Animal Tracking Data Analysis¶
Organism tracking is performed through the MCAM GUI resulting in .CSV output files containing tracking data. This section explores concepts relating to loading data from the CSVs, plotting data, and filtering data.
Output Files¶
Output files are saved in a folder with the same name as the input file and this folder is created in the parent directory of the input file.
Raw Tracking Data - tracking_data.csv - CSV file
containing 8 key-points per fish, x, y coordinate and
confidence for each keypoint. Note: This file is likely
too large to be opened in Excel or other spreadsheet
software due to the large number of columns in the
data array. This file can be opened and manipulated
using Python.
Plotted Tracks -
plotted_tracks.png- Visualization of movement over time from blue (earliest, cold) to red (most recent, hot).Distance Traveled Data -
distance_traveled_metrics.csv- Distance traveled and speed calculated for each frame.Aggregate Metrics -
distance_traveled_key_metrics.csv- Distance traveled and speed calculated for each frame.Video Composite -
composite_tracked_video.mp4- MP4 video containing key-point and skeleton labeled fish for all wells of a well plate.
Units¶
Unless otherwise specified, exported units implicitly:
Distance or length: meters
Time: seconds
Velocity or speed: meters/second
Orientation/Angle: degrees