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Tracker.m
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Tracker.m
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% Run without any inputs to open the GUI.
% Run with 2 or more inputs to run in batch mode.
%
% Batch Mode
% Input ('String', value) pairs
% 'String' is the variable value is assigned to.
% Ex: 'Raw Images Path', 'C:\Images\'
%
% "Default" <none>
% "Raw Images Path" <String>
% "Segmented Images Path" <String>
% "Tracked Images Path" <String>
% "Segmented Images Common Name" <String>
% "Raw Images Common Name" <String>
% "Tracked Images Common Name" <String>
% "Weight Overlap" <numeric>
% "Weight Centroids" <numeric>
% "Weight Size" <numeric>
% "Max Centroids Distance" <numeric>
% "Frames To Track" <String>
% "Min Mitotic Overlap" <numeric>
% "Daughter Size Similarity" <numeric>
% "Daughter Aspect Ratio Similarity" <numeric>
% "Circularity Index" <numeric>
% "Number Frames to Check Circularity" <numeric>
% "Enable Cell Mitosis" <boolean>
% "Min Cell Life CI Threshold" <numeric>
% "Cell Death Delta Centroid Threshold" <numeric>
% "Cell Density Affects CI" <boolean>
% "Border Cell Affects CI" <boolean>
% "Cell Fusion Min Area" <numeric>
% "Min Cell Fusion Overlap" <numeric>
% "Enable Cell Fusion" <boolean>
function Lineage_Mapper(varargin)
if ~isdeployed
addpath([pwd filesep 'src']);
addpath([pwd filesep 'imgs']);
addpath([pwd filesep 'doc']);
end
% ----------------------------------------------------------------------
% Folder path params
raw_images_path = '';
segmented_images_path = '';
tracked_images_path = '';
segmented_images_common_name = '';
raw_images_common_name = '';
tracked_images_common_name = '';
% Cost function params
weight_overlap = 100;
weight_centroids = 50;
weight_size = 20;
max_centroids_distance = 50;
frames_to_track = 'All';
% Mitotic params
division_overlap_threshold = 20;
daughter_size_similarity = 50;
daughter_aspect_ratio_similarity = 70;
circularity_threshold = 30;
number_of_frames_check_circularity = 5;
enable_cell_mitosis_flag = 1;
% Confidence Index params
cell_life_threshold = 32;
cell_apoptosis_delta_centroid_thres = 10;
cell_density_ci_flag = 1;
border_cell_ci_flag = 1;
% Fusion params
cell_size_threshold = 100;
fusion_overlap_threshold = 20;
enable_cell_fusion_flag = 0;
% Non-user params
frames_to_track_nb = 0;
nb_frames = 0;
max_cell_num = 12000;
params = {'raw_images_path',...
'segmented_images_path',...
'tracked_images_path',...
'segmented_images_common_name',...
'raw_images_common_name',...
'tracked_images_common_name',...
'weight_overlap',...
'weight_centroids',...
'weight_size',...
'max_centroids_distance',...
'frames_to_track',...
'division_overlap_threshold',...
'daughter_size_similarity',...
'daughter_aspect_ratio_similarity',...
'circularity_threshold',...
'number_of_frames_check_circularity',...
'enable_cell_mitosis_flag',...
'cell_life_threshold',...
'cell_apoptosis_delta_centroid_thres',...
'cell_density_ci_flag',...
'border_cell_ci_flag',...
'cell_size_threshold',...
'fusion_overlap_threshold',...
'enable_cell_fusion_flag'};
batch_mode = false;
if nargin > 0
% This runs batch mode
batch_mode = true;
% Input String, Type, Variable Name
batchmode_inputs = {{'Default', 'none', ''},...
{'Raw Images Path', 'char', 'raw_images_path'},...
{'Segmented Images Path', 'char', 'segmented_images_path'},...
{'Tracked Images Path', 'char', 'tracked_images_path'},...
{'Segmented Images Common Name', 'char', 'segmented_images_common_name'},...
{'Raw Images Common Name', 'char', 'raw_images_common_name'},...
{'Tracked Images Common Name', 'char', 'tracked_images_common_name'},...
{'Weight Overlap', 'numeric', 'weight_overlap'},...
{'Weight Centroids', 'numeric', 'weight_centroids'},...
{'Weight Size', 'numeric', 'weight_size'},...
{'Max Centroids Distance', 'numeric', 'max_centroids_distance'},...
{'Frames To Track', 'char', 'frames_to_track'},...
{'Min Mitotic Overlap', 'numeric', 'division_overlap_threshold'},...
{'Daughter Size Similarity', 'numeric', 'daughter_size_similarity'},...
{'Daughter Aspect Ratio Similarity', 'numeric', 'daughter_aspect_ratio_similarity'},...
{'Circularity Index', 'numeric', 'circularity_threshold'},...
{'Number Frames to Check Circularity', 'numeric', 'number_of_frames_check_circularity'},...
{'Enable Cell Mitosis', 'logical', 'enable_cell_mitosis_flag'},...
{'Min Cell Life CI Threshold', 'numeric', 'cell_life_threshold'},...
{'Cell Death Delta Centroid Threshold', 'numeric', 'cell_apoptosis_delta_centroid_thres'},...
{'Cell Density Affects CI', 'logical', 'cell_density_ci_flag'},...
{'Border Cell Affects CI', 'logical', 'border_cell_ci_flag'},...
{'Cell Fusion Min Area', 'numeric', 'cell_size_threshold'},...
{'Min Cell Fusion Overlap', 'numeric', 'fusion_overlap_threshold'},...
{'Enable Cell Fusion', 'logical', 'enable_cell_fusion_flag'} };
% parse inputs
% If the user is passing values into this function, that means they are attempting to use this in batch mode without the GUI being displayed
indx = 1;
while indx <= nargin
% loop over the arguments passed in using varargin
if isa(varargin{indx}, 'char')
cur_str = varargin{indx}; % extract the current variable name string
% remove any non alphanumberic values
cur_str = regexprep(cur_str,'[^a-zA-Z0-9]+','');
% loop over possible values for this input string
found_flag = false;
for k = 1:numel(batchmode_inputs)
cmp_str = strrep(batchmode_inputs{k}{1},' ' ,'');
if strcmpi(cur_str, cmp_str)
% match found
if strcmpi(batchmode_inputs{k}{2}, 'none')
% set the default params
batchmode_set_default_parameters();
indx = indx - 1;
found_flag = true; break;
end
% test that the value portion of the string value pair is the correct type
if indx < nargin
val = varargin{indx+1};
switch batchmode_inputs{k}{2}
case 'char'
if isa(val, 'char')
eval([batchmode_inputs{k}{3} '=val;']);
found_flag = true; break;
end
if isa(val, 'numeric')
eval([batchmode_inputs{k}{3} '=num2str(val);']);
found_flag = true; break;
end
case 'numeric'
if isa(val, 'char')
eval([batchmode_inputs{k}{3} '=str2num(val);']);
found_flag = true; break;
end
if isa(val, 'numeric')
eval([batchmode_inputs{k}{3} '=' num2str(val) ';']);
found_flag = true; break;
end
case 'logical'
if isa(val, 'char')
eval([batchmode_inputs{k}{3} '=logical(str2num(val));']);
found_flag = true; break;
end
if isa(val, 'logical') || isa(val, 'numeric')
eval([batchmode_inputs{k}{3} '=logical(' num2str(val) ');']);
found_flag = true; break;
end
end
end
end
end
if found_flag
indx = indx + 1; % skip the next index as it was already used
else
cur_str = varargin{indx}; % extract the current variable name string
error('Cell_tracker_GUI_v4:argCk',['Invalid Input String <' cur_str '>']);
end
end
indx = indx + 1;
end
if ~check_input_batchmode(), return; end
start_tracking_Callback();
return;
end
% check if the GUI is already open, if so do nothing and return
open_fig_handle = findobj('type','figure','name','Lineage_Mapper');
if ~isempty(open_fig_handle)
figure(open_fig_handle); %brings the figure to front
return;
end
% Define General colors
lt_gray = [0.86,0.86,0.86];
dark_gray = [0.7,0.7,0.7];
green_blue = [0.0,0.3,0.4];
TabLabels = {'Main'; 'Folders'; 'Tracking Parameters'; 'Results'; 'Help'};
% Number of tabs to be generated
NumberOfTabs = length(TabLabels);
% indicator of tabs callback
tab_index = zeros(NumberOfTabs,1);
tab_index(3) = 1;
% Get user screen size
SC = get(0, 'ScreenSize');
MaxMonitorX = SC(3);
MaxMonitorY = SC(4);
main_tabFigScale = 0.5;
gui_ratio = 0.6; % height/width
MaxWindowX = round(MaxMonitorX*main_tabFigScale);
MaxWindowY = MaxWindowX*gui_ratio;
% Set the figure window size values and calculate center of the screen position for the lower left corner
gui_width = round(MaxMonitorX/2); % Gui is half the screen wide
gui_height = round(gui_width*gui_ratio); % fix the ratio of the GUI height to width
% if the users screen resolution is not the same as their screen size the GUI will be placed off center
% of possibly out of view
offset = 0;
if (SC(2) ~= 1)
offset = abs(SC(2));
end
left_bottom_corner_x_coordinate = (MaxMonitorX-MaxWindowX)/2 - offset;
left_bottom_corner_y_coordinate = (MaxMonitorY-MaxWindowY)/2 + offset;
hctfig = figure(...
'units', 'pixels',...
'Position',[left_bottom_corner_x_coordinate, left_bottom_corner_y_coordinate, gui_width, gui_height],...
'Name','Lineage_Mapper',...
'NumberTitle','off',...
'Menubar','none',...
'Toolbar','none',...
'Resize', 'on');
%--------------------------------------------------------------------------
% Panel tabs
%--------------------------------------------------------------------------
h_tabpanel = zeros(NumberOfTabs,1);
h_tabpb = zeros(NumberOfTabs,1);
tab_label_text_size = 0.5;
% Create main menu tab, 'Main'
h_tabpanel(1) = uipanel('Units', 'normalized', 'Parent', hctfig,'Visible', 'off', 'Backgroundcolor', lt_gray,'BorderWidth',1, 'Position', [0,0,1,1] );
h_tabpanel(2) = uipanel('Units', 'normalized', 'Parent', hctfig, 'Visible', 'off', 'Backgroundcolor', lt_gray, 'BorderWidth',1, 'Position', [0,0,1,1]);
h_tabpanel(3) = uipanel('Units', 'normalized', 'Parent', hctfig,'Visible', 'off', 'Backgroundcolor', lt_gray,'BorderWidth',1,'Position', [0,0,1,1]);
h_tabpanel(4) = uipanel('Units', 'normalized','Parent', hctfig, 'Visible', 'off', 'Backgroundcolor', lt_gray, 'BorderWidth',1, 'Position', [0,0,1,1]);
h_tabpb(1) = push_button(hctfig, [0 0.95 0.23 0.05], TabLabels(1), 'center', 'k', dark_gray, tab_label_text_size, 'serif', 'bold', 'on', {@first_tab_callback} );
h_tabpb(2) = push_button(hctfig, [0.23 0.95 0.23 0.05], TabLabels(2), 'center', 'k', dark_gray, tab_label_text_size, 'serif', 'bold', 'on', {@second_tab_callback} );
h_tabpb(3) = push_button(hctfig, [0.46 0.95 0.23 0.05], TabLabels(3), 'center', 'k', dark_gray, tab_label_text_size, 'serif', 'bold', 'off', {@third_tab_callback} );
h_tabpb(4) = push_button(hctfig, [0.69 0.95 0.23 0.05], TabLabels(4), 'center', 'k', dark_gray, tab_label_text_size, 'serif', 'bold', 'off', {@fourth_tab_callback} );
% Create main menu tab, 'Help'
push_button(hctfig, [0.92 0.95 0.08 0.05], TabLabels(5), 'center', 'k', dark_gray, tab_label_text_size, 'serif', 'bold', 'on', {@Open_Help_PDF_callback} );
function Open_Help_PDF_callback(varargin)
winopen('GUI_HELP.pdf');
end
%-----------------------------------------------------------------------------------
%-----------------------------------------------------------------------------------
% Main
%-----------------------------------------------------------------------------------
label(h_tabpanel(1), [0.12 0.865 0.75 0.07], 'Lineage Mapper', 'center', green_blue, lt_gray, .7, 'serif', 'bold');
% Time t
label(h_tabpanel(1), [0.2 0.15 0.1 0.04], 'Time t', 'center', 'k', lt_gray, .7, 'sans serif', 'bold');
% Time T + 1
label(h_tabpanel(1), [0.66 0.15 0.15 0.04], 'Time t + 1', 'center', 'k', lt_gray, .7, 'sans serif', 'bold');
% Push button: Start Tracking
start_tracking_pb = push_button(h_tabpanel(1), [0.04 0.005 0.22 0.06], 'Start Tracking', 'center', 'k', 'default', .4, 'sans serif', 'bold', 'off', {@start_tracking_Callback});
push_button(h_tabpanel(1), [0.3 0.005 0.22 0.06], 'Load Tracking Parameters', 'center', 'k', 'default', .4, 'sans serif', 'bold', 'on', {@load_tracking_workspace});
% handle to the intro figure
axes('Parent', h_tabpanel(1), 'Units', 'normalized', 'position', [0.05 0.088 0.87 0.87]);
imshow(imread('celltracker_image_v1.png'), []);
axes('Parent', h_tabpanel(1), 'Units', 'normalized', 'Position', [0.83 -.03 0.16 0.2]);
imshow('Logo.tif');
%-----------------------------------------------------------------------------------
% / End Main
%-----------------------------------------------------------------------------------
%-----------------------------------------------------------------------------------------
% Input pathnames
%-----------------------------------------------------------------------------------------
input_panel = sub_panel(h_tabpanel(2), [0.025,0.45,.95,.45], 'Input', 'lefttop', green_blue, lt_gray, 14, 'serif');
output_panel = sub_panel(h_tabpanel(2), [0.025,0.15,.95,.25], 'Output', 'lefttop', green_blue, lt_gray, 14, 'serif');
% Input Folder Parameters:
% -- Input Help
push_button(input_panel, [0.95 0.925 0.04 0.1], '?', 'center', 'k', 'default', .6, 'sans serif', 'bold', 'on', {@Input_help_callback});
function Input_help_callback(varargin)
winopen('Input_help.pdf');
end
% -- Segmented
label(input_panel, [0.001 0.72 0.22 0.126], 'Segmented Images', 'right', 'k', lt_gray, .5, 'sans serif', 'normal');
segmented_images_path_edit = editbox(input_panel, [0.23 0.74 0.61 0.126], segmented_images_path, 'left', 'k', 'w', .5, 'normal');
push_button(input_panel, [0.851 0.74 0.12 0.126], 'Open', 'center', 'k', 'default', .5, 'sans serif', 'normal', 'on', {@select_folder_segmented_images_Callback});
label(input_panel, [0.001 0.54 0.22 0.126], 'Common segmented name', 'right', 'k', lt_gray, .5, 'sans serif', 'normal');
segmented_images_common_name_edit = editbox(input_panel, [0.23 0.56 0.25 0.126], segmented_images_common_name, 'left', 'k', 'w', .5, 'normal');
% -- Raw Images
label(input_panel,[0.001 0.25 0.22 0.126], 'Raw Images', 'right', 'k', lt_gray, .5, 'sans serif', 'normal');
raw_images_path_edit = editbox_check(input_panel, [0.23 0.28 0.61 0.126], raw_images_path, 'left', 'k', 'w', .5, 'normal', {@save_parameters});
push_button(input_panel, [0.851 0.28 0.12 0.126], 'Open', 'center', 'k', 'default', .5, 'sans serif', 'normal', 'on', {@select_folder_raw_images_Callback});
label(input_panel, [0.001 0.08 0.22 0.126], 'Common raw name', 'right', 'k', lt_gray, .5, 'sans serif', 'normal');
raw_images_common_name_edit = editbox(input_panel, [0.23 0.1 0.25 0.126], raw_images_common_name, 'left', 'k', 'w', .5, 'normal');
% Output Folder Parameters:
% -- Output Help
push_button(output_panel, [0.95 0.84 0.04 0.22], '?', 'center', 'k', 'default', .55, 'sans serif', 'bold', 'on', {@Output_help_callback});
function Output_help_callback(varargin)
winopen('Output_help.pdf');
end
% -- Output Folder
label(output_panel, [0.001 0.47 0.22 0.25], 'Tracked Images', 'right', 'k', lt_gray, .54, 'sans serif', 'normal');
tracked_images_path_edit = editbox(output_panel, [0.23 0.5 0.61 0.25], tracked_images_path, 'left', 'k', 'w', .54, 'normal');
push_button(output_panel, [0.851 0.5 0.12 0.25], 'Open', 'center', 'k', 'default', .54, 'sans serif', 'normal', 'on', {@select_folder_tracked_images_Callback});
label(output_panel, [0.001 0.12 0.22 0.25], 'Common tracked name', 'right', 'k', lt_gray, .54, 'sans serif', 'normal');
tracked_images_common_name_edit = editbox(output_panel, [0.23 0.15 0.25 0.25], tracked_images_common_name, 'left', 'k', 'w', .54, 'normal');
% Push Button: Save User Input
push_button(h_tabpanel(2), [0.04 0.005 0.22 0.06], 'Start Tracking', 'center', 'k', 'default', .4, 'sans serif', 'bold', 'on', {@start_tracking_Callback});
% Push Button: Cancel
push_button(h_tabpanel(2), [0.3 0.005 0.22 0.06], 'Cancel', 'center', 'k', 'default', .4, 'sans serif', 'bold', 'on', {@pb_cancel_pathnames_Callback});
%-----------------------------------------------------------------------------------------
% /End Input pathnames
%-----------------------------------------------------------------------------------------
%------------------------------------------------------------------------------------------
% Tracking Parameters
%------------------------------------------------------------------------------------------
% UI panels for tracking parameters
cost_function_parameters_panel = sub_panel(h_tabpanel(3), [0.032 0.42 0.45 0.5], 'Cost Function Parameters', 'lefttop', green_blue, lt_gray, 13, 'serif');
mitotic_parameters_panel = sub_panel(h_tabpanel(3), [0.518 0.42 0.45 0.5], 'Mitotic Parameters', 'lefttop', green_blue, lt_gray, 13, 'serif');
confidence_index_parameters_panel = sub_panel(h_tabpanel(3), [0.032 0.1 0.45 0.3], 'Confidence Index Parameters', 'lefttop', green_blue, lt_gray, 13, 'serif');
fusion_parameters_panel = sub_panel(h_tabpanel(3), [0.518 0.1 0.45 0.3], 'Fusion Parameters', 'lefttop', green_blue, lt_gray, 13, 'serif');
%-------------------------------------------------------------------------------------------------------------------------------------------
% Cost Function Parameters
%-------------------------------------------------------------------------------------------------------------------------------------------
x_pos = 0.03; y_pos = 0.2; hgt = 0.1;
% edit boxes
eb_pos = x_pos + 0.6;
% unit labels
u_pos = eb_pos + 0.15;
% uicontrol margin
bm = hgt + .05; % bottom margin
% Weight of Overlap
label(cost_function_parameters_panel, [x_pos y_pos+bm*4-.01 0.53 hgt], 'Weight of Cell Overlap', 'right', 'k', lt_gray, .55, 'sans serif', 'normal');
weight_overlap_edit = editbox_check(cost_function_parameters_panel, [eb_pos y_pos+bm*4 0.15 hgt], weight_overlap, 'center', 'k', 'w', .55, 'normal', {@save_parameters});
label(cost_function_parameters_panel, [u_pos y_pos+bm*4-.015 0.1 hgt], '%', 'center', 'k', lt_gray, .55, 'sans serif', 'normal');
% Weight of Centroids Distance
label(cost_function_parameters_panel, [x_pos y_pos+bm*3-.01 0.53 hgt], 'Weight of Centroids Distance', 'right', 'k', lt_gray, .55, 'sans serif', 'normal');
weight_centroids_edit = editbox_check(cost_function_parameters_panel, [eb_pos y_pos+bm*3 0.15 hgt], weight_centroids, 'center', 'k', 'w', .55, 'normal', {@save_parameters});
label(cost_function_parameters_panel, [u_pos y_pos+bm*3-.015 0.1 hgt], '%', 'center', 'k', lt_gray, .55, 'sans serif', 'normal');
% Weight of cell Size
label(cost_function_parameters_panel, [x_pos y_pos+bm*2-.01 0.53 hgt], 'Weight of Cell Size', 'right', 'k', lt_gray, .55, 'sans serif', 'normal');
weight_size_edit = editbox_check(cost_function_parameters_panel, [eb_pos y_pos+bm*2 0.15 hgt], weight_size, 'center', 'k', 'w', .55, 'normal', {@save_parameters});
label(cost_function_parameters_panel, [u_pos y_pos+bm*2-.015 0.1 hgt], '%', 'center', 'k', lt_gray, .55, 'sans serif', 'normal');
% Max_centroids_distance
label(cost_function_parameters_panel, [x_pos y_pos+bm-0.1 0.53 hgt], 'Max Centroids Distance', 'right', 'k', lt_gray, .55, 'sans serif', 'normal');
max_centroids_distance_edit = editbox_check(cost_function_parameters_panel, [eb_pos y_pos+bm-0.09 0.15 hgt], max_centroids_distance, 'center', 'k', 'w', .55, 'normal', {@save_parameters});
label(cost_function_parameters_panel, [u_pos y_pos+bm-0.1 0.1 hgt], 'px', 'center', 'k', lt_gray, .55, 'sans serif', 'normal');
% Frames to track
label(cost_function_parameters_panel, [x_pos y_pos-0.1 0.53 hgt], 'Frames To Track', 'right', 'k', lt_gray, .55, 'sans serif', 'normal');
frames_to_track_edit = editbox_check(cost_function_parameters_panel, [eb_pos y_pos-0.09 0.15 hgt], frames_to_track, 'center', 'k', 'w', .55, 'normal', {@save_parameters});
% Cost Function Help
push_button(cost_function_parameters_panel, [0.92 0.925 0.07 hgt], '?', 'center', 'k', 'default', .6, 'sans serif', 'bold', 'on', {@cost_function_help});
function cost_function_help(varargin)
winopen('Cost_Function_Parameters.pdf');
end
%-------------------------------------------------------------------------------------------------------------------------------------------
%-------------------------------------------------------------------------------------------------------------------------------------------
% Mitotic Parameters
%-------------------------------------------------------------------------------------------------------------------------------------------
x_pos = 0.03; y_pos = 0.2; hgt = 0.1;
% edit boxes
eb_pos = x_pos + 0.6;
% unit labels
u_pos = eb_pos + 0.15;
% uicontrol margin
bm = hgt + .05; % bottom margin
% Min Mitotic Overlap (%size)
label(mitotic_parameters_panel, [x_pos y_pos+bm*4-.01 0.53 hgt], 'Min Mitotic Overlap', 'right', 'k', lt_gray, .55, 'sans serif', 'normal');
division_overlap_threshold_edit = editbox_check(mitotic_parameters_panel, [eb_pos y_pos+bm*4 0.15 hgt], division_overlap_threshold, 'center', 'k', 'w', .55, 'normal', {@save_parameters});
label(mitotic_parameters_panel, [u_pos y_pos+bm*4-.015 0.1 hgt], '%', 'center', 'k', lt_gray, .55, 'sans serif', 'normal');
% Daughter Size Similarity
label(mitotic_parameters_panel, [x_pos y_pos+bm*3-.01 0.53 hgt], 'Daughter Size Similarity', 'right', 'k', lt_gray, .55, 'sans serif', 'normal');
daughter_size_similarity_edit = editbox_check(mitotic_parameters_panel, [eb_pos y_pos+bm*3 0.15 hgt], daughter_size_similarity, 'center', 'k', 'w', .55, 'normal', {@save_parameters});
label(mitotic_parameters_panel, [u_pos y_pos+bm*3-.015 0.1 hgt], '%', 'center', 'k', lt_gray, .55, 'sans serif', 'normal');
% Daughter Aspect Ratio Similarity
label(mitotic_parameters_panel, [x_pos y_pos+bm*2-.01 0.53 hgt], 'Daughter Aspect Ratio Similarity', 'right', 'k', lt_gray, .55, 'sans serif', 'normal');
daughter_aspect_ratio_similarity_edit = editbox_check(mitotic_parameters_panel, [eb_pos y_pos+bm*2 0.15 hgt], daughter_aspect_ratio_similarity, 'center', 'k', 'w', .55, 'normal', {@save_parameters});
label(mitotic_parameters_panel, [u_pos y_pos+bm*2-.015 0.1 hgt], '%', 'center', 'k', lt_gray, .55, 'sans serif', 'normal');
% Circularity Index
label(mitotic_parameters_panel, [x_pos y_pos+bm-.01 0.53 hgt], 'Mother Circularity Index', 'right', 'k', lt_gray, .55, 'sans serif', 'normal');
circularity_threshold_edit = editbox_check(mitotic_parameters_panel, [eb_pos y_pos+bm 0.15 hgt], circularity_threshold, 'center', 'k', 'w', .55, 'normal', {@save_parameters});
label(mitotic_parameters_panel, [u_pos y_pos+bm-.015 0.1 hgt], '%', 'center', 'k', lt_gray, .55, 'sans serif', 'normal');
% Number of frames
label(mitotic_parameters_panel, [x_pos y_pos-.01 0.53 hgt], '# of Frames to Check Circularity', 'right', 'k', lt_gray, .55, 'sans serif', 'normal');
number_of_frames_check_circularity_edit = editbox_check(mitotic_parameters_panel, [eb_pos y_pos 0.15 hgt], number_of_frames_check_circularity, 'center', 'k', 'w', .55, 'normal', {@save_parameters});
% Enable Cell Mitosis
enable_cell_mitosis_checkbox = checkbox(mitotic_parameters_panel, [x_pos-0.01 y_pos-0.18 0.43 hgt], 'Enable Cell Mitosis', 'right', 'k', lt_gray, .55, 'sans serif', 'normal', {@cell_mitosis_callback});
function cell_mitosis_callback(varargin)
enable_cell_mitosis_flag = get(enable_cell_mitosis_checkbox, 'value');
if(enable_cell_mitosis_flag)
set(daughter_size_similarity_edit, 'enable', 'on');
set(daughter_aspect_ratio_similarity_edit, 'enable', 'on');
set(circularity_threshold_edit, 'enable', 'on');
set(number_of_frames_check_circularity_edit, 'enable', 'on');
else
set(daughter_size_similarity_edit, 'enable', 'off');
set(daughter_aspect_ratio_similarity_edit, 'enable', 'off');
set(circularity_threshold_edit, 'enable', 'off');
set(number_of_frames_check_circularity_edit, 'enable', 'off');
end
end
% Mitotic Help
push_button(mitotic_parameters_panel, [0.92 0.925 0.07 hgt], '?', 'center', 'k', 'default', .6, 'sans serif', 'bold', 'on', {@mitotic_help});
function mitotic_help(varargin)
winopen('Mitotic_Parameters.pdf');
end
%-------------------------------------------------------------------------------------------------------------------------------------------
%-------------------------------------------------------------------------------------------------------------------------------------------
% Confidence Index Parameters
%-------------------------------------------------------------------------------------------------------------------------------------------
x_pos = 0.03; y_pos = 0.2; hgt = 0.18;
% edit boxes
eb_pos = x_pos + 0.6;
% uicontrol margin
bm = hgt + .05; % bottom margin
% Min Cell Life (nb frames)
label(confidence_index_parameters_panel, [x_pos y_pos+bm*2-.015 0.53 hgt], 'Min Cell Life (nb frames)', 'right', 'k', lt_gray, .55, 'sans serif', 'normal');
cell_life_threshold_edit = editbox_check(confidence_index_parameters_panel, [eb_pos y_pos+bm*2 0.15 hgt], cell_life_threshold, 'center', 'k', 'w', .55, 'normal', {@save_parameters});
% Max delta centroid distance to be considered dead cell
label(confidence_index_parameters_panel, [x_pos y_pos+bm-.015 0.53 hgt], 'Cell Death Delta Centroid Thres', 'right', 'k', lt_gray, .55, 'sans serif', 'normal');
cell_apoptosis_cent_thres_edit = editbox_check(confidence_index_parameters_panel, [eb_pos y_pos+bm 0.15 hgt], cell_apoptosis_delta_centroid_thres, 'center', 'k', 'w', .55, 'normal', {@save_parameters});
% Cell Density
cell_density_checkbox = checkbox(confidence_index_parameters_panel, [x_pos-0.01 y_pos-0.18 0.43 hgt], 'Surrounding Density ', 'right', 'k', lt_gray, .55, 'sans serif', 'normal', {@cell_density_callback});
function cell_density_callback(varargin)
cell_density_ci_flag = get(cell_density_checkbox, 'value');
end
% Distance To Border
border_cell_checkbox = checkbox(confidence_index_parameters_panel, [x_pos+0.45 y_pos-0.18 0.5 hgt], 'Touching FOV Border ', 'right', 'k', lt_gray, .55, 'sans serif', 'normal', {@border_cell_callback});
function border_cell_callback(varargin)
border_cell_ci_flag = get(border_cell_checkbox, 'value');
end
% Confidence Help
push_button(confidence_index_parameters_panel, [0.915 0.87 0.07 hgt], '?', 'center', 'k', 'default', .6, 'sans serif', 'bold', 'on', {@confidence_help});
function confidence_help(varargin)
winopen('Confidence_Index_Parameters.pdf');
end
%-------------------------------------------------------------------------------------------------------------------------------------------
%-------------------------------------------------------------------------------------------------------------------------------------------
% Fusion Parameters
%-------------------------------------------------------------------------------------------------------------------------------------------
x_pos = 0.03; y_pos = 0.2; hgt = 0.18;
% edit boxes
eb_pos = x_pos + 0.6;
% unit labels
u_pos = eb_pos + 0.15;
% uicontrol margin
bm = hgt + .05; % bottom margin
% Min Fusion Overlap (%size)
label(fusion_parameters_panel, [x_pos y_pos+bm*2-.015 0.53 hgt], 'Min Fusion Overlap', 'right', 'k', lt_gray, .55, 'sans serif', 'normal');
fusion_overlap_threshold_edit = editbox_check(fusion_parameters_panel, [eb_pos y_pos+bm*2 0.15 hgt], fusion_overlap_threshold, 'center', 'k', 'w', .55, 'normal', {@save_parameters});
label(fusion_parameters_panel, [u_pos y_pos+bm*2-.02 0.1 hgt], '%', 'center', 'k', lt_gray, .55, 'sans serif', 'normal');
% Min Cell Area (pixels)
label(fusion_parameters_panel, [x_pos y_pos+bm-.015 0.53 hgt], 'Min Cell Area', 'right', 'k', lt_gray, .55, 'sans serif', 'normal');
cell_size_threshold_edit = editbox_check(fusion_parameters_panel, [eb_pos y_pos+bm 0.15 hgt], cell_size_threshold, 'center', 'k', 'w', .55, 'normal', {@save_parameters});
label(fusion_parameters_panel, [u_pos y_pos+bm-.015 0.1 hgt], 'px', 'center', 'k', lt_gray, .55, 'sans serif', 'normal');
% Disable fusion
enable_fusion_checkbox = checkbox(fusion_parameters_panel, [x_pos-0.01 y_pos-0.18 0.43 hgt], 'Enable Cell Fusion', 'right', 'k', lt_gray, .55, 'sans serif', 'normal', {@fusion_flag_callback});
function fusion_flag_callback(varargin)
enable_cell_fusion_flag = get(enable_fusion_checkbox, 'value');
if enable_cell_fusion_flag
set(cell_size_threshold_edit, 'enable', 'off');
else
set(cell_size_threshold_edit, 'enable', 'on');
end
end
% Fusion Help
push_button(fusion_parameters_panel, [0.915 0.87 0.07 hgt], '?', 'center', 'k', 'default', .6, 'sans serif', 'bold', 'on', {@fusion_help});
function fusion_help(varargin)
winopen('Fusion_Parameters.pdf');
end
%-------------------------------------------------------------------------------------------------------------------------------------------
% Push Button: Save User Input
push_button(h_tabpanel(3), [0.04 0.005 0.22 0.06], 'Start Tracking', 'center', 'k', 'default', .4, 'sans serif', 'bold', 'on', {@start_tracking_Callback});
% Push Button: Cancel
push_button(h_tabpanel(3), [0.3 0.005 0.22 0.06], 'Cancel', 'center', 'k', 'default', .4, 'sans serif', 'bold', 'on', {@pb_tracking_cancel_Callback});
% Push Button: Default Parameters
push_button(h_tabpanel(3), [0.56 0.005 0.22 0.06], 'Default Parameters', 'center', 'k', 'default', .4, 'sans serif', 'bold', 'on', {@default_parameters});
%------------------------------------------------------------------------------------------
% / End Tracking Parameters
%------------------------------------------------------------------------------------------
%------------------------------------------------------------------------------------------
% Result Tab
%------------------------------------------------------------------------------------------
% Examining Tracking Results
label(h_tabpanel(4), [0.12 0.865 0.75 0.07], 'Examining Tracking Results', 'center', green_blue, lt_gray, .7, 'serif', 'bold');
review_data_subpanel = sub_panel(h_tabpanel(4), [.032 .7 .928 .17], 'Tracking Data', 'lefttop', green_blue, lt_gray, 13, 'serif');
% Tracking Data Help
push_button(h_tabpanel(4), [.925 .795 0.03 .045], '?', 'center', 'k', 'default', .6, 'sans serif', 'bold', 'on', {@Tracking_Data_help});
function Tracking_Data_help(varargin)
winopen('Tracking_Data.pdf');
end
x_pos = .008;
y_pos = 0.15;
w = 0.19;
h = 0.47;
% left margin
lm = w + .008;
% Show Confidence Index
push_button(review_data_subpanel, [x_pos y_pos w h], 'Confidence Index', 'center', 'k', 'default', .4, 'sans serif', 'bold', 'on', {@Show_Confidence_Index_callback});
% Show Birth and Death
push_button(review_data_subpanel, [x_pos+lm y_pos w h], 'Birth and Death', 'center', 'k', 'default', .4, 'sans serif', 'bold', 'on', {@show_birth_and_death_callback});
% Show Division Matrix
show_division_matrix_button = push_button(review_data_subpanel, [x_pos+lm*2 y_pos w h], 'Division Matrix', 'center', 'k', 'default', .4, 'sans serif', 'bold', 'on', {@show_division_matrix_callback});
% Show Fusion Matrix
show_fusion_matrix_button = push_button(review_data_subpanel, [x_pos+lm*3 y_pos w h], 'Fusion Matrix', 'center', 'k', 'default', .4, 'sans serif', 'bold', 'off', {@show_fusion_matrix_callback});
% Show Cell Apoptosis
push_button(review_data_subpanel, [x_pos+lm*4 y_pos w h], 'Cell Apoptosis', 'center', 'k', 'default', .4, 'sans serif', 'bold', 'on', {@Show_Cell_Apoptosis_callback});
% Text: Plot Cell Migration (2D)
plot_migration_handle = sub_panel(h_tabpanel(4), [0.032 0.11 0.42 0.56], 'Plot Cell Migration (2D)', 'centertop', green_blue, lt_gray, 13, 'serif');
% Plot Cell Migration (2D) Help
push_button(plot_migration_handle, [0.92 0.925 0.07 0.09], '?', 'center', 'k', 'default', .6, 'sans serif', 'bold', 'on', {@Plot_Cell_Migration_help});
function Plot_Cell_Migration_help(varargin)
winopen('Plot_Cell_Migration.pdf');
end
% Plot cell Migration image
axes('Parent',plot_migration_handle, 'Units', 'normalized', 'position', [0.03 0.33 0.92 0.55]);
imshow(imread('Cell_Migration.png'),[])
% Cell Numbers to Plot
label(plot_migration_handle, [0.25 0.2 0.42 0.1], 'Cell Numbers to Plot:', 'center', 'k', lt_gray, .5, 'sans serif', 'bold');
plot_cell_nb_migration_edit = editbox(plot_migration_handle, [0.66 0.22 0.09 0.1], 'All', 'center', 'k', 'w', .5, 'normal');
push_button(plot_migration_handle, [0.25 0.05 0.5 0.12], 'Plot Cell Migration', 'center', 'k', 'default', .4, 'sans serif', 'bold', 'on', {@Plot_Cell_Migration_callback});
% Plot Cell Lineage
plot_cell_lineage_handle = sub_panel(h_tabpanel(4), [0.54 0.11 0.42 0.56], 'Plot Cell Lineage', 'centertop', green_blue, lt_gray, 13, 'serif');
% Plot Cell Migration (2D) Help
push_button(plot_cell_lineage_handle, [0.92 0.925 0.07 0.09], '?', 'center', 'k', 'default', .6, 'sans serif', 'bold', 'on', {@Plot_Cell_Lineage_help});
function Plot_Cell_Lineage_help(varargin)
winopen('Plot_Cell_Lineage.pdf');
end
% Plot cell lineage image
axes('Parent', plot_cell_lineage_handle, 'Units', 'normalized', 'position', [0.03 0.33 0.92 0.55]);
imshow(imread('Cell_Lineage.png'),[])
% Text: Cell Numbers to Plot
label(plot_cell_lineage_handle, [0.25 0.2 0.42 0.1], 'Cell Numbers to Plot:', 'center', 'k', lt_gray, .5, 'sans serif', 'bold');
plot_lineage_nb_edit = editbox(plot_cell_lineage_handle, [0.66 0.22 0.09 0.1], 'All', 'center', 'k', 'w', .5, 'normal');
push_button(plot_cell_lineage_handle, [0.01 0.05 0.48 0.12], 'Plot Division Lineage', 'center', 'k', 'default', .4, 'sans serif', 'bold', 'on', {@Plot_Division_Lineage_callback});
plot_fusion_linage_pb = push_button(plot_cell_lineage_handle, [0.51 0.05 0.48 0.12], 'Plot Fusion Lineage', 'center', 'k', 'default', .4, 'sans serif', 'bold', 'off', {@Plot_Fusion_Lineage_callback});
% Return To Main
% push_button(h_tabpanel(4), [0.183 0.01 0.27 0.06], '<--- Return To Main', 'center', 'k', 'default', .4, 'sans serif', 'bold', 'on', {@first_tab_callback});
% Explore Tracked Images
push_button(h_tabpanel(4), [0.36 0.01 0.28 0.07], 'Explore Tracked Images', 'center', 'k', 'default', .34, 'sans serif', 'bold', 'on', {@Explore_Tracked_Images_callback});
%--------------------------------------------------------------------------------------------------
% / End Result tab
%--------------------------------------------------------------------------------------------------
%--------------------------------------------------------------------------------------------------
% Pushbutton Callbacks
%--------------------------------------------------------------------------------------------------
function start_tracking_Callback(varargin)
d = dir([segmented_images_path '*' segmented_images_common_name '*.tif']);
nb_frames = length(d);
if nb_frames >0
if ~batch_mode
tab_index(2) = 0;
second_tab_callback();
end
else
errordlg('Segmented Images Folder is empty');
return;
end
% truncate frames_to_track_nb
frames_to_track_nb( frames_to_track_nb > nb_frames) = [];
% Save user input and check for errors
if ~batch_mode
set(h_tabpb(4), 'enable', 'off');
if ~save_parameters(), return; end
end
% check if there exists a tracked images folder
% if so query the user for overwrite permission
if ~batch_mode && exist([tracked_images_path tracked_images_common_name sprintf('%d',nb_frames) '.tif'],'file')
overwrite_button = questdlg('Tracked Images Exist! Overwrite?', 'Warning','Yes','Cancel','Yes');
if ~strcmp(overwrite_button,'Yes')
% if the user did not select yes for overwrite, abort tracking
return;
end
print_to_command('Tracked Images Exist, overwriting...', tracked_images_path);
end
write_metadata_to_log_file();
% Track the segmented images
finished_tracking = start_tracking(segmented_images_path, segmented_images_common_name, tracked_images_path,...
tracked_images_common_name, max_centroids_distance, weight_size/100, weight_centroids/100, weight_overlap/100, fusion_overlap_threshold/100, division_overlap_threshold/100,...
cell_life_threshold, max_cell_num, nb_frames, daughter_size_similarity/100, daughter_aspect_ratio_similarity/100, cell_size_threshold, enable_cell_fusion_flag, ...
frames_to_track_nb, cell_density_ci_flag, border_cell_ci_flag, number_of_frames_check_circularity, circularity_threshold/100, cell_apoptosis_delta_centroid_thres, enable_cell_mitosis_flag);
if finished_tracking
if ~batch_mode
set(h_tabpb(4), 'enable', 'on');
fourth_tab_callback();
end
% write the CSV file for Confidence Index, Birth, Death, Division, and potentially Fusion to disk
Write_Metadata_to_CSV_File(tracked_images_path, enable_cell_fusion_flag);
write_parameters_to_mat_file();
end
end
%--------------------------------------------------------------------------------------------------
%--------------------------------------------------------------------------------------------------
function write_metadata_to_log_file()
print_to_command('', tracked_images_path);
print_to_command(' -------- Lineage Mapper GUI --------',tracked_images_path);
print_to_command('Folder Tab Parameters',tracked_images_path);
print_to_command([' Raw Images Directory: ' raw_images_path],tracked_images_path);
print_to_command([' Segmented Images Directory: ' segmented_images_path],tracked_images_path);
print_to_command([' Tracked Images Directory: ' tracked_images_path],tracked_images_path);
print_to_command([' Metadata Directory: ' tracked_images_path],tracked_images_path);
print_to_command([' Raw Image Common Name: <' raw_images_common_name '>'],tracked_images_path);
print_to_command([' Segmented Image Common Name: <' segmented_images_common_name '>'],tracked_images_path);
print_to_command([' Tracked Image Common Name: <' tracked_images_common_name '>'],tracked_images_path);
print_to_command('Tracking Parameters: ',tracked_images_path);
print_to_command(' Cost Function Parameters: ',tracked_images_path);
print_to_command([' Weight Cell Overlap: <' num2str(weight_overlap) '>'],tracked_images_path);
print_to_command([' Weight Centroids Distance: <' num2str(weight_centroids) '>'],tracked_images_path);
print_to_command([' Weight Cell Size: <' num2str(weight_size) '>'],tracked_images_path);
print_to_command([' Max Centroids Distance: <' num2str(max_centroids_distance) '>'],tracked_images_path);
print_to_command([' Frames to Track: <' frames_to_track '>'],tracked_images_path);
print_to_command(' Mitotic Parameters: ',tracked_images_path);
print_to_command([' Min Mitotic Overlap: <' num2str(division_overlap_threshold) '>'],tracked_images_path);
print_to_command([' Circularity Index: <' num2str(circularity_threshold) '>'],tracked_images_path);
print_to_command([' Daughter Size Similarity: <' num2str(daughter_size_similarity) '>'],tracked_images_path);
print_to_command([' Daughter Aspect Ratio Similarity: <' num2str(daughter_aspect_ratio_similarity) '>'],tracked_images_path);
print_to_command([' Enable Cell Mitotis: <' num2str(enable_cell_mitosis_flag) '>'],tracked_images_path);
print_to_command([' Number of Frames: <' num2str(number_of_frames_check_circularity) '>'],tracked_images_path);
print_to_command(' Confidence Index Parameters: ',tracked_images_path);
print_to_command([' Min Cell Life: <' num2str(cell_life_threshold) '>'],tracked_images_path);
print_to_command([' Cell Death Delta Centroid: <' num2str(cell_apoptosis_delta_centroid_thres) '>'],tracked_images_path);
print_to_command([' Cell Density CI Flag: <' num2str(cell_density_ci_flag) '>'],tracked_images_path);
print_to_command([' Border Cell CI Flag: <' num2str(border_cell_ci_flag) '>'],tracked_images_path);
print_to_command(' Fusion Parameters: ',tracked_images_path);
print_to_command([' Min Cell Area: <' num2str(cell_size_threshold) '>'],tracked_images_path);
print_to_command([' Min Fusion Overlap: <' num2str(fusion_overlap_threshold) '>'],tracked_images_path);
print_to_command([' Enable Fusion: <' num2str(enable_cell_fusion_flag) '>'],tracked_images_path);
end
function write_parameters_to_mat_file()
if numel(params) > 0
save([tracked_images_path 'parameters.mat'], params{1});
for i = 1:numel(params)
save([tracked_images_path 'parameters.mat'], params{i}, '-append');
end
end
end
%--------------------------------------------------------------------------------------------------
%--------------------------------------------------------------------------------------------------
function select_folder_raw_images_Callback(varargin)
% get directory
sdir = uigetdir(pwd,'Select Folder:');
if sdir ~= 0
try
raw_images_path_loc = validate_filepath(sdir);
catch err
if (strcmp(err.identifier,'validate_filepath:notFoundInPath')) || ...
(strcmp(err.identifier,'validate_filepath:argChk'))
errordlg('Invalid directory selected');
return;
else
rethrow(err);
end
end
set(raw_images_path_edit, 'String', raw_images_path_loc);
end
end
%--------------------------------------------------------------------------------------------------
function select_folder_segmented_images_Callback(varargin)
% get directory
sdir = uigetdir(pwd,'Select Folder:');
if sdir ~= 0
try
segmented_images_path_loc = validate_filepath(sdir);
catch err
if (strcmp(err.identifier,'validate_filepath:notFoundInPath')) || ...
(strcmp(err.identifier,'validate_filepath:argChk'))
errordlg('Invalid directory selected');
return;
else
rethrow(err);
end
end
set(segmented_images_path_edit, 'String', segmented_images_path_loc);
end
end
%----------------------------------------------------------------------------
function select_folder_tracked_images_Callback(varargin)
% get directory
sdir = uigetdir(pwd,'Select Folder:');
if sdir ~= 0
try
tracked_images_path_loc = validate_filepath(sdir);
catch err
if (strcmp(err.identifier,'validate_filepath:notFoundInPath')) || ...
(strcmp(err.identifier,'validate_filepath:argChk'))
errordlg('Invalid directory selected');
return;
else
rethrow(err);
end
end
set(tracked_images_path_edit, 'String', tracked_images_path_loc);
end
end
%------------------------------------------------------------------------------------
function pb_cancel_pathnames_Callback(varargin)
set(raw_images_path_edit,'string',raw_images_path);
set(raw_images_common_name_edit,'string',raw_images_common_name);
set(segmented_images_path_edit,'string',segmented_images_path);
set(segmented_images_common_name_edit,'string',segmented_images_common_name);
set(tracked_images_path_edit,'string',tracked_images_path);
set(tracked_images_common_name_edit,'string',tracked_images_common_name);
end
%-----------------------------------------------------------------------------------------------
function pb_tracking_cancel_Callback(varargin)
set(weight_overlap_edit,'String',weight_overlap);
set(weight_centroids_edit,'String',weight_centroids);
set(weight_size_edit,'String',weight_size);
set(max_centroids_distance_edit,'String',max_centroids_distance);
if (strcmp(frames_to_track, '0'))
set(frames_to_track_edit,'String','All');
else
set(frames_to_track_edit,'String',frames_to_track);
end
set(division_overlap_threshold_edit,'String',division_overlap_threshold);
set(daughter_size_similarity_edit,'String',daughter_size_similarity);
set(daughter_aspect_ratio_similarity_edit,'String',daughter_aspect_ratio_similarity);
set(circularity_threshold_edit,'String',circularity_threshold);
set(number_of_frames_check_circularity_edit, 'String', number_of_frames_check_circularity);
set(enable_cell_mitosis_checkbox, 'value', enable_cell_mitosis_flag);
set(cell_life_threshold_edit,'String',cell_life_threshold);
set(cell_apoptosis_cent_thres_edit, 'String', cell_apoptosis_delta_centroid_thres);
set(cell_density_checkbox, 'value', cell_density_ci_flag);
set(border_cell_checkbox, 'value', border_cell_ci_flag);
set(cell_size_threshold_edit,'String',cell_size_threshold);
set(fusion_overlap_threshold_edit,'String',fusion_overlap_threshold);
set(enable_fusion_checkbox,'Value',enable_cell_fusion_flag);
end
%------------------------------------------------------------------------------------
function batchmode_set_default_parameters()
% Cost function params
weight_overlap = 100;
weight_centroids = 50;
weight_size = 20;
max_centroids_distance = 50;
frames_to_track = 'All';
% Mitotic params
division_overlap_threshold = 20;
daughter_size_similarity = 50;
daughter_aspect_ratio_similarity = 70;
circularity_threshold = 30;
number_of_frames_check_circularity = 5;
enable_cell_mitosis_flag = 1;
% Confidence Index params
cell_life_threshold = 32;
cell_apoptosis_delta_centroid_thres = 10;
cell_density_ci_flag = 1;
border_cell_ci_flag = 1;
% Fusion params
cell_size_threshold = 100;
fusion_overlap_threshold = 20;
enable_cell_fusion_flag = 0;
end
function default_parameters(varargin)
% Cost function params
weight_overlap_loc = 100;
weight_centroids_loc = 50;
weight_size_loc = 20;
max_centroids_distance_loc = 50;
frames_to_track_loc = 'All';
% Mitotic params
division_overlap_threshold_loc = 20;
daughter_size_similarity_loc = 50;
daughter_aspect_ratio_similarity_loc = 70;
circularity_threshold_loc = 30;
number_of_frames_check_circularity_loc = 5;
enable_cell_mitosis_flag = 1;
% make sure edit boxes are enabled
if enable_cell_mitosis_flag
set(daughter_size_similarity_edit, 'enable', 'on');
set(daughter_aspect_ratio_similarity_edit, 'enable', 'on');
set(circularity_threshold_edit, 'enable', 'on');
set(number_of_frames_check_circularity_edit, 'enable', 'on');
else
set(daughter_size_similarity_edit, 'enable', 'off');
set(daughter_aspect_ratio_similarity_edit, 'enable', 'off');
set(circularity_threshold_edit, 'enable', 'off');
set(number_of_frames_check_circularity_edit, 'enable', 'off');
end
% Confidence Index params
cell_life_threshold_loc = 32;
cell_apoptosis_delta_centroid_thres_loc = 10;
cell_density_ci_flag = 1;
border_cell_ci_flag = 1;
% Fusion params
cell_size_threshold_loc = 100;
fusion_overlap_threshold_loc = 20;
enable_cell_fusion_flag = 0;
if enable_cell_fusion_flag
set(cell_size_threshold_edit, 'enable', 'off');
else
set(cell_size_threshold_edit, 'enable', 'on');