stitch_2020_09_16.m

% cd to the folder containing this file, set up the path properly
this_file_path = mfilename('fullpath') ;
this_folder_path = fileparts(this_file_path) ;
cd(this_folder_path) ;
modpath ;

% Specify the input/output folders
sample_date = "2020-09-16"  %#ok<NOPTS>
tile_folder_path = sprintf('/groups/mousebrainmicro/mousebrainmicro/data/%s', sample_date)  %#ok<NOPTS>
pipeline_output_folder = sprintf('/nrs/mouselight/pipeline_output/%s', sample_date)  %#ok<NOPTS> 
stitching_output_folder_path = sprintf('/groups/mousebrainmicro/mousebrainmicro/cluster/Reconstructions/%s/stitching-output', sample_date)  %#ok<NOPTS>

% Call the function that does the real work
stitch(tile_folder_path, pipeline_output_folder, stitching_output_folder_path) ;