Sleep Scoring 1.4.0 Latest Release:
Sleep Scoring Workflow:
To start a new project:
- Adjust your Sleep_Scoring.json file (I recommend making a local copy for yourself on your desktop)
- Below is an example of the .json file with explanations of each variable
{ "rawdat_dir": "/Volumes/yaochen/Active/Jacob Amme/jaLC_FLiPAKAREEGEMG004/jaLC_FLiPAKAREEGEMG004_data/", #This is where your raw EEG is "model_dir": "/Users/lizzie/Desktop/Remote_Git/neuroscience_sleep_scoring/model/", #This is the directory with the Sleep Scoring model "video_dir": "/Users/lizzie/Box/ChenLab/Jacob Amme/FLiP Videos/jaLC_FLiPAKAREEGEMG004/", #This is the directory wiht videos "modellog_dir": "/Users/lizzie/Desktop/", #This is where the model log is saved, will be the same as the model dir "personallog_dir": "/Volumes/yaochen/Active/Jacob Amme/" #This is where your personal log file will be "species": "mouse", #species of animal used (just in case rats are eventually used in the future) "mod_name": "mouse", #I wouldn't change this "mouse_name": "1225-9", #Animal name (not experiment name) "epochlen": 4, #This is the bin size for scoring (cannot go lower than 4) "fs": 400, #Sampling rate of raw data "fsd": 200, #Downsampled rate "emg": 1, #1 if you used EMG, 0 if you did not "vid": 1, #if you used motion tracking, 0 if you did not "movement": 1, #if you used video, 0 if you did not "EEG channel": 0, #Auxillary channel that will be used for the spectrogram (either 0 or 2) "EMG channel": 3, #Auxillary channel that will be used for the EMG "Acquisition": [ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 ], #Which acquisitions you would like to score "Filter High": 100, #High-pass filter for the EEG and EMG "Filter Low": 0.5, #Low-pass filter for the EEG and EMG "savedir": "/Volumes/yaochen/Active/Jacob Amme/jaLC_FLiPAKAREEGEMG004/jaLC_FLiPAKAREEGEMG004_extracted_data/", #directory where your extracted data will go "Bonsai Version": 3 #The Bonsai workflow that you used for the experiment }
2)Run the command below to extract and downsample the lfp
python /path/to/sleep/scoring/package/extract_data.py /path/to/json/file
- Once you have run the above line (only once per experiment), run the lone below to start the sleep scoring engine:
python /Users/lizzie/Desktop/Remote_Git/neuroscience_sleep_scoring/New_SWS.py /Users/lizzie/Desktop/Remote_Git/neuroscience_sleep_scoring/Score_Setting.json
- Follow the prompts the load up the acquisition that you want
A few notes about the program:
- Scoring Mode should be used for a new hour
- Checking Mode should be used for an hour that has no scoring
- Press "d" to exit checking mode and "q" to exit scoring mode
- Press "v" to click out of a movie early