ThorImage/ThorSync_2P-analysis

Notebook to synchronize and analyze ThorImage + ThorSync 2-photon calcium imaging data with light stimulation.

The notebook requires the user to draw ROIs as described here. The ROIs are drawn on an automatically computed sum projection. The stimulation information is automatically obtained from the ThorSync file.

Output returned by notebook:

1. Dataframe containing information per frame in the format:

Channel + Sample	Filename	Frame	Mean pixel value in ROI	Mean pixel value in bkg area	Norm_mean_pixel_value_in_ROI	Time passed (s)	dF/F0	LED (ON/OFF)
ChanA (001_001_001)	ChanA_001_001_001	1.0	542.6812468577175	541.7430997876858	0.9381470700317323.	0.0	0.95	0
. . .	. . .	. . .	. . .	. . .	. . .	. . .	. . .	. . .

2. Pickled dictionary containing raw and analyzed data, including ROI coordinates

3. dF/F0 over time showing stimulation:

The notebook also returns raw mean and background normalized mean traces.

4. dF/F0 heatmap (sum over all frames):

5. dF/F0 heatmap movie over time showing stimulation:

example_video_short.mp4

6. ROIs drawn for area of interest and background: