Troubleshooting: Arenas and zones

Issues

▪How do I know the coordinates of the arenas, points and zones?

▪Tracking does not start when the animal is inside the shelter

▪The animal is in the hidden zone but the data show “missing sample”

▪How do I view the analysis results for hidden zones?

▪What if a hidden zone is part of a larger (overlapping) zone?

▪I get a warning that two zones point to the same region, when in fact they don’t

▪I want to repeat calibration but I do not see the ‘+’ cursor anymore

 

How do I know the coordinates of the arenas, points and zones?

1.Open the Arena Settings.

2.Position the mouse pointer on one vertex of the arena/zone outline or on a point of interest.

 

3.Do not move the mouse. In the Status bar, locate the World point (for the coordinates in calibrated units, for example cm) or Pixel point (for the coordinates in pixels).

 

tips

▪If you do not see the Status bar, choose View > Status bar.

▪Zoom in the arena for a more precise positioning of the mouse pointer.

▪You can use the point coordinates to calculate the coordinates of the subject relative to a point of interest. See an example in Troubleshooting: How can I merge heatmaps generated in different arenas? 

▪See also The x-y coordinate system in the arena

Tracking does not start when the animal is inside the shelter

In an experiment with a hidden zone, for example a shelter, it is possible that the animal is already inside that zone when you start the trial. In that case, the trial will only start when the animal first exits the hidden zone. If you want the trial to start straight away, recording the animal inside the hidden zone, you can make a second entry zone, somewhere where you can put, for instance, your finger.

If you cannot get close to the shelter, you can draw a zone that runs along the arena side:

 

After starting the trial, put your finger in that zone in such a way that EthoVision detects it (so the trial can start), then remove it (but make sure that the finger only appears and disappears in this entry zone, not the rest of the arena. This way EthoVision assumes that the animal has entered the hidden zone).

 

The animal is in the hidden zone but the data show “missing sample”

You may encounter this issue in the Track Editor or in the Track Visualization/Integrated Visualization. Normally this happens when the last recorded position of the animal immediately before disappearing from view is outside the entry zone. There are at least two possible reasons for that to occur:

▪The entry zone is too narrow and too near the hidden zone. So chance increases that the last data point occurs outside the entry zone, before the subject disappears from view.

▪Another reason is that Track noise reduction is applied during tracking. In such a situation, the position of the subject at any time is smoothed using the last 12 samples. Especially when the subject moves fast, the data points may “lag behind” the image of the moving subject (you can check this in the Integrated Visualization). It can happen that the last smoothed position is calculated outside the entry zone.

In both cases there is some chance that the last data point before the subject goes missing is still outside the entry zone. For this reason, EthoVision XT considers the subject missing, not in the hidden zone.

To solve the issue, do at least one of the following:

▪Make the entry zone larger. Duplicate the Arena Settings, enlarge the entry zone in such a way that the last position is likely to be inside that zone, and then use the new Arena Settings for the next trials.

▪Increase the sample rate. Especially if the animals move fast, increase the sample rate. This increases the chance that at least one point position is determined inside the entry zone.

▪Disable Track noise reduction. If you use Track noise reduction, duplicate the Detection Settings, under Smoothing set Track noise reduction to Off, and use the new Detection Settings to acquire the next trials.

How do I view the analysis results for hidden zones?

To calculate the time that the subject spent in a hidden zone, choose In zone in the Analysis profile and select the hidden zone.

What if a hidden zone is part of a larger (overlapping) zone?

▪If the hidden zone is part of a larger zone, the results for that zone do not include the time spent in the hidden zone. This is because the time in the hidden zone is always calculated separately.

▪If an entry zone is part of a larger zone, the time in the entry zone is also included in the time spent in the larger zone.

In practice: if a zone includes a hidden zone, in order to know the total time spent in that zone, including the time spent in the hidden zone, you must sum up the times shown in the results table. See a note under the topic In zone

I get a warning that two zones point to the same region, when in fact they don’t

This is caused by very sharp corners of one or more zones. Using the Point edit tool (press P), move single points so that sharp corners are removed. For instance by adding a point just next to the sharp corner. See Move, rotate and resize a shape

I want to repeat calibration but I do not see the ‘+’ cursor anymore

Click the 1. Draw Scale to Calibrate button at the top-right corner of the screen.