Knowledge Base

A Special features and notes

A Special Features And Notes

Edit The Calibration Images

Make a white marker well detectable

When one or more markers is not detected properly during calibration. For example, when a marker is too close to a bright object, the blue cross symbol is placed far from the center of the associated marker. This means that CentroidFinder also includes at least part of the bright object in the detected marker. Do the following: 1. Open the calibration image in a program like Paint or Paint.net and remove the bright regions around the markers. 2. Save the image with a new name. Choose BMP (bitmap) as file type and choose 24 as Bit Depth. 3. Repeat the steps above for the second calibration image. 4. Re-do calibration using the new images.

For water tanks: invert the colors

When filming the calibration frame in water tanks, the calibration markers appear black over a white background. You must convert the image to one where the markers appear white over a black background. 1. In Paint.net, open the calibration image and choose Adjustments > Invert colors. 2. Select Adjustments > Brightness/ Contrast. 3. Adjust the values to increase the white/black contrast. A Special features and notes If necessary, remove the white spots that are too close to the markers. The image should look like this: 4. Save the image with a new name. Choose BMP (bitmap) as file type and choose 24 as Bit Depth. 5. Re-do calibration using this new image.

Additional Lens Correction

Distortion is a divergence from rectilinear projection of an object on a video image. In a rectilinear projection, straight lines in a scene remain straight in a video image. If the level of barrel distortion (fish eye effect) in your video image is not acceptable, you can enter values of focal length, principal point and radial corrections in Track3D. To obtain such values for your cameras, follow the procedure: 1. Download the programs named DLR CalDe and DLR CalLab from the web page: A Special features and notes https://www.dlr.de/rm-neu/desktopdefault.aspx/tabid-3925/ 6084_read-9197/ and follow the instructions to install the program on your PC. 2. Make a checkerboard pattern. 3. Browse to the following web page and follow the instructions on

own_calib.html to create a number of pictures of the checkerboard

in various orientations and for both cameras: https://data.caltech.edu/records/jx9cx-fdh55 Note: Each individual camera lens is unique, resulting in calibration parameters different from that of lenses of the same model. Make sure that each lens is mounted on the corresponding camera. 4. Run the programs and import the calibration pictures for camera 1.

Follow the steps on the page example.html located in

https://data.caltech.edu/records/jx9cx-fdh55 Repeat the procedure for the other camera. See also the documentation coming with the programs. 5. You get the following parameters: - Focal length (x and y) - The x and y values should be equal if the pixels are perfectly square. Copy the first two values given by the program to the corresponding fields under focal length in Track3D. - Principal points - The program calculates the coordinates of the projection point of the focus. This point does not necessarily coincide with the center of the screen, an can differ between A Special features and notes camera 1 and camera 2. Copy the first two values to the corresponding fields under principal point in Track3D. - Distortion kc - The program calculates distortion coefficients of order 2, 4 to correct for radial distortion. Copy the first two values to the radial corrections fields in Track3D. More information on the calibration parameters can be found in

the file parameters.html located in

https://data.caltech.edu/records/jx9cx-fdh55

Draw An Oblique Cone

If you want the cone's main axis to be oblique, you have to set the coordinates of the axis point position in such a way that the cone axis forms the required angle with the x axis. For example if you want the cone pointing upward: 1. Choose the Xtop, Ytop, Ztop coordinates of the cone top position. 2. For the axis point position: - Xaxis= Xtop + cos() A Special features and notes - Yaxis= Ytop - Zaxis= Ztop + sin()

Notes On Filtering

Filtering replaces the coordinates in the 2D track files with values using a smoothing polynomial function. It helps smoothing your data and removing artifacts due to noise. The coordinates exported from EthoVision XT are in fractions of pixels, thus the effect of filtering is very small. The effect is negligible when you smooth the tracks in EthoVision XT before exporting them. In the case of tracking of mosquitoes, when applying filtering about 90% of your data differ by less than 0.5 mm from the original, non- filtered data. However, if the animal is large (e.g. a moth), its center point may move at a high rate due to random noise. We recommend to use filtering when you have not smoothed the tracks in EthoVision XT. If you use data exported from EthoVision 3.1, the coordinates are rounded off to whole pixels, increasing the likelihood of high-frequency movements with no biological significance. In this case, always enable filtering.

Cut off frequency - A low cut off frequency means that a

smoother line will be calculated. A high cut off frequency means that high frequency movements of the animal's center are kept in the data. Be careful not to exclude frequencies that can be important in your study by setting too low a cut off frequency.

Cut off frequency and sample rate - If you set a low sample rate,

for example 5 samples per second, setting a cut off frequency higher than the sample rate is not meaningful.

Butterworth filter - In contrast with other frequency filters, a

Butterworth filter preserves a uniform sensitivity for the passband frequencies (the magnitude response is maximally flat in the passband zone). A second-order filter decreases the signal at 16 dB A Special features and notes per halving of a frequency. The transfer function (magnitude ratio of output to input) of a Butterworth filter is: Where n is the filter order and the c the cutoff frequency. For more information, see: https://en.wikipedia.org/wiki/Butterworth_filter.

Calibration Check

After selecting a calibration file in Track3D, you can check the quality of calibration by looking at the three images opening on the screen:

Calibration check of camera 1

Calibration check of camera 2

Calibration check 3D

The first two images refer to the markers found in the calibration images for camera 1 and 2, respectively. The third image combines the two data sets. H i - 2n A Special features and notes Each red dot is the center of a marker that the calibration program estimated by analyzing the degree of white of the pixels in the calibration images around the clicked point. A line, if visible, connects this dot with the expected position (that is, the position of that marker when taking into account the position of the other markers; the software builds a "model" of the calibration frame assuming that the markers are on straight lines). For most markers the line is not visible as the error is rather small. A black triangle marks the largest error among the markers of each calibration image.

Calibration Error

Statistics of calibration quality (Residual Mean Square (RSM) error and

Maximum error) are given on top of the pictures. The measurement unit of the error is:

pixels for Calibration check of camera 1 and Calibration check of

camera 2

and mm for the Calibration check 3D.

Notes

You can move the calibration check windows after clicking OK in the

Statistics window.

The pictures displayed in Calibration check of camera 1 and

Calibration check of camera 2 are 2D images of the calibration

markers. If you close the calibration check windows, you can re-open them by running analysis again (select New calibration). A Special features and notes

Settings For Mediarecorder

MediaRecorder is set to ensure that EthoVision XT works with video of the best quality. This is usually done by Noldus when installing your system. The settings for the MediaRecorder are stored in a file called Track3D.mrs which is located in the following folder: C:\Users\Public\Public Documents\Noldus\MediaRecorder Make sure you do not edit this file. If you wish to change any settings, save them under a different name: choose File > Save Configuration As.

To go back to the default configuration, choose File > Open

Configuration, and select the file Track3D.mrs.

Optimize the settings file

If for any reason the file Track3D.mrs is missing, do the following: 1. Browse to C:\Users\Public\Public Documents\Noldus\

MediaRecorder, right click the file Default.mrs, and select Open

with the Notepad. 2. The content of the file displays. Change the following values: - GOPsize= 2 - Quality= 100 3. Choose File > Save As... and save the file as Track3D.mrs. 4. Before making the next recordings, start MediaRecorder and choose File > Open Configuration, and select the file Track3D.mrs.

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Source: Track3D 2 - Reference Manual (March 2025)