Track

The 'Track' tab allows automated tracking of a single animal in trials either just the animals' centre point or, for rodents, three point tracking of nose, centre and tail-base.

Terms:
What is a Region?
What is a Zone?

Zones:
How do I create a zone?
Can I change the name of a zone?
What does "Min. time to Constitute entry" mean?
What happens if I delete a zone?
If I create a new zone on already tracked data, do I need to re-track?

Region:
How do I create a region?
What do I draw?
What are the drawing tools?
What is the difference between zones and regions?
What happens if I change a region?
What does copy / paste do?

Measurement:
What is measurement?
What is the rule?
Do I have to draw the region and set the rule for every trial?

Tracking:
What point of the animal is tracked?
How should I film a trial to ensure tracking will work best?
What is tracking config?
What does set background do?
Do I have to set the background?
Why can't I play the video on the tracking screen?
What are the possible status values?
What happens when I track?
Do I have to stay logged in while tracking is in progress?
How do I know that track is working?
What if track isn't working?
How many videos can I track at once?

Terms:

What is a Region?
A region is a part of some apparatus or object that you want to identify the animal interacting with from the video. An example of a region would be one of the arms of an Elevated Plus Maze.

What is a Zone?
A zone is a group of regions within the video. For example if using an Elevated Plus Maze, the "open arms" would be a zone, made up of two "regions", one for each open arm.

Zones:

How do I create a zone?
Select Zones from the Track tab, and click "Add Zone" to add a new zone, you'll have to enter a name and the minimum time to constitute a zone entry

Can I change the details of a zone?
Yes, to change the name of a zone select the Edit action from the zones list within the track tab.You can change the name, color, and time to constitute entry.

What does "Min. time to Constitute entry" mean?
The minimum time to constitute entry means the amount of time the animal needs to consecutively be in the zone to count as a zone entry.

What happens if I delete a zone?
If you delete a zone, all regions of this zone in all trials, will be deleted.

If I create a new zone on already tracked data, do I need to re-track?
No, if the video is already tracked there is no need to retrack after changing zones or regions. Just generate a new report and it will give results based on the updated zones and/or regions.

Region:

How do I create a region?
The create regions tab under the Track tab allows regions to be created. To create a region for an existing zone, first select the correct trial and zone using the drop down boxes, then use the drawing tools along the top of the video to draw the region on the video. Once you have completed drawing all of the regions you require you must click save to store these permenantly.

What do I draw?
Using the drawing tools it is possible to draw any shape on the video indicating the region required to get the results you need from each trial.

What are the drawing tools?
The drawing tools are (left to right): rectangle, circle, polygon, move. rotate-left, rotate-right, delete, and scale

What is the difference between zones and regions?
Zones are groups of one or more regions that are grouped together for calculating results with. If there is a zone with two regions then the animal will be counted as in the zone if it is in either region for the amount of time specified.

What happens if I change a region?
You can change a region by selecting the region from the drop down menu on the top right and making any changes you require. There's no need to retrack the trial after changing the regions - just generate a new report to get the updated results.

What does copy / paste do?
So you don't have to draw regions for every identical trial set-up you can click copy the regions from one trial then select another trial and click paste within an experiment. All of the regions and the ruler information will be copied to the trial, you can then click save to save the region informatoin for that trial.

Measurement:

What is measurement?
To give real-world values in our results we need to be able to convert pixel numbers into SI units. The measurement feature allows us to do this by getting the real-world value for one point in the video.

What is the rule?
The rule is on the screen and can be moved and resized to an area of known length within the video. This known length should then be entered in the "Length of Rule". The results will then be presented in SI units.

Do I have to draw the region and set the rule for every trial?
No, often multiple trials are undertaken without moving the camera and so the settings will be the same for multiple trials. To make it easier when setting up tracking we've introduced copy/paste functionality to copy the region and measurement config from one trail to another - this ensures consistency between trials while saving time during the setup.

Tracking:

What point of the animal is tracked?
The centre of mass of the animal is tracked

How should I film a trial to ensure tracking will work best?
To enable optimum tracking, see our list of requirements for tracking videos and also check out our advice for filming experiments.

What is tracking config?
We've tried to make the tracking setup as easy as possible but there are a few optional settings which help improve the quality of the tracking results - these are included in the tracking config list.

What does "Set Background" do?
"Set Background" allows selecting a frame of the video which contains an empty arena (i.e. where no animal is present). Note: It is important that the lighting in the background frame is similar to the lighting throughout the trial, and that it does not contain the animal.

Do I have to set the background?
No, it's optional, but if there is a frame of the video which contains an empty arena then it is best to complete this as it helps improve the tracking accuracy.

Why can't I play the video on the tracking screen?
The video on the tracking screen can only be played up to the point where there are tracking results. If you have not yet tracked the trial then you will not be able to view the video. If you wish to view the video this can be done from the trial list.

What are the possible status values?
Tracking can have three different status values:
"Trial has not been tracked"
"Tracking in progress"
"Tracking Complete"

What happens when I track?
When you track the status will change to "Tracking in Progress" and tracking will start in the background. You will be able to see the progress of tracking displayed in the progress bar. Note: tracking can take some time to complete, so don't worry if there is little or no progress for a couple of minutes.

Do I have to stay logged in while tracking is in progress?
No, once tracking as started you can leave the application and it will continue in the background. Next time you log in you'll see the progress of the tracking.

How do I know that track is working?
The tracking progress bar will show the amount of the trial that has been tracked so far. You can play the video up to the point that tracking has completed and the tracking results up to that point will be overlaid and the video will play demonstrating the points that have been tracked.

What if track isn't working?
If you have any problems with tracking of your video, please contact us and we'll suggest how you can get the results you are looking for.

How many videos can I track at once?
There is no limit to the number of videos that can be tracked at once, however the system can only process a few tracking jobs at a time so the tracking jobs will be added to a queue until there is space to process them. This can take up to a couple of hours so don't worry if the progress bar shows 0% for a long time.