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

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
clear all; clc;
close all;
warning off;

%% load data

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

px_to_mu = 0.065;
t_int = 3.0;

%% 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
        cell_g2_id = fnames_channel{j,1};
        cell_g2_temp = struct_tmp.cell_list.(cell_g2_id);

        length_g2_temp = double(px_to_mu*cell_g2_temp.lengths_w_div);

%         if cell_g2_temp.birth_label ==1 && isfield(cell_g2_temp,'initiation_time') == 1 && cell_g2_temp.lengths_w_div(end) < 20 && ismember(cell_g2_temp.daughters(1,:),fnames_channel) %&& cell_g2_temp.peak > 0 && cell_g2_temp.peak < 2000  %filter out filamentous cells
        if cell_g2_temp.birth_label ==1 && isfield(cell_g2_temp,'initiation_time') == 1 && isfield(cell_g2_temp,'initiation_time_n') == 1 && cell_g2_temp.lengths_w_div(end) < 20 && ismember(cell_g2_temp.daughters(1,:),fnames_channel) %&& cell_g2_temp.peak > 0 && cell_g2_temp.peak < 2000  %filter out filamentous cells
%         if cell_g2_temp.birth_label ==1 && isfield(cell_g2_temp,'initiation_time') == 1 && isfield(cell_g2_temp,'initiation_time_n') == 1 && isfield(cell_g2_temp,'initiation_time_n2') == 0 && cell_g2_temp.n_oc_n == 2 && cell_g2_temp.lengths_w_div(end) < 20 && ismember(cell_g2_temp.daughters(1,:),fnames_channel) %&& cell_g2_temp.peak > 0 && cell_g2_temp.peak < 2000  %filter out filamentous cells


            cell_g3_id = cell_g2_temp.daughters(1,:);
            cell_g3_temp = struct_tmp.cell_list.(cell_g3_id);

            length_g3_temp = double(px_to_mu*cell_g3_temp.lengths_w_div);

%             if cell_g2_temp.lengths_w_div(end) < 20 && isfield(cell_g3_temp,'initiation_time') == 1 && cell_g3_temp.lengths_w_div(end) < 20 %filter out filamentous cells
            if cell_g2_temp.lengths_w_div(end) < 20 && isfield(cell_g3_temp,'initiation_time') == 1  && isfield(cell_g3_temp,'initiation_time_n') == 1 && cell_g3_temp.lengths_w_div(end) < 20 %filter out filamentous cells
%             if cell_g2_temp.lengths_w_div(end) < 20 && isfield(cell_g3_temp,'initiation_time') == 1  && isfield(cell_g3_temp,'initiation_time_n') == 1 && isfield(cell_g3_temp,'initiation_time_n2') == 0 && cell_g3_temp.n_oc_n == 2 && cell_g3_temp.lengths_w_div(end) < 20 %filter out filamentous cells


                %----------parameters for mother generation--------
                generation_time_g2( mother_cell_counter ) = double( cell_g2_temp.tau ) ;

                newborn_length_g2( mother_cell_counter ) = cell_g2_temp.sb;
                newborn_width_g2( mother_cell_counter ) = cell_g2_temp.widths_w_div(1);

                division_length_g2( mother_cell_counter ) = cell_g2_temp.sd;
                division_width_g2( mother_cell_counter ) = cell_g2_temp.widths_w_div(end);

                newborn_volume_g2( mother_cell_counter ) = (newborn_length_g2( mother_cell_counter )-newborn_width_g2( mother_cell_counter ))*pi*(newborn_width_g2( mother_cell_counter )/2)^2+(4/3)*pi*(newborn_width_g2( mother_cell_counter )/2)^3;
                division_volume_g2( mother_cell_counter ) = (division_length_g2( mother_cell_counter )-division_width_g2( mother_cell_counter ))*pi*(division_width_g2( mother_cell_counter )/2)^2+(4/3)*pi*(division_width_g2( mother_cell_counter )/2)^3;

                added_length_g2( mother_cell_counter ) = division_length_g2( mother_cell_counter ) - newborn_length_g2( mother_cell_counter );

                added_volume_g2( mother_cell_counter ) = division_volume_g2( mother_cell_counter ) - newborn_volume_g2( mother_cell_counter );

                cell_width_g2( mother_cell_counter ) = mean(cell_g2_temp.widths_w_div(1:end));

                septum_position_g2( mother_cell_counter ) = cell_g2_temp.septum_position;

                birth_time_g2( mother_cell_counter) = t_int*double(cell_g2_temp.birth_time);
                division_time_g2( mother_cell_counter) = t_int*double(cell_g2_temp.division_time);

                growth_rate_g2( mother_cell_counter ) = 60*log(division_volume_g2( mother_cell_counter )/newborn_volume_g2( mother_cell_counter ))/generation_time_g2( mother_cell_counter );
                elongation_rate_g2( mother_cell_counter ) = 60*log(division_length_g2( mother_cell_counter )/newborn_length_g2( mother_cell_counter ))/generation_time_g2( mother_cell_counter );

                if length(length_g2_temp)>2
                    ft1 = fittype('a*x+b');
                    Growth_time = t_int*double( cell_g2_temp.times_w_div - cell_g2_temp.times_w_div(1) );
                    Growth_length = px_to_mu*cell_g2_temp.lengths_w_div;

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

                    elongation_rate_fit_g2( mother_cell_counter ) = 60*fit_temp.a;
                elseif length(length_g2_temp)==2
                    elongation_rate_fit_g2( mother_cell_counter ) = 60*elongation_rate_g2( mother_cell_counter );
                end

                initiation_time_g2_m( mother_cell_counter ) = t_int*double(cell_g2_temp.initiation_time); %note the change in definitions
                initiation_time_g2( mother_cell_counter ) = t_int*double(cell_g2_temp.initiation_time_n);
                termination_time_g2( mother_cell_counter ) = t_int*double(cell_g2_temp.termination_time);

                initiation_mass_g2_m( mother_cell_counter ) = cell_g2_temp.initiation_mass; %note the change in definitions
                initiation_mass_g2( mother_cell_counter ) = cell_g2_temp.initiation_mass_n;
                termination_mass_g2( mother_cell_counter ) = cell_g2_temp.termination_mass;

                B_period_g2( mother_cell_counter ) = t_int*double(cell_g2_temp.initiation_time - cell_g2_temp.birth_time_m);
                C_period_g2( mother_cell_counter ) = t_int*double(cell_g2_temp.termination_time - cell_g2_temp.initiation_time);
                D_period_g2( mother_cell_counter ) = t_int*double(cell_g2_temp.division_time - cell_g2_temp.termination_time);
                tau_cyc_g2( mother_cell_counter ) = t_int*double(cell_g2_temp.division_time - cell_g2_temp.initiation_time);


                %----------parameters for daughter generation--------
                generation_time_g3( mother_cell_counter ) = double( cell_g3_temp.tau ) ;

                newborn_length_g3( mother_cell_counter ) = cell_g3_temp.sb;
                newborn_width_g3( mother_cell_counter ) = cell_g3_temp.widths_w_div(1);

                division_length_g3( mother_cell_counter ) = cell_g3_temp.sd;
                division_width_g3( mother_cell_counter ) = cell_g3_temp.widths_w_div(end);

                newborn_volume_g3( mother_cell_counter ) = (newborn_length_g3( mother_cell_counter )-newborn_width_g3( mother_cell_counter ))*pi*(newborn_width_g3( mother_cell_counter )/2)^2+(4/3)*pi*(newborn_width_g3( mother_cell_counter )/2)^3;
                division_volume_g3( mother_cell_counter ) = (division_length_g3( mother_cell_counter )-division_width_g3( mother_cell_counter ))*pi*(division_width_g3( mother_cell_counter )/2)^2+(4/3)*pi*(division_width_g3( mother_cell_counter )/2)^3;

                added_length_g3( mother_cell_counter ) = division_length_g3( mother_cell_counter ) - newborn_length_g3( mother_cell_counter );

                added_volume_g3( mother_cell_counter ) = division_volume_g3( mother_cell_counter ) - newborn_volume_g3( mother_cell_counter );

                cell_width_g3( mother_cell_counter ) = mean(cell_g3_temp.widths_w_div(1:end));

                septum_position_g3( mother_cell_counter ) = cell_g3_temp.septum_position;

                birth_time_g3( mother_cell_counter) = t_int*double(cell_g3_temp.birth_time);
                division_time_g3( mother_cell_counter) = t_int*double(cell_g3_temp.division_time);

                growth_rate_g3( mother_cell_counter ) = 60*log(division_volume_g3( mother_cell_counter )/newborn_volume_g3( mother_cell_counter ))/generation_time_g3( mother_cell_counter );
                elongation_rate_g3( mother_cell_counter ) = 60*log(division_length_g3( mother_cell_counter )/newborn_length_g3( mother_cell_counter ))/generation_time_g3( mother_cell_counter );

                if length(length_g3_temp)>2
                    ft1 = fittype('a*x+b');
                    Growth_time = t_int*double( cell_g3_temp.times_w_div - cell_g3_temp.times_w_div(1) );
                    Growth_length = px_to_mu*cell_g3_temp.lengths_w_div;

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

                    elongation_rate_fit_g3( mother_cell_counter ) = 60*fit_temp.a;
                elseif length(length_g3_temp)==2
                    elongation_rate_fit_g3( mother_cell_counter ) = 60*elongation_rate_g3( mother_cell_counter );
                end

                initiation_time_g3_m( mother_cell_counter ) = t_int*double(cell_g3_temp.initiation_time); %note the change in definitions
                initiation_time_g3( mother_cell_counter ) = t_int*double(cell_g3_temp.initiation_time_n);
                termination_time_g3( mother_cell_counter ) = t_int*double(cell_g3_temp.termination_time);

                initiation_mass_g3_m( mother_cell_counter ) = cell_g3_temp.initiation_mass; %note the change in definitions
                initiation_mass_g3( mother_cell_counter ) = cell_g3_temp.initiation_mass_n;
                termination_mass_g3( mother_cell_counter ) = cell_g3_temp.termination_mass;

                B_period_g3( mother_cell_counter ) = t_int*double(cell_g3_temp.initiation_time - cell_g3_temp.birth_time_m);
                C_period_g3( mother_cell_counter ) = t_int*double(cell_g3_temp.termination_time - cell_g3_temp.initiation_time);
                D_period_g3( mother_cell_counter ) = t_int*double(cell_g3_temp.division_time - cell_g3_temp.termination_time);
                tau_cyc_g3( mother_cell_counter ) = t_int*double(cell_g3_temp.division_time - cell_g3_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_md_GUI_noc2.mat');