Track workflow: Repair

Sometimes WormLab incorrectly identifies the head as the tail and vice-versa after a worm emerges from an omega bend or fold. To correct this problem as follows:

1. Click a worm to select it.
2. Select Entire track OR To end of track.
   • Entire track: Swaps the head and tail in all frames for the selected worm.
   • To end of track: Swaps the head and tail from the current frame displayed until the end of track for the selected worm.
3. Click Swap head/tail.

Choose how you want to define the deletion of worm tracks:

• This frame: Remove all detected worm from the current frame.

• All frames Remove all detected worms from all frames.

• Range Remove all detected worms from video frame "n" to frame "n+x".

• on Label Remove all detected worms from inside a manually drawn label through all frames.

  This tool was developed to delete artifacts that are interpreted as worms by WormLab software. Note that the object detected as a worm must remain inside the label for the entire track in order to be deleted.

To connect the end of a track to the beginning of another track do the following:

1. Enter the track numbers to join:
   • If the numbers are consecutive, use a dash (1-3).
   • If the numbers are not consecutive, use commas.
2. Click Join Tracks. WormLab joins the secondary worm track and the original, primary worm track. The newly created worm track is assigned the original, primary track number.
3. Click Re-Index Worms to reassign worm tracks in consecutive numerical order (and avoid empty columns in data tables).

To connect a track that is interrupted at frame "n" and resumed at frame "n+x" to tracks generated between frame "n" and frame "n+x":

1. Use Split Tracks to "end" the interrupted track 1 at frame "n"

2. Use Join Tracks to connect the interrupted track to the other tracks

1. Use the slider to navigate to the desired frame.
2. Click a worm to select its track.
3. Click Split Tracks .
4. WormLab software splits the original (primary) track and creates a new (secondary) track for the worm.
5. Click Re-Index Worms to reassign worm tracks in consecutive numerical order (and avoid empty columns in data tables).

Use Assign ID to swap the ID number of a selected worm track.

1. Use the slider to navigate to the desired frame.
2. Click a worm to select it.
3. Enter the desired ID number for the worm track.
4. Click Assign ID.

Click a worm then click Delete selected track to delete a worm model and its data. Click Re-Index Worms to reassign worm tracks in consecutive numerical order (and avoid empty columns in data tables).

Click Undo to undo the last operation:

• After deleting a track: Restore the track and the data.
• After joining or splitting: Return to previous state.

Click Track auto-connect to automatically join discontinuous worm tracks throughout the entire video. Tracks are joined based on the user defined tolerance percentage for position (midpoint shift) and shape (length and width).

• Interaction Events: click Previous and Next to quickly jump to worm-interactions, including entanglements and self-overlap, throughout the video.

  To include coiling as an interaction, check Include coiling.

• Track event (start/termination): click Previous and Next to quickly jump to the beginning and end of worm tracks throughout the entire video.

Click Re-Index Worms to reassign worm tracks in consecutive numerical order after deleting, joining, or splitting tracks. Re-Indexing worms after modifying the number of worm tracks is a good idea because otherwise, there will be empty columns in data tables corresponding to tracks that are no longer present in the analysis.