!!! 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
- Add the pipeline folder and all its subfolders to matlab path.
- If this is the first time, run cnmfe_setup.m to set up environment.
- 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.
- The mouse_id variable in pipescript.m should be a char array with the mouse id.
- The session_type variable in pipescript.m should be a char array of the type of session being recorded (hab,def1, ...).
- 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.
- 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.
- 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.