NEURAL PREPROCESSING: all of these and dependencies are made publicly available at https://github.com/HoweLab/MultifiberProcessing

cxd2tif.m: converts raw .cxd files into .tif
motion_correct.m: motion correction (courtesty of Dr. Jason R. Climer, jason.r.climer@gmail.com)
load_tiffs_fast.m: fast tiff reader (courtesty of Dr. Jason R. Climer, jason.r.climer@gmail.com)
write_tiff_fast.m: fast tiff writer (courtesty of Dr. Jason R. Climer, jason.r.climer@gmail.com)

The following scripts (.m + .fig files comprise a GUI) are used to create new ROI maps or fit existing ROI maps onto neural data movies and extract fluorescence:
create_ROI_map.m & create_ROI_map.fig
fit_ROI_map.m & fit_ROI_map.fig
refine_ROI_map.m & refine_ROI_map.fig




BEHAVIORAL PREPROCESSING:

split_and_bin_grid_behav_files.m bins the 2kHz behavioral data to match the the neural imaging sampling rate using the incoming TTLs from the neural imaging camera(s)

split_frames_by_LED: in cases where imaging was acquired using alternating LED excitation, this splits the behavioral file (after running split_and_bin_grid_behav_files.m) to align with the respective imaging channels

