cell_processing_main.m

clc;
clear;
close all;
warning('off','all')
set(0,'defaultAxesFontSize',10)
set(0,'defaultAxesFontName', 'DejaVu Sans')
set(0,'defaultTextFontName', 'DejaVu Sans')

addpath(genpath('common_codes'));
% =========================================================================

raw_data_dir = uigetdir('ADD YOUR FOLDER DIRECTORY CONTAIING THE STACKED TIFF FILES');
disp(['Data directory: ',raw_data_dir])

case_list = dir(fullfile(raw_data_dir,'*.tif'));

N_cases = length(case_list);

case_set = 1:N_cases;

optionProcessing = 1;
optionPostprocessing = 0;
optionVideo = 1;

if optionProcessing
    plot_dir = 'results';
    mkdir(plot_dir)
    window_range = zeros(N_cases,4);

    basic_t = zeros(N_cases,1);
    peak_min = zeros(N_cases,1);
    area_min = zeros(N_cases,1);
    area_max = zeros(N_cases,1);
    time_step = zeros(N_cases,1); 
    d_acc_threshold = zeros(N_cases,1);
    
    
    for i = case_set
        close all
        figure('position',[200 100 800 800])
        C = strsplit(case_list(i).name,'.');
        case_string = strrep(C{1},'_',' ');
        img_fname = fullfile(case_list(i).folder,case_list(i).name);%fullfile(raw_data_dir,case_list(i).name);
        img = imread(img_fname, 1);
        imagesc(img); hold on;
        axis equal
        title(['Select region for case: ',case_string]);
        [x,y] = ginput(2);
        x0 = min(round(x));
        x1 = max(round(x));
        y0 = min(round(y));
        y1 = max(round(y));
        rectangle('Position',[x0 y0 x1-x0 y1-y0],'EdgeColor','r','LineWidth',3,'linestyle','--')
        print(fullfile(plot_dir,[case_string,'_ROI']),'-dtiff','-r300')
        window_range(i,:) = [x0 x1 y0 y1];
        
        close all
        prompt = {'Basic intensity thresholding:',...
            'Minimum peak intensity:',...
            'Minimum cell area:',...
            'Maximum cell area:',...
            'Time step (min) between frames:',...
            'd_acc to threshold motile cells:'};
        tt = 'Processing parameters';
        dims = [1 35];
        definput = {'20','25','3','1000','30','50'};
        answer = inputdlg(prompt,tt,dims,definput);
        basic_t(i) = str2double(answer{1});
        peak_min(i) = str2double(answer{2});
        area_min(i) = str2double(answer{3});
        area_max(i) = str2double(answer{4});
        time_step(i) = str2double(answer{5});
        d_acc_threshold(i) = str2double(answer{6});
        
    end
        
    
    props = [];    
    props.optionFigure = 0;
    props.downsample_factor = 7;
  
    for i = case_set
        
        C = strsplit(case_list(i).name,'.');
        case_string = C{1};
        disp(['Processing case: ',case_string])
        
        props.case_string = case_string;
        props.window_range = window_range(i,:);        
        props.img_fname = fullfile(case_list(i).folder,case_list(i).name);
        props.peak_min = peak_min(i);        
        props.basic_t = basic_t(i);
        props.area_min = area_min(i);
        props.area_max = area_max(i);    
        props.optionDebug = 0;
        props.connectivity = 4;
        
        cell_downsample_Hessian_segmentation(props);
        cell_parameterization(props);
        cell_tracking(case_string);
        cell_connect_tracks(case_string);        
        
    end
end

if optionPostprocessing
    
    props = [];  
    props.roseBins = 8;
    props.plot_UV_max = 10;
    props.plot_dXdY_max = 200;    
    props.plot_cell_num_max = 1000; 
    
    for i = case_set
        close all
        C = strsplit(case_list(i).name,'.');
        props.case_string = C{1};
        
        props.time_step = time_step(i);
        props.d_acc_threshold = d_acc_threshold(i); 
        cell_postprocessing(props);
        
    end
end

if optionVideo
    time_step = 1;
    for i = case_set
        close all
        C = strsplit(case_list(i).name,'.');
        case_string = C{1};
        
        cell_plot_sequence(case_string,time_step);
        
    end
end