Complete analysis pipeline

Details about the script run_pipeline.m that demonstrates how to perform the full analysis pipeline (motion correction, source extraction, activity deconvolution):

1. The user specifies a folder where all the datasets are located and the extension of the files.
2. The datasets are first motion corrected using the NoRMCorre. Every registered file gets saved at the same folder in an hdf5 format, and the corresponding shifts as a mat file. The flag non_rigid specifies whether the algorithm should correct for rigid (faster) or for non-rigid (more accurate but slower) motion.
3. Downsampling and memory mapping: The hdf5 files are read sequentially, downsampled in time by a factor tsub and the downsampled data is saved as a single memory mapped file named ds_data.mat