Knowledge Base

The X-Y Coordinate System in the Arena

The Default Coordinate System

By default, the x- and y-coordinates of your track are expressed relative to the center point of the background image. The positive x-axis points to the right, and the positive y-axis points upward.

Position of Shapes in the Coordinate System

After calibrating the arena, the Shape Size and Position section at the bottom of the Arena Settings pane shows the real-world coordinates X and Y of the object currently selected. If the arena is not calibrated yet, the coordinates X and Y are given in pixels.

• If you click the calibration arrow line, the X and Y values are the coordinates of the center of the arrow.
• If you click an object like a zone, X and Y are the coordinates of the geometric center of the object. Width and Height are the width and height of the rectangle around the object, respectively.
• Remember that the value of X and Y depend on where the origin (0,0) is placed. In the default coordinate system, a negative value means that the center of the object is to the left (for X) or below (for Y) the center of the background image.

World Point / Pixel Point

In the Status bar, World Point and Pixel Point indicate the current position of the mouse pointer. You can use this function to know the exact position of an object. If you do not see the Status bar, choose View > Status Bar.

• World Point gives you the coordinates of a point based on the calibration scale and origin, and the distance unit chosen in the Experiment Settings. The world coordinates can be positive or negative depending on where your axis origin is.
• Pixel Point gives you the coordinates of a point in pixels. The 0,0 coordinates correspond to the top-left corner of the video image. The pixel coordinates are always positive.

Modify the Coordinate System of the Arena

Aim

To use a coordinate system different from the default one. For example:

• You want to export the real-world coordinates expressed relative to a point of reference in the real world that is not in the middle of your image.
• You want the dependent variables that use angle (Head Direction, Heading, Meander, Turn Angle) to be expressed relative to a reference line different from the default one (horizontal and pointing to the right). For example, if you have an external cue to the north-east of your arena and want to express the animal's orientation relative to this cue, rotate the Calibration Axes so the x-axis points towards the cue.

Use the Calibration Axes object to specify the orientation of the real-world coordinate system and to specify the real-world coordinates for one pixel point.

To Modify the Coordinate System

1. Click the Create Calibration Axes button at the bottom of the Arenas and Zones section.
2. Optionally, in the Calibration Coordinate System window, type the real-world origin of the x-axis (Origin X) and of the y-axis (Origin Y) relative to the current position of the origin on your screen. Do this if you know the origin of the coordinate system is outside the background image. For example, if you type 10 cm for Origin X, it means the origin (0,0) of your calibration system is shifted 10 cm to the left relative to the center of the video image.
3. Click and drag the Calibration Axes object to reposition the axes origin. To flip the y-axis of the Calibration Axes object, double-click it and select Flipped Y-Axis. Move the Rotation Mode arrow to rotate the calibration axes.

To Return to the Default Coordinate System

Select the Calibration Axes object and press Delete.

Check the Video Aspect Ratio

The Video Aspect Ratio

The video aspect ratio is the relation of the horizontal to vertical size of a video image. When you pre-record video from analog cameras, the aspect ratio of the resulting video files is not the same as that of the source camera. This results in a distorted background image. In such cases, a perfectly circular Morris water maze may look ellipse-like in EthoVision XT after you grab a background image from the video file.

When Is the Video Aspect Ratio Not Correct?

The problem of the aspect ratio occurs in the following situations:

• When you record video with a program other than EthoVision XT, such as MediaRecorder, and from analog cameras.
• When you recorded video with EthoVision XT and you use that video in a new experiment.

If you record video and do tracking within the same experiment, the video aspect ratio is always correct.

How to Identify a Distorted Video Aspect Ratio

• The shape of the test enclosure as displayed in the background deviates from the expected shape. For example, a circular water maze looks like an ellipse, or a square open field looks like a rectangle.
• Place a sheet with a circle under the camera and grab this image as the background image. In Arena Settings, draw a three-point circle. If the aspect ratio of the image is correct, the three-point circle fits over the circle from the camera image.

Calculate the Correct Aspect Ratio in a Video Image

1. After grabbing the background image, locate the bitmap file of your background image in the Bitmap Files folder of your experiment folder.
2. Open the file in an image editing program such as Paint.NET.
3. Draw a shape exactly around the arena and note the dimensions of the shape you have drawn.

If the ratio (for instance, width/height) of the dimensions of the drawn shape deviates from the ratio of the real-world dimensions of the arena, the image is distorted.

Example 1: You have a perfectly circular water maze with a diameter of 100 cm. When you open the background image in an image editing program and draw an ellipse around the maze, the ratio of width/height is 1.019 instead of exactly 1. This means you need to adjust the aspect ratio by dividing the width of the image by 1.019 in the Adjust Aspect Ratio window. Do not change the height.

Example 2: You have a square open field measuring 40 x 40 cm. When you open the background image and draw a rectangle around the open field, the ratio of width/height is 0.8 instead of exactly 1. This means you need to adjust the aspect ratio by dividing the width of the image by 0.8 in the Adjust Aspect Ratio window. Do not change the height.