% batch preprocess DiSPIM images
% either cd into data parent directory or modify below
data_dir = fullfile('data/');
input_dir = fullfile(data_dir,'images/');
preprocessed_dir = fullfile(data_dir,'preprocessed/');
seeds_dir = fullfile(data_dir,'seeds/');
% preprocess images
load(fullfile(data_dir,'DiSPIM_preprocess_options.mat'),'options');
CERW_batch_preprocess(input_dir, preprocessed_dir, options);
% generate seeds
load(fullfile(data_dir,'DiSPIM_seeds_options.mat'),'options');
CERW_batch_seeds(preprocessed_dir,seeds_dir,options);