Analysis Module Outputs

Data Structures

Behavior.mat - struct containing all behaviors analyzed. Within each behavior struct:

- Bouts: start and stop frames of each behavior bout
- Count: number of behavior bouts
- Length: duration of each behavior bout
- Vector:  behavior vector across all frames
- Results: results table for spatial classifiers (e.g. EPM)
- Spatial: information about each behavior in custom ROIs, if selected
- Temporal: information about each behavior with respect to user-provided cue file

Special Classifiers

• Some classifiers do not output in the above format and instead report analysis specific to each classifier
• The most common example is for behavior recorded in special arenas, such as the Elevated Plus Maze or Open Field Test
• These classifiers output a results table, containing information relevant to the classifier (e.g. time spent/number entries in open/closed arms of EPM)
• Additionally, these classifiers report bout-wise and vectorized information about time spent in classifier ROIs

Metrics.mat - a struct containing information about speed, movement, and velocity of the tracked parts

- Diff: contains the location differential across frames for various points
- Velocity: the velocity at each frame
- Acceleration: the acceleration at each frame
- Dist: contains distance measurements between various sets of tracked points (e.g. head and tailbase)
- Location:  location of animal
- Movement:  movement speed in cm/sec
- DistanceTraveled: total distance traveled in cm

Params.mat - a struct containing information about parameters used during analysis

- [BehaviorName]: contains specific parameter values used for each classifier run in the Analysis Module
- Video: contains information about the video (video name, total frames, fps, etc.)
- Cutoff Threshold: threshold value for throwing away low quality tracking data (to be replaced via interpolation)
- Hampel: whether or not hampel filter was applied
- Smoothing: parameters used for smoothing
- px2cm: distance calibration value in pixels/centimeter
- Other miscellaneous parameters (e.g. part names, batch session)

Tracking.mat - a struct containing the location of each tracked part

- Raw: contains the original pose estimation data collected from the input file 
- Smooth: contains the location of each tracked part after smoothing
- Data are stored as matrix: Tracking.Smooth.(keypoint) = [x/y coordinate by frame number]

Plots & Figures

Spatiotemporal Maps

• Spatiotemporal maps plot the trajectory of the subject from the beginning to end of the analyzed session. Color data shows the progression of time.

Spatiotemporal Maps with Behavior

• These maps include spatiotemporal trajectory with additional symbols representing locations of tracked behaviors.
  

Behavior Plots

• These plots show the results of applied behavior classifiers throughout the session.