!!! Remember to put all the source codes from https://github.com/zhoupc/CNMF_E in the same path of cnmfe_setup.m before running it

1. Add the pipeline folder and all its subfolders to matlab path.
2. If this is the first time, run cnmfe_setup.m to set up environment.
3. The input variable in pipescript.m should be a char array with they path to the folder with all the .avi files to be converted.
4. The mouse_id variable in pipescript.m should be a char array with the mouse id.
5. The session_type variable in pipescript.m should be a char array of the type of session being recorded (hab,def1, ...).
6. The hour variable in pipescript.m should be a char array of the time associated with this session. It should be formated as hour_minute_second.
7. The cnmfe_home variable in pipejoin.m should be a char array of the path where the cnmfe analysis should be outputted. This will also be where the merged .avi file and the .tif file are generated.
8. Run with by running pipescript on the matlab command window.

• This code does not work with behavCam videos. It has only been tested with msCam videos.
• All the input values should be in the form of char arrays. NO STRINGS. This will lead to an error when the code runs saveastif.m.
• Some files are very large and will take a long time to process. for these files, if the connection to the external drive is broken, then the output will be a broken tiff file. The error you will get will be fl:filesystem:SystemError. All you need to do is re-establish the connection and re-run the preprocessing algorithm.

• If you wish to supress or delete the .avi file, remove the percent symbols in pipenormcorre.m on lines 52
• To delete the files, run del_files.m with tiff_name as input

• Filenames are in italics.
• Variables are in bold.

This is the notebook for aligning neuron and behavior data by their timestamp. Used as a preprocessor to clean and prepare the integrated data for DL/ML models.