EpiTools_CommandLine.m

%% Simple pipeline to show how to use EpiTools from Matlab Consolse

% Please proceed through the code sections individually instead of running
% the entire script at once.

% Used data: /8bitDataset/test_set.tif (206x * 199y * 30z * 8t) 
% Generated ouptut: /8bitDataset/Analysis/

% In order to run the EpiTools *GUI* after the execution of this test
% please make sure to remove the ds-settings data structure from the Workspace 
% before launching the gui. 

%% Function loading (Current directory should be the epitools home directory)

file_path = pwd;
cd([file_path,'/src']);
LoadEpiTools();

cd(file_path);

%% Logging setup [ mandatory, w/o it the programm will crash ]

log_settings.log_level = {'INFO', 'PROC', 'GUI', 'WARN', 'ERR'};
log_settings.log_device = 3;
assignin('base', 'log_settings', log_settings);

%% Data Structure setup (ds = Data Settings object) needed for GUI

TestData = [pwd,'/Tests/8bitDataSet/'];

ds = settings();

ds.data_analysisindir = [TestData,'Analysis'];
ds.data_analysisoutdir = [TestData,'Analysis'];
ds.data_imagepath = TestData;
ds.data_benchmarkdir = [TestData,'Benchmark'];
ds.exec_commandline = true;
ds.platform_units = 1;

strModuleName = 'Main';
ds.CreateModule(strModuleName);

LoadEtMetaData(ds);

%% Surface Projection

strModuleName = 'Projection';
ds.CreateModule(strModuleName);

% how much smoothing to apply to original data - default 1 [1-5]
ds.AddSetting(strModuleName, 'SmoothingRadius', 1.0); 
% 1st surface fitting, surface stiffness - default 100 [50 - 200]
ds.AddSetting(strModuleName, 'SurfSmoothness1', 30);        
% 2nd surface fitting, stiffness          - default 30 [10 - 50]
ds.AddSetting(strModuleName, 'SurfSmoothness2', 20);
% how much up/down to gather data from surface - default 1.2 [1 - 3]
ds.AddSetting(strModuleName, 'ProjectionDepthThreshold', 1.2);
% show fit or not
ds.AddSetting(strModuleName, 'InspectResults', false);

Projection(ds);

%% Time Series Registration
strModuleName = 'Stack_Registration';
ds.CreateModule(strModuleName);

ds.AddSetting(strModuleName, 'SkipFirstRegStep', true); 
ds.AddSetting(strModuleName, 'useStackReg', true); 

Registration(ds); 

%% Apply CLAHE
strModuleName = 'Contrast_Enhancement';
ds.CreateModule(strModuleName);

ds.AddSetting(strModuleName, 'enhancement_limit', 0.02);
ds.AddSetting(strModuleName, 'enhancement_width',30);

ImproveContrast(ds);

%% Segmentation parameters:
strModuleName = 'Segmentation';
ds.CreateModule(strModuleName);

% area of cell in pixels
ds.AddSetting(strModuleName, 'mincellsize', 25); 
% smoothing to be applied, needed to get rid of as much noise as poss 
% without loosing the actual features we are looking for)
ds.AddSetting(strModuleName, 'sigma1', 1);         
ds.AddSetting(strModuleName, 'threshold', 25);               

% Grow cells
ds.AddSetting(strModuleName, 'sigma3', 2);
ds.AddSetting(strModuleName, 'LargeCellSizeThres', 3000);
% default 0.35 .. have to play with it
ds.AddSetting(strModuleName, 'MergeCriteria', 0.35);   

% Final joining ,  30 for YM data
ds.AddSetting(strModuleName, 'IBoundMax', 30); 

% Performance Options (show=show_steps)
ds.AddSetting(strModuleName, 'debug', false);
ds.AddSetting(strModuleName, 'Parallel', false);
ds.AddSetting(strModuleName, 'SingleFrame', false);

Segmentation(ds);

%% Execute tracking correction

strModuleName = 'Tracking';
ds.CreateModule(strModuleName);
ds.AddSetting(strModuleName, 'TrackingRadius', 15);

TrackingLauncher(ds);

%% ReSegment with applied changes

strModuleName = 'ReSegmentation';
ds.CreateModule(strModuleName);

ReSegmentation(ds);

%% Export the segmentation

strModuleName = 'Skeletons';
ds.CreateModule(strModuleName);
SkeletonConversion(ds);