Tracking settings - Z2S

There are four SET functions that need to be included in the script for tracking to occur. Standard tracking settings for various the model organisms are shown below. These values have been tested and are reliable in tracking most animals. However, the values may need to be adjusted for your specific animals.

If you are using software before May 2022, please see the Tracking settings - Z1 page for details on the additional SET functions needed. These additional functions will continue to work on the latest software version. The settings found on this page are intended to simplify the use and adjustment of previous tracking commands.

Tracking setting commands

There are two tracking settings which are placed at the beginning of the script. These settings tell the unit how to find and track the organism(s).

SET(TARGET_SIZE,#) 
SET(DETECTOR_THRESHOLD,#)

SET(TARGET_SIZE,#) - This is the command where the size of the organism is set. This is set as the diameter of the organism in mm.

SET(DETECTOR_THRESHOLD,#) - This is the level at which the unit will properly detect the organism (and not other artefacts in the arena).

• The higher the detector threshold, the less sensitive the tracking will be. Therefore, the animal might not be detected if set too high. This can be indicated by the target marker being absent.
• If the threshold is set too low the tracking can pick up other signals in the arena (e.g., shadows, reflections, or biological material), creating 'noisy' tracking and the target marker may jump around the arena(s).

Reference image setting commands

There are two reference image settings which tell the unit how to capture the tracking reference image and how long to take to create the final image. The image is best achieved when the animals have moved during the AUTOREF period, as it works by removing the animal from the background image. Tracking is achieved by looking for significant differences, of suitable size and strength, between this 'empty' image and the current video image.

SET(AUTOREF_MODE,MOVEMENT)
SET(AUTOREF_TIMEOUT,#)
 
AUTOREFERENCE()

SET(AUTOREF_MODE,MOVEMENT) - This command sets the method for capturing the reference image.

• NOTE: We recommend that you use SET(AUTOREF_MODE,MOVEMENT), which is based on the animal moving during the autoref period.

SET(AUTOREF_TIMEOUT,#) - A reference image is complied by filming for the period of time set in this command. If an animal is unlikely to move much (e.g., a young larval fish), increasing this setting to a larger amount of time allows for a greater possibility of the system capturing movement.

AUTOREFERENCE() - this function is used to execute the above settings in an attempt to create the reference image. This image is stored as autoref.bmp in the assets directory. This should be included at the point in the script where you want the reference image created. This typically occurs within ACTION MAIN at the start of your experiment. However, this function can be included at any point in the script and can occur more than once during an experiment.

Tracking settings in the MWP units

Larval zebrafish

SET(TARGET_SIZE,2) 
SET(DETECTOR_THRESHOLD,6) 
 
SET(AUTOREF_MODE,MOVEMENT) 
SET(AUTOREF_TIMEOUT,60)

Adult Drosophila

SET(TARGET_SIZE,5) 
SET(DETECTOR_THRESHOLD,3) 
 
SET(AUTOREF_MODE,MOVEMENT) 
SET(AUTOREF_TIMEOUT,30)

Daphnia

SET(TARGET_SIZE,1) 
SET(DETECTOR_THRESHOLD,5) 
 
SET(AUTOREF_MODE,MOVEMENT) 
SET(AUTOREF_TIMEOUT,10) 

Tracking settings in the AD or LT units

Adult zebrafish

SET(TARGET_SIZE,15) 
SET(DETECTOR_THRESHOLD,5) 
 
SET(AUTOREF_MODE,MOVEMENT) 
SET(AUTOREF_TIMEOUT,30)

The test begins with the TARGET_SIZE set to 1 and the DETECTOR_THRESHOLD set to 0. For each of 10 target sizes (1-10), there are 11 detector thresholds which run through (0-10). This allows you to test various target size and detector threshold settings quickly. You will need to place animals onto your well plate and into the system. Once the script reaches the appropriate settings for your particular animal, you will be able to see the target marker surrounding the animal and not jumping around to 'noise'. A video is created, as well as a data file of the findings. 

Target_Size and Detector_Threshold demo script

The script begins with the TARGET_SIZE set to 1 and the DETECTOR_THRESHOLD set to 0. For each of 10 target sizes (1-10), there are 11 detector thresholds which run through (0-10). This allows you to test various target size and detector threshold settings quickly. 

You will need to place animals onto your well plate and into the system. Once the script reaches the appropriate settings for your particular animal, you will be able to see the target marker surrounding the animal and not jumping around to 'noise'. A video is created, as well as a data file of the findings.

Script download

To download the target_size_detector_threshold_testing script as a .zs file (file type Zantiks software reads), choose the Save File As option in the right-click dialogue box. Clicking on the script name hyperlink will open a read-only version of the script.

Script download:

target_size_detector_threshold_testing.zs

Assets

You will need to upload the asset into the Asset directory on your Zantiks Control Console and ensure the correct asset name is in the LOAD(ZONES,"name_of_asset") command in the script.

See the Calibrating your Zantiks unit page and Asset building in the MWP unit page for details on how to create assets customised to your system.