matlab_foci_GUI/stat_cell_param.m at master · junlabucsd/matlab_foci_GUI · GitHub

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clear all; clc;
close all;
warning off;


%% load data
parameters

dir_name = [data_dir 'picked/'];
fnames = dir( [ dir_name '/*.mat' ]);

% px_to_mu = 0.11;
t_int = 1; % leave as 1

%% extract and calculate all cell data

mother_cell_counter = 1;

for i=1:numel(fnames)
    struct_tmp = load([dir_name fnames(i).name]);
    fnames_channel = fieldnames(struct_tmp.cell_list);
    L_channles = length(fnames_channel(:,1));

    for j=1:L_channles
        fname_rec = fnames_channel{j,1};
        cell_temp = struct_tmp.cell_list.(fname_rec);

        length_temp = double(px_to_mu*cell_temp.lengths_w_div);

        if cell_temp.birth_label ==1 && isfield(cell_temp,'initiation_time') == 1
%             if (cell_temp.division_time - cell_temp.termination_time) > 10

                % && isfield(cell_temp,'initiation_time_n') == 1  && cell_temp.lengths_w_div(end) < 20 %&& cell_temp.peak > 0 && cell_temp.peak < 2000  %only look at mother cells and only those have cell cycle information; %filter out filamentous cells

            cell_id( mother_cell_counter ) = {cell_temp.id} ;

            generation_time( mother_cell_counter ) = double( cell_temp.tau ) ;

            newborn_length( mother_cell_counter ) = cell_temp.sb;
            newborn_width( mother_cell_counter ) = cell_temp.widths_w_div(1);
%             newborn_width( mother_cell_counter ) = mean(cell_temp.widths_w_div(1:end));

            division_length( mother_cell_counter ) = cell_temp.sd;
            division_width( mother_cell_counter ) = cell_temp.widths_w_div(end);
%             division_width( mother_cell_counter ) = mean(cell_temp.widths_w_div(1:end));

            newborn_volume( mother_cell_counter ) = (newborn_length( mother_cell_counter )-newborn_width( mother_cell_counter ))*pi*(newborn_width( mother_cell_counter )/2)^2+(4/3)*pi*(newborn_width( mother_cell_counter )/2)^3;
%             division_volume( mother_cell_counter ) = (division_length( mother_cell_counter )-division_width( mother_cell_counter ))*pi*(division_width( mother_cell_counter )/2)^2+(4/3)*pi*(division_width( mother_cell_counter )/2)^3;
            division_volume( mother_cell_counter ) = (division_length( mother_cell_counter )-2*division_width( mother_cell_counter ))*pi*(division_width( mother_cell_counter )/2)^2+2*(4/3)*pi*(division_width( mother_cell_counter )/2)^3;

            added_length( mother_cell_counter ) = division_length( mother_cell_counter ) - newborn_length( mother_cell_counter );

            added_volume( mother_cell_counter ) = division_volume( mother_cell_counter ) - newborn_volume( mother_cell_counter );

            cell_width( mother_cell_counter ) = mean(cell_temp.widths_w_div(1:end));

            septum_position( mother_cell_counter ) = cell_temp.septum_position;

            birth_time( mother_cell_counter) = t_int*double(cell_temp.birth_time);
            division_time( mother_cell_counter) = t_int*double(cell_temp.division_time);

            growth_rate( mother_cell_counter ) = 60*log(division_volume( mother_cell_counter )/newborn_volume( mother_cell_counter ))/generation_time( mother_cell_counter );
            elongation_rate( mother_cell_counter ) = 60*log(division_length( mother_cell_counter )/newborn_length( mother_cell_counter ))/generation_time( mother_cell_counter );

            if length(length_temp)>2
            ft1 = fittype('a*x+b');
            Growth_time = t_int*double( cell_temp.times_w_div - cell_temp.times_w_div(1) );
            Growth_length = px_to_mu*cell_temp.lengths_w_div;

            fit_temp = fit(Growth_time',log(Growth_length)',ft1);

            elongation_rate_fit( mother_cell_counter ) = 60*fit_temp.a;
            elseif length(length_temp)==2
            elongation_rate_fit( mother_cell_counter ) = 60*elongation_rate( mother_cell_counter );
            end

            initiation_time_m( mother_cell_counter ) = t_int*double(cell_temp.initiation_time); %note the change in definitions
%             initiation_time( mother_cell_counter ) = t_int*double(cell_temp.initiation_time_n);
            termination_time( mother_cell_counter ) = t_int*double(cell_temp.termination_time);

            initiation_mass_m( mother_cell_counter ) = cell_temp.initiation_mass; %note the change in definitions
%             initiation_mass( mother_cell_counter ) = cell_temp.initiation_mass_n;
            termination_mass( mother_cell_counter ) = cell_temp.termination_mass;

            % calculate occ of mother cell for volumn calculation
            n_oc( mother_cell_counter) = cell_temp.n_oc ;

            B_period( mother_cell_counter ) = t_int*double(cell_temp.initiation_time - cell_temp.birth_time_m);
            C_period( mother_cell_counter ) = t_int*double(cell_temp.termination_time - cell_temp.initiation_time);
            D_period( mother_cell_counter ) = t_int*double(cell_temp.division_time - cell_temp.termination_time);
            tau_cyc( mother_cell_counter ) = t_int*double(cell_temp.division_time - cell_temp.initiation_time);


            mother_cell_counter = mother_cell_counter + 1;
%             end

        end

    end
    if mod(i,10)==0
        i
    end
end

% save('../../analysis/cell_cycle_stat_GUI.mat');