ParameterFile.txt

* General
Name = '<NAME-OF-RUN>' % Fill in the name of the session, will be used to make output folder
emailAddress = '<EMAIL-ADDRESS>' % OPTIONAL - will notify by email when the run is finished

* Flags
WriteVideo = true; % Should be true in order to write outputs
SaveCheckPoints = 10; % Save checkpoints of the run, in case some problem occures during the run
LoadCheckPoints = false; % Continue from a saved checkpoint

% FALGS FOR DEBUGGING - NO NEED TO CHANGE
deleteIfErr = false;
saveCode = false;
profile = false;
SaveDebug = 0;

* load_data_params
data_path = fullfile('<PATH-TO-DATA-DIRECTORY>'); % Path the the directory of the raw images
extention = '*.TIF'; % Extension of the raw images should be in the format '*.<EXTENSION>'
expr = 'M20150416_w2CFP_s102_t(\d+).TIF' % Experesion of filenames. Replace the time index with (\d+)
tagged_data_path = fullfile('<PATH-TO-INIT-SEG-DIR>');% Path the the directory of the segmentation of the first two frames
tagged_extention = '*.tif'; % Extension of the raw images should be in the format '*.<EXTENSION>'
tagged_expr = 'ManualSeg_s102_(\d+).tif' % Experesion of filenames. Replace the time index with (\d+)

* parameters
cellPrior = 0.8; % Paramter for tuning foreground/background probabilities. parameter Alpha in the paper
minCellSize = 70; % Parameter for minimum cell size
stop_frame = inf % Stoping frame. In order to run all frames in the set insert inf.

% ADVANCED PARAMETERS
maxItr = 4;
minErr = 10;
solidityThr = 0.5;
patchSize = 150;
edgeQ = 2;
edgeK = 5;
geoOnly = false;