Worm_optogenetics

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This script is for analyzing Optogenetics experiment data.

Input data type

sequential images (.jpg, .png)

How to analysis

1. Image subtraction analysis (quantify the mobility)
   1. run "Image_subtraction_analysis_multiple.py"
   2. select the upper directory of seq images.
   3. wait for several minutes (depends on CPU)
2. Find the stimulation timing
   1. Open a sequential images with Fiji (NIH)
   2. check images and write down the blue light stimulation timing
3. Analyze the behavior with script
   1. Open "Optogenetics_analysis.py"
   2. put the stimulation timing (e.g. stimuli_list = [1346, 1884, 2259, 2727, 3122])
   3. run the script
   4. select the subtraction analysis file (e.g. "locomotor_activity_th=7.csv")

Output

following files are positioned under dfs

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Licence

[MIT]

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Author

[Shinichi Miyazaki] https://github.com/Rukaume