Freeze Analysis
The freeze analysis module allows the user to automatically score an animal's motion and freezing while in a conditioning chamber. It was designed with side-view recording in mind, and with the intention of being able to crop the top of a video frame to remove the influence of fiberoptic/miniscope cables. In the case where no cables are to be used, recording should be capable from above the animal.
- Run FreezeAnalysis_Calibration.ipynb on a short video of a chamber with no animal in it (~10 sec). This allows detection of basal fluctuation in pixel grayscale values. A suggested cutoff for use with subsequent steps is provided.
- Process several individual behavior videos with FreezeAnalysis_Individual.ipynb. This will allow extensive visualization of results in order to ensure confidence in selected parameters.
- Once you are comfortable with parameters, use FreezeAnalysis_BatchProcess.ipynb on a whole folder of videos.