MicrotubuleGenerator.m

% Code for generating 3D microtubule model
% INPUT
% ************************************************************************
% xsize, ysize, zsize: size of output matrix
% sim_num: number of microtubules
% step_num: total step used for simulation (length?)
%
% OUTPUT
% ************************************************************************
% img: 3D matrix
%
% originally from Fang Huang and Jiaxi Zhao, 
% modified by HAO, Xiang
% Aug 31, 2016

function img = MicrotubuleGenerator(xsize,ysize,zsize,sim_num,step_num)
%% parameters
l = 1;  % nm
KT = 4.1;   % pN/nm
A = 1000;
forces = zeros(1,sim_num);

%% Part 1: Construct a random microtubule map from result generated by WLC

[wlcseries] = WLCmicrotubules(forces,KT,A,l,step_num);
len = size(wlcseries,3);

wlc_centers=mean(wlcseries,1);
normalized_wlc=wlcseries-repmat(wlc_centers,[step_num 1 1]);
randomshift=rand(size(wlc_centers))*1000-500;
random_wlc=normalized_wlc+repmat(randomshift,[step_num 1 1]);

%% Part 2: Shift Origin & normalize chain
% randomized
% shift origin
random_wlc(:,1,:) = random_wlc(:,1,:)-min(min(random_wlc(:,1,:)));
random_wlc(:,2,:) = random_wlc(:,2,:)-min(min(random_wlc(:,2,:)));
random_wlc(:,3,:) = random_wlc(:,3,:)-min(min(random_wlc(:,3,:)));

% normalize chain
random_wlc(:,1,:) = random_wlc(:,1,:)/max(max(abs(random_wlc(:,1,:))));
random_wlc(:,2,:) = random_wlc(:,2,:)/max(max(abs(random_wlc(:,2,:))));
random_wlc(:,3,:) = random_wlc(:,3,:)/max(max(abs(random_wlc(:,3,:))));

% plot randomized chain
figure
hold on
for ii=1:len
    plot(random_wlc(:,1,ii),random_wlc(:,2,ii),'color',rand(3,1),'linewidth',2)
end

% normalized
% shift origin
normalized_wlc(:,1,:) = normalized_wlc(:,1,:)-min(min(normalized_wlc(:,1,:)));
normalized_wlc(:,2,:) = normalized_wlc(:,2,:)-min(min(normalized_wlc(:,2,:)));
normalized_wlc(:,3,:) = normalized_wlc(:,3,:)-min(min(normalized_wlc(:,3,:)));

% normalize chain
normalized_wlc(:,1,:) = normalized_wlc(:,1,:)/max(max(abs(normalized_wlc(:,1,:))));
normalized_wlc(:,2,:) = normalized_wlc(:,2,:)/max(max(abs(normalized_wlc(:,2,:))));
normalized_wlc(:,3,:) = normalized_wlc(:,3,:)/max(max(abs(normalized_wlc(:,3,:))));

% plot normalized chain (normalized)
figure
hold on
for ii=1:len
    plot(normalized_wlc(:,1,ii),normalized_wlc(:,2,ii),'color',rand(3,1),'linewidth',2)
end

%% Part 3: Generate 3D image
img_original = zeros(xsize,ysize,zsize);
for i = 1:sim_num
    for j = 1:step_num
        xcart = round(xsize*normalized_wlc(j,1,i)) + 1;
        ycart = round(ysize*normalized_wlc(j,2,i)) + 1;
        zcart = round(zsize*normalized_wlc(j,3,i)) + 1;
        img_original(xcart,ycart,zcart) = 1;
    end
end

img_original = img_original(1:xsize,1:ysize,1:zsize);
img = img_original;
% img = imgaussfilt3(img_original,1);
% 
% mkdir('./result');
% save(['./result/microtubule_model_',num2str(sim_num),'_' date '.mat'],'img','img_original','-v7.3');
% threeDViewer(img);
end