overlap matrix
% postIND: indexing to seperate different type of post synaptic cells
% postType: numbers specify the type of post-synaptic cell
% one group (about 1/3) of PV+ interneurons in layer4 project to layer 2/3
% assume the same connection and synaptic properties as the PV+ cells in
% L2/3
% keyboard
% connectivity matrix need to be calculated for each type of post synaptic
% cell
for i = 1:length(postIND) - 1
temp = ADO_Mat(postIND(i)+1:postIND(i+1), :);
ADO_temp = temp;
DM = DMs(postIND(i)+1:postIND(i+1), :);
DR = DendRatio(postIND(i)+1:postIND(i+1));
switch postType(i)
case(1) % post-synaptic cell is pyramidal
CM(postIND(i)+1:postIND(i+1), :) = simConn_L4toL23_FsPVtoPyr(temp, AxonRatio, DendRatio(postIND(i)+1:postIND(i+1)));
case{2, 3} % post-synaptic cell is FsPV or chandiler
CM(postIND(i)+1:postIND(i+1), :) = simConn_L4toL23_FsPVtoFsPV(temp, AxonRatio, DendRatio(postIND(i)+1:postIND(i+1)));
case(4) % post-synaptic cell is RsPV
CM(postIND(i)+1:postIND(i+1), :) = simConn_L4toL23_FsPVtoRsPV(temp, AxonRatio, DendRatio(postIND(i)+1:postIND(i+1)));
case{5, 6} % post-synaptic cell is MarSOM
CM(postIND(i)+1:postIND(i+1), :) = simConn_L4toL23_FsPVtoMarSOM(temp, AxonRatio, DendRatio(postIND(i)+1:postIND(i+1)));
case{7, 8} % post-synaptic cell is BipVIP
CM(postIND(i)+1:postIND(i+1), :) = simConn_L4toL23_FsPVtoBipVIP(temp, AxonRatio, DendRatio(postIND(i)+1:postIND(i+1)));
case(9) % post-synaptic cell is BipCR
CM(postIND(i)+1:postIND(i+1), :) = simConn_L4toL23_FsPVtoBipCR(temp, AxonRatio, DendRatio(postIND(i)+1:postIND(i+1)));
case(10) % post-synaptic cell in SbcCR
CM(postIND(i)+1:postIND(i+1), :) = simConn_L4toL23_FsPVtoSbcCR(temp, AxonRatio, DendRatio(postIND(i)+1:postIND(i+1)));
case(11) % post-synaptic cell in NG cells
CM(postIND(i)+1:postIND(i+1), :) = simConn_L4toL23_FsPVtoNG(temp, AxonRatio, DendRatio(postIND(i)+1:postIND(i+1)));
end
end
%% nested function
function CMs = simConn_L4toL23_FsPVtoPyr(ADO_temp, AR, DR)
% map axon-dendrite overlapping index into connectivity matrix
% the value is normalized to meausre average connection probability
% from experiment; for Pyr-Pyr connection, within 50 micron p =
% 0.19
% also total number of connection is controlled by the axon and
% dendrite ratio in the model region
% assuming a total convengenc/divergence rate of 140 for total
% connection
pConn = ADO_temp/3.2454e-12*0.5;
% convert pConn into binary connectivity matrix
RI = rand(size(pConn));
CMs = zeros(size(pConn));
CMs(RI < pConn) = 1;
CMs = conn_reduction(CMs, 700*AR', 60*DR');
end
function CMs = simConn_L4toL23_FsPVtoFsPV(ADO_temp, AR, DR)
% for Pyr-FsPV connection, within 50 micron p =
% 0.85
% assuming a total convengenc rate of 700 and divergence rate of 90
pConn = ADO_temp/3.9171e-12*0.40;
% convert pConn into binary connectivity matrix
RI = rand(size(pConn));
CMs = zeros(size(pConn));
CMs(RI < pConn) = 1;
CMs = conn_reduction(CMs, 50*AR', 50*DR');
end
function CMs = simConn_L4toL23_FsPVtoRsPV(ADO_temp, AR, DR)
% for Pyr-FsPV connection, no connections
% assuming a total convengenc rate of 240 and divergence rate of 40
% pConn = ADO_temp/1.2930e-12*0.4;
% convert pConn into binary connectivity matrix
% RI = rand(size(pConn));
CMs = zeros(size(ADO_temp));
% CMs(RI < pConn) = 1;
%
% CMs = conn_reduction(CMs, 45*AR', 210*DR');
end
function CMs = simConn_L4toL23_FsPVtoMarSOM(ADO_temp, AR, DR)
% for Pyr-MarSOM connection, no connection
% assuming a total convengenc rate of 700 and divergence rate of 90
%
% pConn = ADO_temp/3.1268e-12*0.7;
% % convert pConn into binary connectivity matrix
% RI = rand(size(pConn));
CMs = zeros(size(ADO_temp));
% CMs(RI < pConn) = 1;
%
% CMs = conn_reduction(CMs, 70*AR', 700*DR');
end
function CMs = simConn_L4toL23_FsPVtoBipVIP(ADO_temp, AR, DR)
% for Pyr-FsPV connection, within 150 micron p =
% 0.21
% assuming a total convengenc rate of 700 and divergence rate of 90
pConn = ADO_temp/4.6968e-12*0.34;
% convert pConn into binary connectivity matrix
RI = rand(size(pConn));
CMs = zeros(size(pConn));
CMs(RI < pConn) = 1;
CMs = conn_reduction(CMs, 40*AR', 40*DR');
end
function CMs = simConn_L4toL23_FsPVtoBipCR(ADO_temp, AR, DR)
% for Pyr-FsPV connection, within 150 micron p =
% 0.183
% assuming a total convengenc rate of 700 and divergence rate of 90
pConn = ADO_temp/4.5486e-12*0.34;
% convert pConn into binary connectivity matrix
RI = rand(size(pConn));
CMs = zeros(size(pConn));
CMs(RI < pConn) = 1;
CMs = conn_reduction(CMs, 40*AR', 40*DR');
end
function CMs = simConn_L4toL23_FsPVtoSbcCR(ADO_temp, AR, DR)
% for Pyr-FsPV connection, within 150 micron p =
% 0.174
% assuming a total convengenc rate of 700 and divergence rate of 90
pConn = ADO_temp/4.6328e-12*0.28;
% convert pConn into binary connectivity matrix
RI = rand(size(pConn));
CMs = zeros(size(pConn));
CMs(RI < pConn) = 1;
CMs = conn_reduction(CMs, 30*AR', 30*DR');
end
function CMs = simConn_L4toL23_FsPVtoNG(ADO_temp, AR, DR)
% for Pyr-FsPV connection, within 150 micron p =
% 0.6
% assuming a total convengenc rate of 700 and divergence rate of 90
pConn = ADO_temp/4.5429e-12*0.45;
% convert pConn into binary connectivity matrix
RI = rand(size(pConn));
CMs = zeros(size(pConn));
CMs(RI < pConn) = 1;
CMs = conn_reduction(CMs, 40*AR', 40*DR');
end
end
% %%
% %check connection probability as a function of distance
% bin = 0:25:500;
% N_all = [0, cumsum(NiN2)];
% Pconn = {};
% for post = 1:length(N_all) - 1
% Pconn{post,1} = PConn_pairs(CM_modified(N_all(post)+1:N_all(post+1),:), ...
% bin, DM(N_all(post)+1:N_all(post+1), :));
% end