MATLABUtilityFunctions/InterpolateStack.m at master · KinneretLab/MATLABUtilityFunctions · GitHub

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addpath ('\\phhydra\data-new\phhydra\data\analysis\users\Yonit\Layer Separation - Matlab\matlabCode');

image_dir='\\phhydra\data-new\phhydra\Analysis\users\Yonit\Layer Separation - Matlab\Examples\2018_10_22_pos4\Original_Files';

out_dir='\\phhydra\data-new\\phhydra\Analysis\users\Yonit\Layer Separation - Matlab\Examples\2018_10_22_pos4\US_Original_Files';

exp_name = '2018_10_22_pos4';

mkdir(out_dir);

cd (image_dir);

tpoints = dir('*.tiff*');

for j = 1:length(tpoints)

    % Read raw data for each time point

    fileName = [image_dir,'\',tpoints(j).name];
    image3D = read3Dstack (fileName,image_dir);

    V = double(image3D);

    [X1,Y1,Z1] = size(V);
    [X,Y,Z] = meshgrid((1:X1),(1:Y1),(1:Z1));
    x_res = 1;
    y_res = 1;
    z_res = 2;

    [Xq,Yq,Zq] = meshgrid(1:(X1*x_res),1:(Y1*y_res),1:(1/z_res):Z1);

    Vq = interp3(X,Y,Z,V,Xq,Yq,Zq);
    Vq_uint16= uint16(Vq);

    first_frame = Vq_uint16(:,:,1);

    t_point_name = strcat(exp_name,'_T_',num2str(j,'%03.f'),'.tiff');

    cd(out_dir);

    imwrite(first_frame,t_point_name,'tiff');

    for i = 2:((Z1-1)*z_res+1)

        next_frame = Vq_uint16(:,:,i);
        imwrite(next_frame,t_point_name,'WriteMode','append');

    end
end