Advanced detection settings: Marker-assisted identification
Prerequisites
▪You have marked the animals with colors.
▪You have optimized lighting as suggested in Tips for color tracking.
To adjust detection settings for marker-assisted identification
1.Put the marked animals in the arena or play the video.
2.In the Detection Settings window, under Video, select the image source and sample rate. See Video file, image quality and sample rate.
3.Use the Automated Setup.
At this stage EthoVision XT detects the subjects, but does not distinguish between the animals yet. When the Automated Setup gives good detection, proceed with the next step. If not, create advanced detection settings, follow the procedure in Advanced detection settings: Method.
When done with the Automated Setup, make sure Marker-assisted identification is selected in the Subject Identification section in the Detection Settings pane. Note:
▪important Make sure you select a point in the video where the animals do not touch!
▪If you use three-body point detection, it is normal that the nose is not correctly identified at this point.
▪If detection is processor intensive and you track from video, the video slows down, so all frames can be analyzed to enable creating good detection settings.
4.In the Subject Identification section, click the name of one of the subjects and click the Identification button.
Result: The Identification [Subject name] window opens. Optionally enlarge the Video window by dragging its bottom-right corner.
5.Move the mouse pointer to the Video window so the pointer becomes an eyedropper.
6.Move the eyedropper on top of the color marker of the subject you want to identify (see the figure below) and click the left mouse button.
The Identification [Subject name] window now displays the color you just picked and the pixels with the initial color are highlighted in the Video window. In the Identification [Subject name] window, you can change the following (see also the figure below):
Hue: Hue is the predominant wavelength of the marker color and represents what is usually referred to as color in everyday life (red, green, blue, etc.). The range of values for Hue of the picked color are shown and this range is represented by the box on the vertical color bar on the right.
Saturation: Saturation represents the purity of a color. Saturation decreases when a pure color is mixed with white; “red” is saturated, “pink” is less saturated. The range of values for Saturation are shown and this range is represented by the width of the box on the Color map.
Brightness: Brightness (or Intensity) represents the amount of light reflected by the colored surface. The range of values for Brightness are shown and this range is represented by the height of the box on the Color map. If you set this range too broad, you will not be able to separate the colors well.
Below: A: Color bar. The box represents Hue which corresponds to an angle on the circle in the HSI color model (for example, 0 degrees means red, 240 degrees means blue). B: Color map. The height of the box represents the Brightness (or Intensity) range which corresponds to the vertical position of the color circle. The width of the box represents the Saturation range which corresponds to the horizontal position on the circle between the center and the edge.
If the marker is not detected completely or not detected in all areas of the arena, expand the range of Hue, Saturation and Brightness slightly.
Change the color range by changing the numbers or by resizing the Hue box on the vertical color bar, or resizing/moving the box in the color map (horizontally to adjust Saturation, vertically to adjust Brightness). As a result, the outline covers (almost) the complete marker.
Below: The color of the marker after fine-tuning the color settings. Most of the marker is now selected as indicated by the white outline.
7.Next, play the video to see in the Video window whether the marker is detected correctly in different parts of the arena.
If the marker 'dances' then your color settings are too sensitive. Go back to step 5 and make the box larger.
8.Continue with setting the following:
▪Marker erosion: Set the number of pixels to erode. By selecting Erode first, then dilate, you can make the marker more round to prevent the center-point of the marker to start jittering.
▪Marker dilation: Set the number of pixels to dilate. By selecting Dilate first, then erode, you can prevent the marker from being masked or divided in two separate markers by, for instance, a grid on top of the arena.
▪Minimal marker size: Set the Minimal marker size to prevent noise to be detected as the marker. First, increase the Minimal marker size until noise is not detected anymore. Next, enter a value for the Minimal marker size that is somewhere in between this lower threshold and the value of the Current marker size.
Marker pointer: Select a Marker pointer from the list. With relatively small markers it is useful to select Cross lines.
Click another subject under Subject Identification, and repeat steps 2-8 for all subjects you want to identify. If you used the Automated Setup, estimates for the settings below have been created. Optionally fine-tune these settings if detection of all subjects does not go well in the entire track.
What next?
Follow the procedure in this order:
1.Advanced detection settings: Smoothing
2.Advanced detection settings: Subject contour
3.Advanced detection settings: Subject size (multiple animals per arena)