Knowledge Base

Advanced Modeled Parameters

Maximum Noise Size

Set the Maximum noise size. The value should be lower than the minimum subject size, but high enough to make sure that small objects with the same contrast as the subject are not detected.

Shape Stability

The Shape stability setting is used when you track animals whose body can be occluded by, for example, cage bars or part of the body of another animal. When this happens, the animal's body consists of two separate objects that are close together.

The Shape stability optimized for slider has two extreme settings:

• Occlusions: When you set the slider close to Occlusions, EthoVision considers separate objects that are close together part of one animal.
• Noise: When you set the slider close to Noise, EthoVision considers separate smaller parts not part of the animal.

If you are not sure which setting to select, leave Shape stability at the default value of 620.

Modeling Effort

The Modeling effort setting is used when two animals touch and EthoVision loses the separate shapes. At this point, EthoVision tries to determine which part of the big merged body fill belongs to either animal, which costs a lot of processing load.

The Modeling effort optimized for slider has two extreme settings:

• Performance: When you set the slider close to Performance, EthoVision is only allowed a short time to determine which part of the merged body fill belongs to which animal. Therefore, modeling quality is low.
• Modelling: When you set the slider to Modelling, EthoVision XT is allowed a longer time per frame to determine which part of the merged body fill belongs to which animal. Therefore, modelling quality is good, but this costs a lot of processor load.

We recommend selecting Modelling only when you have a computer that exceeds the minimum system requirements. When you are not sure which setting to select, leave Modeling effort at the default value of 500.

Tips for Setting the Subject Size

• Make sure you do not set the Tolerance too small; it is better to get a wrong body size/shape than a wrong location of the animal.
• It is better to set the Average subject size slightly bigger than the actual subject size, especially when you carry out nose-tail tracking.
• If you want to carry out live tracking with multiple similarly-sized animals, it is recommended to first introduce one animal into the arena and make the Subject Size settings for this animal.
• If the subject size changes a lot between trials, it is recommended to create new Detection Settings for this new size.

Advanced Detection Settings for Color Marker Tracking

Aim

To specify which colors EthoVision XT should follow when tracking color markers.

Prerequisites

• You have marked the animals.
• In the Experiment Settings under Tracked Features you selected Color marker tracking (treat marker as center-point).

Note that with this option you track only the marker, while the animal's shape is ignored.

Procedure

1. Put the marked animals in the arena or play the video. Optimize the camera setup, lighting conditions and marker characteristics. See Tips for color tracking.
2. In the Detection Settings window, under Video, select the image source and sample rate. See Video file, image quality and sample rate.
3. In the Detection Settings window, click Subject Identification.
4. Carry out steps 4 to 9 in Advanced detection settings: Marker-assisted identification for all subjects.

No additional settings are necessary. EthoVision XT tracks the markers and makes no estimate of the body contours.

Detect the Nose and the Tail Base

Learn About

• Overview of nose-tail base detection
• Optimize nose-tail base detection

When Do I Need This Information?

In the Experiment Settings, under Tracked features, you chose Center-point, nose-point and tail-base detection. Choose the procedure based on what you selected under Body point detection technique.

Contour-Based Technique

Follow the procedure in this order:

1. Adjust the settings for nose-tail base detection (Contour-based)
2. Adjust Advanced detection settings: Smoothing
3. Adjust Subject contour for nose-tail base detection
4. Adjust Subject size for nose-tail base detection

Deep Learning

Follow the procedure: Adjust the settings for nose-tail base detection (Deep learning).

Note: Subject size and contour do not affect the performance of the Deep learning algorithm. Therefore, EthoVision XT should be able to find the nose and tail base points also when the detection of the subject's body is not optimal. However, we advise you to adjust the settings for size and contour, especially if you want to analyze the body's mobility.

Overview of Nose-Tail Base Detection

When you set an experiment for Nose-tail base detection, EthoVision XT analyzes the contour of the area detected as subject at each sample, and assigns Nose-point and Tail-base to two specific pixels of the contour. Furthermore, it determines the direction the animal is supposed to point to (Head direction).

Nose-tail base detection is optimized for rodents and for adult fish, depending on the method used.

Nose- and Tail-Base Points

The two points are detected independently through one of two complex algorithms. The nose-point is found in all cases, except when the center-point is not found either. The tail-base may not be found in a few cases if detection is good.

Reliable tracking of nose and tail-base is limited by the size of the video image. You can mix four camera images like in the case of a group of PhenoTypers, with good results. Mixing 16 camera images makes the subjects too small for reliable nose and tail-base tracking.

Head Direction

Once the nose-point has been found, two points are determined along the contour lying at a specific distance from the nose-point. The Head direction is the line dividing equally the angle formed by the center and those additional points.

Important: If you use Nose-tail tracking with two or more subjects per arena, track from video file instead of live.