An easy-to-use GUI to extract immobility and freezing episodes
Uses the motion output from the tracking GUI and the original movie to extract freezing episodes and display the results. Parameters can then be adjusted to give the best results. The same parameters are usually usable for different animals in the same conditions.
- Uses a motion threshold to detect freezing episodes
- Allows to merge episodes closer than a defined gap
- Defines a minimum freezing duration
- Allows manual editing/removal of single episodes (e.g. sometimes to remove grooming detected as freezing)
Output: a new variable in the .mat tracking file with the start/end times of each freezing episode
The current version has not been tested for compatibility and dependencies; in particular, it might not run under MATLAB versions older than R2018a. Also, unlike the tracking GUI, it needs the frames timestamps, that are currently either retrieved from the tracking file or a file generated by our acquisition system. This will soon be expanded to accommodate different systems.
- Expand the manual
- Switch from function to class for more robustness and ease of use on successive files
- Make the overall code less dependent on the recording system
- Use the calibration option from the tracking GUI to get an even more absolute freezing threshold (here it is influenced by the real pixel size, that depends on the camera distance)
- Take into account potential differences in screen resolutions/sizes
- Add inputs checking
- Adjust some parameters to get a smooth browsing (some movies have ridiculous FPS and resolution that are too heavy to handle like this)
- Add the possibility to compute a "moving" background