Knowledge Base

Optogenetics Experiments

Detection Settings

Choose Setup > Detection Settings.

We assume that you followed the procedure in detection settings on page 17.

Set the Sample Rate

In the Video section, check that the sample rate is set to:

• Rats: 5 samples/second.
• Mice: 12.5 samples/second.

However, when tracking the nose-point, center-point and tail-base point of the rodents, always choose the highest possible sample rate, for example 25 or 30 samples/s, depending on your camera.

Remove the Effect of Cables and Fibers

When working with physiology and optogenetics setups, the cables and fibers often make detection of the subject impossible with the default settings.

To filter fibers out of the video image, use the Subject Contour options. If the fiber is the same color as the subject, then increase the value in the first Erosion filter until the fiber is no longer detected. Increase Dilation to make the entire body fully detected. Leave the second Erosion filter to zero.

If the fiber has a different color and "cuts" the yellow blob in two, try first Dilation, and then increase the second Erosion filter.

In Zone Conditions and Zone Exit Threshold

When the previous condition is met, turn off the LED.

Note: You can also base the "In Zone" conditions on the statistic "Current". However, in such case when the subject walks along the zone border its center point will jitter between somewhere outside the zone and inside the zone. For this reason the "Current" value of the In Zone variable will rapidly change from true to false and vice versa, therefore the conditions based on this variable become true and false very often.

To prevent this from happening, in the "In Zone" Condition window click Settings and enter a Zone exit threshold. This way the subject is still considered in the zone (Current In Zone = true) if its body point is found within the threshold distance from the zone border. The subject is only considered out of the zone (Current In Zone = false) if it crosses the threshold.

Tip: Reduce the zone by a distance half of the exit threshold. For example, if the exit threshold is 4 cm, reduce the zone border by 2 cm. This way you do not overestimate the size of the zone when using the exit threshold. For details, in the EthoVision XT Help see Dependent Variables in Detail > In Zone.

Source: EthoVision XT 18 - Application Manual, Noldus Information Technology