Inputs - DeNardoLab/BehaviorDEPOT GitHub Wiki

Data Requirements

BehaviorDEPOT requires a video file and associated pose-estimation file for each session to be run. DeepLabCut is the default pose-estimation software for BehaviorDEPOT. v1.3 includes a conversion script for SLEAP and we are committed to providing support for new pose formats when requested by users.

When performing batch analysis, BehaviorDEPOT accepts a single directory as input. Within the input directory, there should be folders for each session you want to analyze, each containing a video and a pose-estimation file.

Video Format

  • Formats currently supported: MP4 and AVI.
    *Other formats can be added; please contact authors if you have a particular format you would like to have integrated.

Pose-estimation File

Cue File (Optional)

  • Input for cue files is required to be a spreadsheet file (.csv, .xlsx), with each event as a row, the start frame in the first column, and the end frame in the second column.

Converting Human Annotations to BehaviorDEPOT Format (hB)

Input Annotation Format

  • BehaviorDEPOT reads in frame-wise annotations of behavior for use in Support Modules.
  • The input format should be a table:
    • Column 1 contains start frames for each behavior bout.
    • Column 2 contains stop frames for each behavior bout.
    • Column 3 contains behavior labels (e.g. Freezing, Grooming).
    • Multiple behaviors may be contained within the same table.
    • Table can be saved as a .MAT or .CSV file.

Converting Annotations

  1. To convert annotations, open the BehaviorDEPOT GUI.
  2. Select the 'Convert Human Annotations' button on the right side of the GUI.
  3. Select the table file (.MAT or .CSV) that you wish to convert.
  4. Type in the total number of frames in the video.
  5. An 'hB' file will be saved in the same directory as the input table.

Output Format